Starting phenix.real_space_refine on Thu Jul 25 22:24:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utp_26786/07_2024/7utp_26786.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utp_26786/07_2024/7utp_26786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utp_26786/07_2024/7utp_26786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utp_26786/07_2024/7utp_26786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utp_26786/07_2024/7utp_26786.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utp_26786/07_2024/7utp_26786.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 19768 2.51 5 N 5299 2.21 5 O 5873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 50": "OE1" <-> "OE2" Residue "G TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 193": "OE1" <-> "OE2" Residue "G PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 405": "OD1" <-> "OD2" Residue "G TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "F PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 237": "OD1" <-> "OD2" Residue "F PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 477": "OD1" <-> "OD2" Residue "F ASP 511": "OD1" <-> "OD2" Residue "F PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 125": "OD1" <-> "OD2" Residue "D PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E ASP 413": "OD1" <-> "OD2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 513": "OD1" <-> "OD2" Residue "E PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 526": "OD1" <-> "OD2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 574": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 31056 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4238 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492} Chain breaks: 2 Chain: "L" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 495 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'TRANS': 98} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 Chain: "H" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 108 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "G" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4238 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492} Chain breaks: 2 Chain: "F" Number of atoms: 4234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4234 Classifications: {'peptide': 531} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 491} Chain breaks: 2 Chain: "D" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2234 Classifications: {'peptide': 276} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 259} Chain breaks: 8 Chain: "E" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4238 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492} Chain breaks: 2 Chain: "I" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4238 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492} Chain breaks: 2 Chain: "C" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2394 Classifications: {'peptide': 299} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 278} Chain breaks: 9 Chain: "B" Number of atoms: 4207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4207 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 489} Chain breaks: 3 Time building chain proxies: 13.49, per 1000 atoms: 0.43 Number of scatterers: 31056 At special positions: 0 Unit cell: (191.4, 177.1, 137.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 5873 8.00 N 5299 7.00 C 19768 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 494 " distance=2.07 Simple disulfide: pdb=" SG CYS G 490 " - pdb=" SG CYS G 494 " distance=2.05 Simple disulfide: pdb=" SG CYS F 490 " - pdb=" SG CYS F 494 " distance=2.04 Simple disulfide: pdb=" SG CYS E 490 " - pdb=" SG CYS E 494 " distance=2.07 Simple disulfide: pdb=" SG CYS I 490 " - pdb=" SG CYS I 494 " distance=2.03 Simple disulfide: pdb=" SG CYS C 490 " - pdb=" SG CYS C 494 " distance=2.03 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 494 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.61 Conformation dependent library (CDL) restraints added in 5.4 seconds 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7424 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 57 sheets defined 10.7% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 116 through 121 removed outlier: 3.809A pdb=" N TRP A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.542A pdb=" N MET A 190 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A 191 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.531A pdb=" N VAL A 241 " --> pdb=" O PRO A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.560A pdb=" N LEU A 285 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 313 removed outlier: 3.583A pdb=" N ARG A 313 " --> pdb=" O GLN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 removed outlier: 3.731A pdb=" N ASP A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.779A pdb=" N PHE A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 562 removed outlier: 3.663A pdb=" N TYR A 561 " --> pdb=" O GLN A 558 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL A 562 " --> pdb=" O PHE A 559 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 61 removed outlier: 4.185A pdb=" N UNK H 60 " --> pdb=" O UNK H 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 91 Processing helix chain 'G' and resid 95 through 99 Processing helix chain 'G' and resid 116 through 121 removed outlier: 3.914A pdb=" N TRP G 120 " --> pdb=" O ALA G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 132 removed outlier: 3.610A pdb=" N THR G 132 " --> pdb=" O LEU G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 191 removed outlier: 3.528A pdb=" N MET G 190 " --> pdb=" O PRO G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 241 Processing helix chain 'G' and resid 245 through 250 removed outlier: 3.524A pdb=" N SER G 249 " --> pdb=" O THR G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 313 removed outlier: 3.727A pdb=" N ARG G 313 " --> pdb=" O GLN G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 413 removed outlier: 3.519A pdb=" N ASP G 413 " --> pdb=" O PRO G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 443 through 448 Processing helix chain 'G' and resid 554 through 558 removed outlier: 3.566A pdb=" N GLN G 558 " --> pdb=" O VAL G 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 116 through 120 Processing helix chain 'F' and resid 122 through 132 removed outlier: 3.644A pdb=" N THR F 132 " --> pdb=" O LEU F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 241 removed outlier: 3.720A pdb=" N VAL F 241 " --> pdb=" O PRO F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 250 removed outlier: 3.550A pdb=" N SER F 249 " --> pdb=" O THR F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 313 removed outlier: 3.762A pdb=" N ARG F 313 " --> pdb=" O GLN F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 413 Processing helix chain 'F' and resid 443 through 448 removed outlier: 4.267A pdb=" N ILE F 447 " --> pdb=" O ASN F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 562 removed outlier: 3.546A pdb=" N ASN F 560 " --> pdb=" O ASN F 557 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR F 561 " --> pdb=" O GLN F 558 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL F 562 " --> pdb=" O PHE F 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 557 through 562' Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 245 through 250 removed outlier: 3.897A pdb=" N VAL D 250 " --> pdb=" O ILE D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 558 Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 95 through 99 removed outlier: 3.805A pdb=" N LEU E 98 " --> pdb=" O ASN E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 121 removed outlier: 4.144A pdb=" N TRP E 120 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 132 removed outlier: 3.551A pdb=" N LEU E 128 " --> pdb=" O GLY E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 241 Processing helix chain 'E' and resid 245 through 250 Processing helix chain 'E' and resid 381 through 385 removed outlier: 4.195A pdb=" N GLY E 385 " --> pdb=" O ARG E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 447 Processing helix chain 'E' and resid 558 through 562 removed outlier: 3.922A pdb=" N VAL E 562 " --> pdb=" O PHE E 559 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 92 removed outlier: 4.070A pdb=" N VAL I 92 " --> pdb=" O ASP I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 99 removed outlier: 3.637A pdb=" N ASP I 99 " --> pdb=" O MET I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 120 Processing helix chain 'I' and resid 122 through 131 removed outlier: 3.505A pdb=" N LEU I 128 " --> pdb=" O GLY I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 241 removed outlier: 3.634A pdb=" N ASP I 240 " --> pdb=" O ASP I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 245 through 250 Processing helix chain 'I' and resid 409 through 413 Processing helix chain 'I' and resid 443 through 447 Processing helix chain 'I' and resid 557 through 561 removed outlier: 3.605A pdb=" N ASN I 560 " --> pdb=" O ASN I 557 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR I 561 " --> pdb=" O GLN I 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 557 through 561' Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 116 through 121 removed outlier: 4.167A pdb=" N TRP C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 241 removed outlier: 3.621A pdb=" N ASP C 240 " --> pdb=" O ASP C 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 122 through 132 removed outlier: 3.546A pdb=" N VAL B 130 " --> pdb=" O TRP B 126 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN B 131 " --> pdb=" O GLN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 3.534A pdb=" N MET B 190 " --> pdb=" O PRO B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 381 through 385 removed outlier: 3.820A pdb=" N GLY B 385 " --> pdb=" O ARG B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'B' and resid 443 through 447 Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.593A pdb=" N VAL B 562 " --> pdb=" O PHE B 559 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 58 through 72 current: chain 'A' and resid 164 through 167 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 84 Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 218 removed outlier: 3.717A pdb=" N GLY A 235 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR A 217 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N TYR A 233 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 276 through 278 removed outlier: 6.237A pdb=" N HIS A 277 " --> pdb=" O ARG A 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 315 through 317 removed outlier: 3.507A pdb=" N GLY A 315 " --> pdb=" O ALA G 379 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE G 398 " --> pdb=" O TYR G 378 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 335 through 336 removed outlier: 6.615A pdb=" N GLU A 335 " --> pdb=" O ALA A 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 354 removed outlier: 3.625A pdb=" N SER A 348 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE F 415 " --> pdb=" O LEU F 430 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 396 through 399 Processing sheet with id=AA9, first strand: chain 'A' and resid 429 through 430 removed outlier: 3.506A pdb=" N SER G 348 " --> pdb=" O GLY G 351 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.612A pdb=" N UNK L 18 " --> pdb=" O UNK L 74 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N UNK L 74 " --> pdb=" O UNK L 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 33 through 36 Processing sheet with id=AB3, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AB4, first strand: chain 'H' and resid 81 through 82 Processing sheet with id=AB5, first strand: chain 'G' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 58 through 72 current: chain 'G' and resid 164 through 167 Processing sheet with id=AB6, first strand: chain 'G' and resid 80 through 84 Processing sheet with id=AB7, first strand: chain 'G' and resid 215 through 217 removed outlier: 5.949A pdb=" N ASP G 215 " --> pdb=" O HIS G 234 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR G 217 " --> pdb=" O ILE G 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE G 232 " --> pdb=" O THR G 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 276 through 278 Processing sheet with id=AB9, first strand: chain 'G' and resid 315 through 317 Processing sheet with id=AC1, first strand: chain 'G' and resid 335 through 336 removed outlier: 6.585A pdb=" N GLU G 335 " --> pdb=" O ALA G 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'G' and resid 429 through 430 removed outlier: 3.729A pdb=" N GLY F 351 " --> pdb=" O SER F 348 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 58 through 72 current: chain 'F' and resid 164 through 167 Processing sheet with id=AC4, first strand: chain 'F' and resid 80 through 84 removed outlier: 3.504A pdb=" N HIS F 102 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 216 through 218 Processing sheet with id=AC6, first strand: chain 'F' and resid 276 through 278 removed outlier: 5.781A pdb=" N HIS F 277 " --> pdb=" O ARG F 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 335 through 336 removed outlier: 6.875A pdb=" N GLU F 335 " --> pdb=" O ALA F 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 44 through 45 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 44 through 45 current: chain 'E' and resid 102 through 112 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 72 current: chain 'D' and resid 164 through 167 Processing sheet with id=AD1, first strand: chain 'D' and resid 80 through 82 Processing sheet with id=AD2, first strand: chain 'D' and resid 379 through 380 Processing sheet with id=AD3, first strand: chain 'E' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 58 through 72 current: chain 'E' and resid 164 through 167 Processing sheet with id=AD4, first strand: chain 'E' and resid 217 through 218 removed outlier: 3.640A pdb=" N THR E 217 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE E 232 " --> pdb=" O THR E 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 335 through 336 removed outlier: 6.637A pdb=" N GLU E 335 " --> pdb=" O ALA E 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 345 through 346 Processing sheet with id=AD7, first strand: chain 'E' and resid 377 through 380 Processing sheet with id=AD8, first strand: chain 'E' and resid 463 through 464 removed outlier: 4.354A pdb=" N TYR E 464 " --> pdb=" O GLU E 574 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E 574 " --> pdb=" O TYR E 464 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'I' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 58 through 72 current: chain 'I' and resid 164 through 167 Processing sheet with id=AE1, first strand: chain 'I' and resid 80 through 84 Processing sheet with id=AE2, first strand: chain 'I' and resid 216 through 218 removed outlier: 3.769A pdb=" N THR I 217 " --> pdb=" O ILE I 232 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE I 232 " --> pdb=" O THR I 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'I' and resid 276 through 277 Processing sheet with id=AE4, first strand: chain 'I' and resid 316 through 317 removed outlier: 3.506A pdb=" N PHE B 380 " --> pdb=" O GLU B 396 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 396 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 335 through 336 removed outlier: 6.762A pdb=" N GLU I 335 " --> pdb=" O ALA I 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'I' and resid 345 through 348 removed outlier: 3.548A pdb=" N SER I 348 " --> pdb=" O GLY I 351 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 377 through 380 Processing sheet with id=AE8, first strand: chain 'I' and resid 429 through 430 removed outlier: 3.529A pdb=" N SER B 348 " --> pdb=" O GLY B 351 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 463 through 464 removed outlier: 4.120A pdb=" N TYR I 464 " --> pdb=" O GLU I 574 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU I 574 " --> pdb=" O TYR I 464 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'I' and resid 470 through 472 removed outlier: 6.717A pdb=" N ASP I 471 " --> pdb=" O CYS I 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 62 through 72 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 62 through 72 current: chain 'C' and resid 164 through 167 No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 80 through 84 Processing sheet with id=AF4, first strand: chain 'C' and resid 216 through 218 removed outlier: 3.714A pdb=" N THR C 217 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C 232 " --> pdb=" O THR C 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AF6, first strand: chain 'B' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 58 through 72 current: chain 'B' and resid 164 through 167 Processing sheet with id=AF7, first strand: chain 'B' and resid 80 through 84 Processing sheet with id=AF8, first strand: chain 'B' and resid 215 through 218 removed outlier: 6.698A pdb=" N ASP B 215 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 232 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 276 through 278 Processing sheet with id=AG1, first strand: chain 'B' and resid 335 through 336 removed outlier: 6.548A pdb=" N GLU B 335 " --> pdb=" O ALA B 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'B' and resid 415 through 416 Processing sheet with id=AG3, first strand: chain 'B' and resid 470 through 472 removed outlier: 6.832A pdb=" N ASP B 471 " --> pdb=" O CYS B 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 295 hydrogen bonds defined for protein. 567 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.98 Time building geometry restraints manager: 11.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 10111 1.34 - 1.48: 8893 1.48 - 1.63: 12721 1.63 - 1.77: 1 1.77 - 1.91: 203 Bond restraints: 31929 Sorted by residual: bond pdb=" C LEU A 422 " pdb=" N PRO A 423 " ideal model delta sigma weight residual 1.333 1.374 -0.041 1.20e-02 6.94e+03 1.18e+01 bond pdb=" CB CYS E 490 " pdb=" SG CYS E 490 " ideal model delta sigma weight residual 1.808 1.907 -0.099 3.30e-02 9.18e+02 9.01e+00 bond pdb=" CA ASN I 505 " pdb=" CB ASN I 505 " ideal model delta sigma weight residual 1.526 1.570 -0.044 1.53e-02 4.27e+03 8.15e+00 bond pdb=" CB LYS I 501 " pdb=" CG LYS I 501 " ideal model delta sigma weight residual 1.520 1.605 -0.085 3.00e-02 1.11e+03 8.06e+00 bond pdb=" C TYR E 409 " pdb=" N PRO E 410 " ideal model delta sigma weight residual 1.335 1.372 -0.037 1.30e-02 5.92e+03 7.99e+00 ... (remaining 31924 not shown) Histogram of bond angle deviations from ideal: 96.84 - 104.36: 723 104.36 - 111.89: 14121 111.89 - 119.41: 11856 119.41 - 126.94: 16324 126.94 - 134.46: 636 Bond angle restraints: 43660 Sorted by residual: angle pdb=" CA PRO E 187 " pdb=" N PRO E 187 " pdb=" CD PRO E 187 " ideal model delta sigma weight residual 112.00 98.11 13.89 1.40e+00 5.10e-01 9.84e+01 angle pdb=" CA CYS E 494 " pdb=" CB CYS E 494 " pdb=" SG CYS E 494 " ideal model delta sigma weight residual 114.40 127.09 -12.69 2.30e+00 1.89e-01 3.04e+01 angle pdb=" CA CYS A 494 " pdb=" CB CYS A 494 " pdb=" SG CYS A 494 " ideal model delta sigma weight residual 114.40 126.98 -12.58 2.30e+00 1.89e-01 2.99e+01 angle pdb=" CA GLN I 213 " pdb=" CB GLN I 213 " pdb=" CG GLN I 213 " ideal model delta sigma weight residual 114.10 124.49 -10.39 2.00e+00 2.50e-01 2.70e+01 angle pdb=" CB GLN F 213 " pdb=" CG GLN F 213 " pdb=" CD GLN F 213 " ideal model delta sigma weight residual 112.60 121.16 -8.56 1.70e+00 3.46e-01 2.54e+01 ... (remaining 43655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 16486 17.96 - 35.92: 1698 35.92 - 53.87: 383 53.87 - 71.83: 66 71.83 - 89.79: 41 Dihedral angle restraints: 18674 sinusoidal: 7165 harmonic: 11509 Sorted by residual: dihedral pdb=" CA ASN F 426 " pdb=" C ASN F 426 " pdb=" N ASP F 427 " pdb=" CA ASP F 427 " ideal model delta harmonic sigma weight residual 180.00 142.59 37.41 0 5.00e+00 4.00e-02 5.60e+01 dihedral pdb=" CB CYS B 490 " pdb=" SG CYS B 490 " pdb=" SG CYS B 494 " pdb=" CB CYS B 494 " ideal model delta sinusoidal sigma weight residual 93.00 41.23 51.77 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CA ASN A 493 " pdb=" C ASN A 493 " pdb=" N CYS A 494 " pdb=" CA CYS A 494 " ideal model delta harmonic sigma weight residual 180.00 -149.80 -30.20 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 18671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4078 0.077 - 0.154: 629 0.154 - 0.231: 52 0.231 - 0.307: 2 0.307 - 0.384: 3 Chirality restraints: 4764 Sorted by residual: chirality pdb=" CB ILE D 204 " pdb=" CA ILE D 204 " pdb=" CG1 ILE D 204 " pdb=" CG2 ILE D 204 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA SER G 226 " pdb=" N SER G 226 " pdb=" C SER G 226 " pdb=" CB SER G 226 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA ASN F 428 " pdb=" N ASN F 428 " pdb=" C ASN F 428 " pdb=" CB ASN F 428 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 4761 not shown) Planarity restraints: 5732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 186 " -0.127 5.00e-02 4.00e+02 1.80e-01 5.21e+01 pdb=" N PRO E 187 " 0.311 5.00e-02 4.00e+02 pdb=" CA PRO E 187 " -0.103 5.00e-02 4.00e+02 pdb=" CD PRO E 187 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 464 " -0.026 2.00e-02 2.50e+03 4.08e-02 3.33e+01 pdb=" CG TYR E 464 " 0.098 2.00e-02 2.50e+03 pdb=" CD1 TYR E 464 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR E 464 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR E 464 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 464 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 464 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 464 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 237 " -0.073 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO E 238 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO E 238 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO E 238 " -0.059 5.00e-02 4.00e+02 ... (remaining 5729 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 564 2.64 - 3.21: 28791 3.21 - 3.77: 46841 3.77 - 4.34: 65177 4.34 - 4.90: 107423 Nonbonded interactions: 248796 Sorted by model distance: nonbonded pdb=" OH TYR A 524 " pdb=" O LEU B 506 " model vdw 2.076 2.440 nonbonded pdb=" OG1 THR D 42 " pdb=" OE1 GLU D 260 " model vdw 2.091 2.440 nonbonded pdb=" O LEU A 506 " pdb=" OH TYR E 524 " model vdw 2.096 2.440 nonbonded pdb=" O THR F 245 " pdb=" OG SER F 249 " model vdw 2.101 2.440 nonbonded pdb=" O VAL D 149 " pdb=" OG SER D 525 " model vdw 2.121 2.440 ... (remaining 248791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 38 through 294 or resid 299 through 584)) selection = (chain 'B' and resid 38 through 584) selection = (chain 'E' and (resid 38 through 294 or resid 299 through 584)) selection = (chain 'F' and (resid 38 through 294 or resid 299 through 584)) selection = (chain 'G' and (resid 38 through 294 or resid 299 through 584)) selection = (chain 'I' and (resid 38 through 294 or resid 299 through 584)) } ncs_group { reference = (chain 'H' and resid 10 through 108) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 69.790 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 31929 Z= 0.449 Angle : 1.104 13.885 43660 Z= 0.591 Chirality : 0.055 0.384 4764 Planarity : 0.009 0.180 5732 Dihedral : 15.953 89.791 11229 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.15 % Rotamer: Outliers : 0.42 % Allowed : 24.76 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 3686 helix: -2.35 (0.41), residues: 92 sheet: -1.04 (0.17), residues: 859 loop : -0.84 (0.11), residues: 2735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 109 HIS 0.020 0.002 HIS F 102 PHE 0.068 0.004 PHE E 243 TYR 0.098 0.003 TYR E 464 ARG 0.017 0.002 ARG F 481 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1544 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1530 time to evaluate : 3.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.7930 (t0) cc_final: 0.7662 (t0) REVERT: A 60 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6924 (tp30) REVERT: A 79 TYR cc_start: 0.8362 (m-80) cc_final: 0.7641 (m-80) REVERT: A 145 ILE cc_start: 0.8856 (mt) cc_final: 0.8576 (mm) REVERT: A 241 VAL cc_start: 0.8220 (m) cc_final: 0.8018 (p) REVERT: A 312 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8092 (mtmt) REVERT: A 335 GLU cc_start: 0.7332 (tt0) cc_final: 0.6277 (tm-30) REVERT: A 346 GLU cc_start: 0.6416 (mt-10) cc_final: 0.5927 (mt-10) REVERT: A 350 GLN cc_start: 0.7384 (mt0) cc_final: 0.6913 (mp10) REVERT: A 380 PHE cc_start: 0.7734 (p90) cc_final: 0.7534 (p90) REVERT: A 396 GLU cc_start: 0.7671 (tt0) cc_final: 0.7266 (tt0) REVERT: A 473 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6664 (mm-30) REVERT: A 501 LYS cc_start: 0.7888 (ttpp) cc_final: 0.7629 (ttpt) REVERT: A 524 TYR cc_start: 0.8165 (p90) cc_final: 0.7942 (p90) REVERT: A 528 TRP cc_start: 0.8260 (m100) cc_final: 0.8000 (m100) REVERT: A 569 MET cc_start: 0.6677 (mmm) cc_final: 0.6432 (tpp) REVERT: A 574 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6761 (mm-30) REVERT: G 62 THR cc_start: 0.8548 (m) cc_final: 0.8066 (t) REVERT: G 73 MET cc_start: 0.7748 (ptm) cc_final: 0.7442 (ptm) REVERT: G 109 TRP cc_start: 0.8347 (m100) cc_final: 0.7646 (m100) REVERT: G 143 GLN cc_start: 0.8067 (mt0) cc_final: 0.7832 (mt0) REVERT: G 193 GLU cc_start: 0.7401 (mp0) cc_final: 0.7143 (mp0) REVERT: G 213 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7169 (tm-30) REVERT: G 327 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6488 (mm-30) REVERT: G 335 GLU cc_start: 0.7231 (tt0) cc_final: 0.6622 (tt0) REVERT: G 342 TYR cc_start: 0.7753 (p90) cc_final: 0.6883 (p90) REVERT: G 345 PHE cc_start: 0.8149 (m-80) cc_final: 0.7467 (m-80) REVERT: G 377 ARG cc_start: 0.8256 (ttt90) cc_final: 0.7653 (tpp80) REVERT: G 398 PHE cc_start: 0.8737 (p90) cc_final: 0.8522 (p90) REVERT: G 479 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8220 (mmtm) REVERT: G 491 GLN cc_start: 0.7503 (mm-40) cc_final: 0.7240 (mm-40) REVERT: G 518 MET cc_start: 0.7710 (ptp) cc_final: 0.7505 (ptp) REVERT: G 530 LYS cc_start: 0.7917 (ttpp) cc_final: 0.7475 (ttpp) REVERT: G 560 ASN cc_start: 0.8248 (m-40) cc_final: 0.7880 (m-40) REVERT: F 65 SER cc_start: 0.8540 (t) cc_final: 0.8158 (p) REVERT: F 73 MET cc_start: 0.7809 (ttp) cc_final: 0.7179 (tmm) REVERT: F 80 ARG cc_start: 0.4416 (tpt90) cc_final: 0.4145 (tpt90) REVERT: F 81 ARG cc_start: 0.5497 (ptp-170) cc_final: 0.3547 (ptp90) REVERT: F 106 VAL cc_start: 0.8873 (t) cc_final: 0.8552 (m) REVERT: F 120 TRP cc_start: 0.8383 (m100) cc_final: 0.7643 (m100) REVERT: F 127 GLN cc_start: 0.8597 (tt0) cc_final: 0.7986 (tp40) REVERT: F 135 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7027 (mp0) REVERT: F 151 LYS cc_start: 0.8310 (mmmm) cc_final: 0.7551 (mmmm) REVERT: F 191 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7973 (mtt90) REVERT: F 225 THR cc_start: 0.7255 (m) cc_final: 0.6876 (p) REVERT: F 230 THR cc_start: 0.8251 (m) cc_final: 0.7935 (p) REVERT: F 335 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6682 (tp30) REVERT: F 386 GLN cc_start: 0.7229 (tt0) cc_final: 0.6809 (tt0) REVERT: F 409 TYR cc_start: 0.8389 (t80) cc_final: 0.8140 (t80) REVERT: F 413 ASP cc_start: 0.7515 (m-30) cc_final: 0.7111 (m-30) REVERT: F 430 LEU cc_start: 0.8801 (tp) cc_final: 0.8542 (tp) REVERT: F 451 TYR cc_start: 0.8548 (t80) cc_final: 0.8276 (t80) REVERT: F 470 TRP cc_start: 0.7642 (p90) cc_final: 0.7380 (p90) REVERT: F 520 ARG cc_start: 0.7583 (mtt90) cc_final: 0.7273 (mtt90) REVERT: F 532 LYS cc_start: 0.8444 (ttmm) cc_final: 0.8025 (ttmm) REVERT: F 545 TRP cc_start: 0.8584 (t-100) cc_final: 0.8347 (t-100) REVERT: F 550 GLN cc_start: 0.8186 (mm110) cc_final: 0.7675 (mm-40) REVERT: F 551 MET cc_start: 0.7481 (ttt) cc_final: 0.6714 (ttt) REVERT: F 562 VAL cc_start: 0.8672 (p) cc_final: 0.8448 (m) REVERT: F 575 LYS cc_start: 0.7833 (mmtt) cc_final: 0.7299 (mmtt) REVERT: D 73 MET cc_start: 0.8165 (ptt) cc_final: 0.7580 (ptp) REVERT: D 256 ARG cc_start: 0.8141 (mtm-85) cc_final: 0.7538 (mtm-85) REVERT: E 60 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6905 (tm-30) REVERT: E 61 ILE cc_start: 0.8165 (mt) cc_final: 0.7898 (mt) REVERT: E 62 THR cc_start: 0.8573 (m) cc_final: 0.8024 (m) REVERT: E 86 ASN cc_start: 0.7162 (p0) cc_final: 0.6846 (p0) REVERT: E 131 ASN cc_start: 0.8206 (m-40) cc_final: 0.7685 (t0) REVERT: E 163 LYS cc_start: 0.7785 (mppt) cc_final: 0.7466 (mppt) REVERT: E 210 TYR cc_start: 0.8624 (p90) cc_final: 0.8304 (p90) REVERT: E 266 PHE cc_start: 0.8179 (t80) cc_final: 0.7937 (t80) REVERT: E 342 TYR cc_start: 0.7312 (p90) cc_final: 0.6745 (p90) REVERT: E 386 GLN cc_start: 0.8340 (tt0) cc_final: 0.8048 (tt0) REVERT: E 387 LYS cc_start: 0.8704 (tptm) cc_final: 0.8119 (tptm) REVERT: E 400 TYR cc_start: 0.8107 (t80) cc_final: 0.7299 (t80) REVERT: E 408 ARG cc_start: 0.5797 (tpm170) cc_final: 0.5553 (tpt170) REVERT: E 469 ILE cc_start: 0.8380 (mp) cc_final: 0.8134 (mp) REVERT: E 471 ASP cc_start: 0.5685 (t0) cc_final: 0.5480 (t0) REVERT: E 479 LYS cc_start: 0.8253 (mptt) cc_final: 0.7866 (mptt) REVERT: E 483 HIS cc_start: 0.7822 (m170) cc_final: 0.6823 (m-70) REVERT: E 532 LYS cc_start: 0.8296 (ttpt) cc_final: 0.7813 (ttpt) REVERT: E 551 MET cc_start: 0.7455 (ttt) cc_final: 0.7004 (ttt) REVERT: I 76 SER cc_start: 0.7994 (t) cc_final: 0.7652 (t) REVERT: I 95 ASN cc_start: 0.8192 (m-40) cc_final: 0.7978 (m-40) REVERT: I 96 MET cc_start: 0.4590 (ptt) cc_final: 0.4351 (ptt) REVERT: I 101 ILE cc_start: 0.8554 (mt) cc_final: 0.8297 (mt) REVERT: I 109 TRP cc_start: 0.8685 (m100) cc_final: 0.8476 (m100) REVERT: I 145 ILE cc_start: 0.8840 (mm) cc_final: 0.8434 (mm) REVERT: I 147 ASN cc_start: 0.7952 (t0) cc_final: 0.7631 (t0) REVERT: I 193 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7088 (mp0) REVERT: I 230 THR cc_start: 0.8484 (m) cc_final: 0.8093 (p) REVERT: I 265 THR cc_start: 0.7519 (p) cc_final: 0.7265 (p) REVERT: I 293 SER cc_start: 0.8605 (m) cc_final: 0.7880 (p) REVERT: I 310 GLN cc_start: 0.8322 (mt0) cc_final: 0.8071 (mt0) REVERT: I 318 GLN cc_start: 0.8299 (mt0) cc_final: 0.8088 (mm-40) REVERT: I 348 SER cc_start: 0.8423 (m) cc_final: 0.8074 (p) REVERT: I 378 TYR cc_start: 0.7965 (m-80) cc_final: 0.7652 (m-80) REVERT: I 382 ARG cc_start: 0.8032 (mtt90) cc_final: 0.7827 (mtt90) REVERT: I 491 GLN cc_start: 0.7345 (mm-40) cc_final: 0.6926 (mm-40) REVERT: I 538 LYS cc_start: 0.8088 (tppt) cc_final: 0.7777 (mmtt) REVERT: C 67 ARG cc_start: 0.6816 (mmt-90) cc_final: 0.6603 (mmt-90) REVERT: C 68 LEU cc_start: 0.8022 (tp) cc_final: 0.7360 (mp) REVERT: C 73 MET cc_start: 0.8112 (ptt) cc_final: 0.7666 (ptt) REVERT: C 115 ASN cc_start: 0.7335 (t0) cc_final: 0.6560 (t0) REVERT: C 509 GLU cc_start: 0.7734 (mm-30) cc_final: 0.6989 (tm-30) REVERT: C 528 TRP cc_start: 0.8423 (m100) cc_final: 0.8017 (m100) REVERT: B 95 ASN cc_start: 0.8322 (t0) cc_final: 0.7568 (t0) REVERT: B 152 THR cc_start: 0.7854 (m) cc_final: 0.7580 (m) REVERT: B 198 TYR cc_start: 0.7172 (m-10) cc_final: 0.6857 (m-10) REVERT: B 256 ARG cc_start: 0.7897 (mtp180) cc_final: 0.7686 (mtp85) REVERT: B 266 PHE cc_start: 0.8186 (t80) cc_final: 0.7947 (t80) REVERT: B 331 MET cc_start: 0.7806 (ttm) cc_final: 0.7537 (ttm) REVERT: B 353 PHE cc_start: 0.8047 (p90) cc_final: 0.7819 (p90) REVERT: B 382 ARG cc_start: 0.7933 (mtt90) cc_final: 0.7607 (mtt90) REVERT: B 400 TYR cc_start: 0.7660 (t80) cc_final: 0.7356 (t80) REVERT: B 415 ILE cc_start: 0.8181 (mt) cc_final: 0.7915 (mt) REVERT: B 416 GLN cc_start: 0.8011 (tt0) cc_final: 0.7594 (mp10) REVERT: B 417 ASN cc_start: 0.8020 (t0) cc_final: 0.7724 (t0) REVERT: B 463 VAL cc_start: 0.8115 (p) cc_final: 0.7800 (m) REVERT: B 473 GLU cc_start: 0.7088 (tt0) cc_final: 0.6732 (tt0) REVERT: B 491 GLN cc_start: 0.7484 (mm-40) cc_final: 0.6803 (mm-40) REVERT: B 510 TYR cc_start: 0.8861 (t80) cc_final: 0.8316 (t80) REVERT: B 536 LYS cc_start: 0.8108 (tmtt) cc_final: 0.7813 (tmtt) REVERT: B 558 GLN cc_start: 0.8201 (tt0) cc_final: 0.7882 (tt0) REVERT: B 569 MET cc_start: 0.6969 (mmm) cc_final: 0.6720 (mmm) REVERT: B 575 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7347 (mmtt) outliers start: 14 outliers final: 5 residues processed: 1534 average time/residue: 0.4486 time to fit residues: 1065.6003 Evaluate side-chains 1506 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1499 time to evaluate : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 570 LYS Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 0.0070 chunk 297 optimal weight: 7.9990 chunk 164 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 307 optimal weight: 1.9990 chunk 118 optimal weight: 30.0000 chunk 186 optimal weight: 0.3980 chunk 228 optimal weight: 9.9990 chunk 355 optimal weight: 0.1980 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS A 277 HIS A 302 ASN A 384 HIS A 426 ASN A 491 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 GLN ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 GLN G 468 GLN G 491 GLN F 93 ASN F 143 GLN F 167 ASN F 234 HIS ** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 GLN F 565 ASN D 517 ASN E 48 GLN E 143 GLN ** E 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 HIS I 383 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31929 Z= 0.161 Angle : 0.581 8.837 43660 Z= 0.293 Chirality : 0.043 0.200 4764 Planarity : 0.005 0.105 5732 Dihedral : 6.026 84.057 4257 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.61 % Allowed : 21.61 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.13), residues: 3686 helix: -1.26 (0.48), residues: 94 sheet: -0.65 (0.16), residues: 906 loop : -0.48 (0.12), residues: 2686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 279 HIS 0.007 0.001 HIS A 384 PHE 0.028 0.002 PHE A 197 TYR 0.027 0.001 TYR A 561 ARG 0.006 0.001 ARG G 520 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1643 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1524 time to evaluate : 3.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.7921 (t0) cc_final: 0.7656 (t0) REVERT: A 60 GLU cc_start: 0.7399 (tt0) cc_final: 0.7055 (tp30) REVERT: A 104 GLN cc_start: 0.8093 (pt0) cc_final: 0.7672 (pt0) REVERT: A 109 TRP cc_start: 0.8565 (m100) cc_final: 0.7992 (m100) REVERT: A 177 LEU cc_start: 0.8413 (tt) cc_final: 0.8193 (tp) REVERT: A 200 TRP cc_start: 0.8371 (p90) cc_final: 0.8073 (p90) REVERT: A 214 TRP cc_start: 0.8324 (p90) cc_final: 0.7361 (p90) REVERT: A 237 ASP cc_start: 0.7828 (t0) cc_final: 0.7316 (t0) REVERT: A 244 TYR cc_start: 0.7093 (m-80) cc_final: 0.6872 (m-80) REVERT: A 260 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7040 (tt0) REVERT: A 312 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8178 (mtmt) REVERT: A 335 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6172 (tm-30) REVERT: A 350 GLN cc_start: 0.7447 (mt0) cc_final: 0.6964 (mp10) REVERT: A 380 PHE cc_start: 0.7533 (p90) cc_final: 0.7171 (p90) REVERT: A 396 GLU cc_start: 0.7450 (tt0) cc_final: 0.7064 (tt0) REVERT: A 414 TRP cc_start: 0.7901 (p90) cc_final: 0.7392 (p90) REVERT: A 446 ASN cc_start: 0.8171 (m110) cc_final: 0.7862 (m110) REVERT: A 473 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6788 (mm-30) REVERT: A 501 LYS cc_start: 0.8323 (ttpp) cc_final: 0.7615 (ttpp) REVERT: A 530 LYS cc_start: 0.8334 (ttmm) cc_final: 0.7880 (ttpp) REVERT: A 540 ARG cc_start: 0.8261 (ptm-80) cc_final: 0.7942 (ptm160) REVERT: A 566 ILE cc_start: 0.8701 (pp) cc_final: 0.8469 (pp) REVERT: A 569 MET cc_start: 0.6704 (mmm) cc_final: 0.6056 (tpp) REVERT: G 50 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: G 54 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8223 (mt) REVERT: G 62 THR cc_start: 0.8398 (m) cc_final: 0.7726 (p) REVERT: G 67 ARG cc_start: 0.7947 (mtt90) cc_final: 0.7645 (mmt-90) REVERT: G 109 TRP cc_start: 0.8388 (m100) cc_final: 0.7792 (m100) REVERT: G 120 TRP cc_start: 0.8558 (m100) cc_final: 0.7951 (m100) REVERT: G 135 GLU cc_start: 0.7033 (tp30) cc_final: 0.6765 (tp30) REVERT: G 144 GLU cc_start: 0.7344 (pm20) cc_final: 0.6905 (pm20) REVERT: G 174 MET cc_start: 0.7608 (mtp) cc_final: 0.7281 (mtp) REVERT: G 193 GLU cc_start: 0.7274 (mp0) cc_final: 0.6836 (mp0) REVERT: G 213 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7026 (tm-30) REVERT: G 266 PHE cc_start: 0.8147 (t80) cc_final: 0.7825 (t80) REVERT: G 283 ARG cc_start: 0.8452 (mtp180) cc_final: 0.8106 (mtp180) REVERT: G 327 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6642 (mm-30) REVERT: G 335 GLU cc_start: 0.7201 (tt0) cc_final: 0.6657 (tt0) REVERT: G 342 TYR cc_start: 0.7751 (p90) cc_final: 0.7133 (p90) REVERT: G 345 PHE cc_start: 0.7916 (m-80) cc_final: 0.7226 (m-80) REVERT: G 346 GLU cc_start: 0.6639 (mm-30) cc_final: 0.6431 (mm-30) REVERT: G 398 PHE cc_start: 0.8748 (p90) cc_final: 0.8369 (p90) REVERT: G 479 LYS cc_start: 0.8615 (mmtm) cc_final: 0.8278 (mmtm) REVERT: G 491 GLN cc_start: 0.7556 (mm110) cc_final: 0.7146 (mm110) REVERT: G 518 MET cc_start: 0.7754 (ptp) cc_final: 0.7458 (ptp) REVERT: G 530 LYS cc_start: 0.8108 (ttpp) cc_final: 0.7397 (ttpp) REVERT: G 532 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7990 (ttpp) REVERT: G 560 ASN cc_start: 0.8317 (m-40) cc_final: 0.7937 (m-40) REVERT: F 65 SER cc_start: 0.8619 (t) cc_final: 0.8139 (p) REVERT: F 73 MET cc_start: 0.7858 (ttp) cc_final: 0.7340 (ttt) REVERT: F 80 ARG cc_start: 0.3732 (tpt90) cc_final: 0.1778 (tpt170) REVERT: F 109 TRP cc_start: 0.8466 (m100) cc_final: 0.7915 (m100) REVERT: F 120 TRP cc_start: 0.8403 (m100) cc_final: 0.7772 (m100) REVERT: F 135 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: F 151 LYS cc_start: 0.8284 (mmmm) cc_final: 0.7920 (mmmm) REVERT: F 197 PHE cc_start: 0.8220 (m-10) cc_final: 0.7602 (m-80) REVERT: F 201 LYS cc_start: 0.8163 (mmpt) cc_final: 0.7763 (mmpt) REVERT: F 213 GLN cc_start: 0.7550 (tm-30) cc_final: 0.7068 (tm-30) REVERT: F 216 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7492 (ptm160) REVERT: F 237 ASP cc_start: 0.8092 (t0) cc_final: 0.7743 (t0) REVERT: F 266 PHE cc_start: 0.8183 (t80) cc_final: 0.7627 (t80) REVERT: F 279 TRP cc_start: 0.8448 (p-90) cc_final: 0.8219 (p-90) REVERT: F 335 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6560 (tp30) REVERT: F 386 GLN cc_start: 0.7174 (tt0) cc_final: 0.6814 (tt0) REVERT: F 409 TYR cc_start: 0.8256 (t80) cc_final: 0.7887 (t80) REVERT: F 451 TYR cc_start: 0.8574 (t80) cc_final: 0.8177 (t80) REVERT: F 470 TRP cc_start: 0.7691 (p90) cc_final: 0.7438 (p90) REVERT: F 520 ARG cc_start: 0.7535 (mtt90) cc_final: 0.7143 (mtt90) REVERT: F 532 LYS cc_start: 0.8406 (ttmm) cc_final: 0.7979 (ttmm) REVERT: F 533 LEU cc_start: 0.8417 (tp) cc_final: 0.7113 (tp) REVERT: F 550 GLN cc_start: 0.8347 (mm110) cc_final: 0.8085 (mm-40) REVERT: F 551 MET cc_start: 0.7394 (ttt) cc_final: 0.6959 (ttt) REVERT: F 562 VAL cc_start: 0.8663 (p) cc_final: 0.8429 (m) REVERT: F 575 LYS cc_start: 0.7796 (mmtt) cc_final: 0.7193 (mmtt) REVERT: D 49 THR cc_start: 0.7838 (m) cc_final: 0.7468 (p) REVERT: D 50 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6605 (tm-30) REVERT: D 73 MET cc_start: 0.8165 (ptt) cc_final: 0.7597 (ptp) REVERT: D 174 MET cc_start: 0.7745 (mtp) cc_final: 0.7251 (mtp) REVERT: D 208 TRP cc_start: 0.7723 (t60) cc_final: 0.7447 (t60) REVERT: D 256 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.8017 (tpp80) REVERT: D 508 ASN cc_start: 0.7989 (p0) cc_final: 0.7428 (p0) REVERT: D 509 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6698 (mm-30) REVERT: E 51 PHE cc_start: 0.8466 (m-80) cc_final: 0.8189 (m-80) REVERT: E 60 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6760 (tm-30) REVERT: E 131 ASN cc_start: 0.8438 (m-40) cc_final: 0.6160 (t0) REVERT: E 142 GLU cc_start: 0.7772 (pt0) cc_final: 0.6804 (pt0) REVERT: E 163 LYS cc_start: 0.7710 (mppt) cc_final: 0.7201 (mppt) REVERT: E 210 TYR cc_start: 0.8515 (p90) cc_final: 0.8083 (p90) REVERT: E 237 ASP cc_start: 0.7608 (t0) cc_final: 0.7311 (t0) REVERT: E 240 ASP cc_start: 0.7204 (m-30) cc_final: 0.6985 (m-30) REVERT: E 247 GLU cc_start: 0.7521 (mp0) cc_final: 0.7024 (mp0) REVERT: E 266 PHE cc_start: 0.8159 (t80) cc_final: 0.7851 (t80) REVERT: E 342 TYR cc_start: 0.7232 (p90) cc_final: 0.6841 (p90) REVERT: E 387 LYS cc_start: 0.8682 (tptm) cc_final: 0.8181 (tptm) REVERT: E 400 TYR cc_start: 0.8105 (t80) cc_final: 0.7262 (t80) REVERT: E 464 TYR cc_start: 0.7688 (t80) cc_final: 0.7083 (t80) REVERT: E 471 ASP cc_start: 0.5838 (t0) cc_final: 0.5523 (t0) REVERT: E 479 LYS cc_start: 0.8266 (mptt) cc_final: 0.7892 (mptt) REVERT: E 483 HIS cc_start: 0.7841 (m170) cc_final: 0.6820 (m-70) REVERT: E 501 LYS cc_start: 0.7738 (tttt) cc_final: 0.7052 (tttt) REVERT: E 520 ARG cc_start: 0.7565 (mtp85) cc_final: 0.6994 (mtp85) REVERT: E 529 TRP cc_start: 0.8247 (t60) cc_final: 0.7265 (t60) REVERT: E 532 LYS cc_start: 0.8244 (ttpt) cc_final: 0.7620 (ttpt) REVERT: E 545 TRP cc_start: 0.8560 (t-100) cc_final: 0.8233 (t-100) REVERT: E 550 GLN cc_start: 0.7496 (mm-40) cc_final: 0.7107 (mm-40) REVERT: E 582 LYS cc_start: 0.6468 (pmtt) cc_final: 0.6133 (pmtt) REVERT: I 53 PHE cc_start: 0.8401 (m-80) cc_final: 0.8194 (m-80) REVERT: I 76 SER cc_start: 0.8085 (t) cc_final: 0.7729 (t) REVERT: I 95 ASN cc_start: 0.8266 (m-40) cc_final: 0.7999 (m-40) REVERT: I 96 MET cc_start: 0.4373 (OUTLIER) cc_final: 0.4040 (ptt) REVERT: I 101 ILE cc_start: 0.8369 (mt) cc_final: 0.8150 (mt) REVERT: I 145 ILE cc_start: 0.8779 (mm) cc_final: 0.8475 (mm) REVERT: I 147 ASN cc_start: 0.7928 (t0) cc_final: 0.7546 (t0) REVERT: I 193 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7037 (mp0) REVERT: I 237 ASP cc_start: 0.7147 (t0) cc_final: 0.6729 (t0) REVERT: I 265 THR cc_start: 0.7448 (p) cc_final: 0.7183 (p) REVERT: I 269 ASP cc_start: 0.6760 (p0) cc_final: 0.6262 (p0) REVERT: I 293 SER cc_start: 0.8570 (m) cc_final: 0.8048 (p) REVERT: I 314 ARG cc_start: 0.8047 (ptp-170) cc_final: 0.7822 (ptp90) REVERT: I 318 GLN cc_start: 0.8604 (mt0) cc_final: 0.8143 (mm-40) REVERT: I 346 GLU cc_start: 0.6638 (mm-30) cc_final: 0.6391 (mm-30) REVERT: I 408 ARG cc_start: 0.7924 (mmt-90) cc_final: 0.7722 (mmt-90) REVERT: I 491 GLN cc_start: 0.7399 (mm-40) cc_final: 0.6782 (mm-40) REVERT: I 529 TRP cc_start: 0.7623 (t60) cc_final: 0.7349 (t60) REVERT: I 565 ASN cc_start: 0.8147 (t0) cc_final: 0.7892 (t0) REVERT: C 67 ARG cc_start: 0.7082 (mmt-90) cc_final: 0.6674 (mmt-90) REVERT: C 68 LEU cc_start: 0.8053 (tp) cc_final: 0.7625 (tp) REVERT: C 73 MET cc_start: 0.8148 (ptt) cc_final: 0.7787 (ptt) REVERT: C 77 GLU cc_start: 0.6832 (tp30) cc_final: 0.6242 (tp30) REVERT: C 115 ASN cc_start: 0.7458 (t0) cc_final: 0.6575 (t0) REVERT: C 200 TRP cc_start: 0.8573 (p90) cc_final: 0.8338 (p90) REVERT: C 509 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6969 (tm-30) REVERT: C 528 TRP cc_start: 0.8527 (m100) cc_final: 0.7950 (m100) REVERT: B 53 PHE cc_start: 0.8233 (m-80) cc_final: 0.7838 (p90) REVERT: B 80 ARG cc_start: 0.8035 (mmm-85) cc_final: 0.7491 (mmm-85) REVERT: B 125 ASP cc_start: 0.7506 (m-30) cc_final: 0.7266 (m-30) REVERT: B 152 THR cc_start: 0.8090 (m) cc_final: 0.7793 (m) REVERT: B 193 GLU cc_start: 0.7688 (tt0) cc_final: 0.6998 (tt0) REVERT: B 216 ARG cc_start: 0.7626 (tpt-90) cc_final: 0.7283 (tpt-90) REVERT: B 400 TYR cc_start: 0.7777 (t80) cc_final: 0.7474 (t80) REVERT: B 415 ILE cc_start: 0.8309 (mt) cc_final: 0.8043 (mt) REVERT: B 416 GLN cc_start: 0.7876 (tt0) cc_final: 0.7535 (mp10) REVERT: B 417 ASN cc_start: 0.8108 (t0) cc_final: 0.7619 (t0) REVERT: B 510 TYR cc_start: 0.8852 (t80) cc_final: 0.8558 (t80) REVERT: B 511 ASP cc_start: 0.8176 (t0) cc_final: 0.7730 (t0) REVERT: B 536 LYS cc_start: 0.8068 (tmtt) cc_final: 0.7655 (tmtt) REVERT: B 569 MET cc_start: 0.7043 (mmm) cc_final: 0.6693 (mmm) REVERT: B 575 LYS cc_start: 0.8003 (mmtt) cc_final: 0.7398 (mmtt) outliers start: 119 outliers final: 76 residues processed: 1549 average time/residue: 0.4639 time to fit residues: 1123.3866 Evaluate side-chains 1561 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1474 time to evaluate : 3.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 546 ASN Chi-restraints excluded: chain A residue 558 GLN Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 70 HIS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 201 LYS Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 494 CYS Chi-restraints excluded: chain I residue 497 GLN Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 549 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.9980 chunk 110 optimal weight: 0.4980 chunk 296 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 356 optimal weight: 2.9990 chunk 385 optimal weight: 0.0980 chunk 317 optimal weight: 0.4980 chunk 353 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 286 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 426 ASN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 GLN G 468 GLN ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN ** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN E 127 GLN E 143 GLN E 166 ASN E 403 HIS ** E 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 403 HIS I 446 ASN I 483 HIS C 102 HIS C 147 ASN B 115 ASN B 468 GLN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31929 Z= 0.133 Angle : 0.542 11.462 43660 Z= 0.269 Chirality : 0.042 0.177 4764 Planarity : 0.005 0.075 5732 Dihedral : 5.222 73.763 4244 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.46 % Allowed : 23.88 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 3686 helix: -0.87 (0.51), residues: 94 sheet: -0.36 (0.17), residues: 858 loop : -0.36 (0.11), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 58 HIS 0.007 0.001 HIS C 102 PHE 0.030 0.001 PHE A 266 TYR 0.019 0.001 TYR A 561 ARG 0.007 0.001 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1637 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1523 time to evaluate : 3.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7375 (tt0) cc_final: 0.6980 (tp30) REVERT: A 79 TYR cc_start: 0.8377 (m-80) cc_final: 0.7798 (m-80) REVERT: A 104 GLN cc_start: 0.8136 (pt0) cc_final: 0.7668 (pt0) REVERT: A 109 TRP cc_start: 0.8528 (m100) cc_final: 0.7959 (m100) REVERT: A 177 LEU cc_start: 0.8421 (tt) cc_final: 0.8218 (tp) REVERT: A 200 TRP cc_start: 0.8424 (p90) cc_final: 0.8047 (p90) REVERT: A 214 TRP cc_start: 0.8278 (p90) cc_final: 0.7357 (p90) REVERT: A 237 ASP cc_start: 0.7687 (t0) cc_final: 0.7250 (t0) REVERT: A 247 GLU cc_start: 0.7683 (mp0) cc_final: 0.7326 (mp0) REVERT: A 260 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7082 (tt0) REVERT: A 266 PHE cc_start: 0.7538 (t80) cc_final: 0.7295 (t80) REVERT: A 312 LYS cc_start: 0.8502 (mtmt) cc_final: 0.8200 (mtmt) REVERT: A 335 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6147 (tm-30) REVERT: A 350 GLN cc_start: 0.7382 (mt0) cc_final: 0.6943 (mp10) REVERT: A 413 ASP cc_start: 0.6859 (OUTLIER) cc_final: 0.6418 (m-30) REVERT: A 414 TRP cc_start: 0.7906 (p90) cc_final: 0.7442 (p90) REVERT: A 446 ASN cc_start: 0.8139 (m110) cc_final: 0.7752 (m110) REVERT: A 473 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6741 (mm-30) REVERT: A 501 LYS cc_start: 0.8464 (ttpp) cc_final: 0.7637 (ttpp) REVERT: A 530 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7727 (ttpp) REVERT: A 538 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7743 (ttmt) REVERT: A 540 ARG cc_start: 0.8259 (ptm-80) cc_final: 0.7893 (ptm160) REVERT: A 566 ILE cc_start: 0.8635 (pp) cc_final: 0.8419 (pp) REVERT: G 60 GLU cc_start: 0.7652 (tp30) cc_final: 0.7139 (tp30) REVERT: G 62 THR cc_start: 0.8314 (m) cc_final: 0.7521 (p) REVERT: G 109 TRP cc_start: 0.8382 (m100) cc_final: 0.7840 (m100) REVERT: G 120 TRP cc_start: 0.8518 (m100) cc_final: 0.8091 (m100) REVERT: G 135 GLU cc_start: 0.6968 (tp30) cc_final: 0.6635 (tp30) REVERT: G 144 GLU cc_start: 0.7423 (pm20) cc_final: 0.6808 (pm20) REVERT: G 174 MET cc_start: 0.7627 (mtp) cc_final: 0.6973 (mtp) REVERT: G 193 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: G 213 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7007 (tm-30) REVERT: G 266 PHE cc_start: 0.8069 (t80) cc_final: 0.7819 (t80) REVERT: G 327 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6628 (mm-30) REVERT: G 335 GLU cc_start: 0.7315 (tt0) cc_final: 0.6772 (tt0) REVERT: G 342 TYR cc_start: 0.7725 (p90) cc_final: 0.7213 (p90) REVERT: G 345 PHE cc_start: 0.7885 (m-80) cc_final: 0.7210 (m-80) REVERT: G 398 PHE cc_start: 0.8714 (p90) cc_final: 0.8287 (p90) REVERT: G 426 ASN cc_start: 0.7958 (t0) cc_final: 0.7265 (t0) REVERT: G 479 LYS cc_start: 0.8581 (mmtm) cc_final: 0.8231 (mmtm) REVERT: G 491 GLN cc_start: 0.7580 (mm110) cc_final: 0.7201 (mm110) REVERT: G 501 LYS cc_start: 0.8145 (ttpp) cc_final: 0.7504 (ttpp) REVERT: G 505 ASN cc_start: 0.7329 (t0) cc_final: 0.6747 (t0) REVERT: G 518 MET cc_start: 0.7755 (ptp) cc_final: 0.7427 (ptp) REVERT: G 521 ILE cc_start: 0.8612 (mt) cc_final: 0.8393 (mt) REVERT: G 530 LYS cc_start: 0.8157 (ttpp) cc_final: 0.7158 (ttpp) REVERT: G 532 LYS cc_start: 0.8204 (ttmm) cc_final: 0.7969 (ttpp) REVERT: G 560 ASN cc_start: 0.8312 (m-40) cc_final: 0.7937 (m-40) REVERT: F 65 SER cc_start: 0.8518 (t) cc_final: 0.8086 (p) REVERT: F 72 ASN cc_start: 0.8163 (t0) cc_final: 0.7930 (t0) REVERT: F 73 MET cc_start: 0.7883 (ttp) cc_final: 0.7145 (tmm) REVERT: F 80 ARG cc_start: 0.3493 (tpt90) cc_final: 0.1548 (tpt170) REVERT: F 109 TRP cc_start: 0.8545 (m100) cc_final: 0.7682 (m100) REVERT: F 120 TRP cc_start: 0.8366 (m100) cc_final: 0.7789 (m100) REVERT: F 135 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: F 151 LYS cc_start: 0.8294 (mmmm) cc_final: 0.7637 (mmmm) REVERT: F 165 TYR cc_start: 0.8522 (m-80) cc_final: 0.8296 (m-80) REVERT: F 167 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7966 (m-40) REVERT: F 197 PHE cc_start: 0.8266 (m-10) cc_final: 0.7698 (m-80) REVERT: F 200 TRP cc_start: 0.8443 (p90) cc_final: 0.8225 (p90) REVERT: F 201 LYS cc_start: 0.8127 (mmpt) cc_final: 0.7725 (mmpt) REVERT: F 213 GLN cc_start: 0.7449 (tm-30) cc_final: 0.6932 (tm-30) REVERT: F 216 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7528 (ptm160) REVERT: F 237 ASP cc_start: 0.8120 (t0) cc_final: 0.7714 (t0) REVERT: F 266 PHE cc_start: 0.8189 (t80) cc_final: 0.7597 (t80) REVERT: F 279 TRP cc_start: 0.8393 (p-90) cc_final: 0.8191 (p-90) REVERT: F 335 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6520 (tp30) REVERT: F 386 GLN cc_start: 0.7069 (tt0) cc_final: 0.6742 (tt0) REVERT: F 409 TYR cc_start: 0.8058 (t80) cc_final: 0.7853 (t80) REVERT: F 431 LEU cc_start: 0.8436 (mt) cc_final: 0.8107 (mm) REVERT: F 439 LYS cc_start: 0.7928 (mmtp) cc_final: 0.7288 (mmtp) REVERT: F 451 TYR cc_start: 0.8569 (t80) cc_final: 0.8345 (t80) REVERT: F 470 TRP cc_start: 0.7733 (p90) cc_final: 0.7395 (p90) REVERT: F 501 LYS cc_start: 0.8063 (ttpp) cc_final: 0.7060 (ttpp) REVERT: F 532 LYS cc_start: 0.8506 (ttmm) cc_final: 0.8057 (ttmm) REVERT: F 533 LEU cc_start: 0.8463 (tp) cc_final: 0.7137 (tp) REVERT: F 540 ARG cc_start: 0.8132 (ptt90) cc_final: 0.7826 (ptm-80) REVERT: F 546 ASN cc_start: 0.8046 (p0) cc_final: 0.7825 (p0) REVERT: F 551 MET cc_start: 0.7186 (ttt) cc_final: 0.6689 (ttt) REVERT: F 562 VAL cc_start: 0.8602 (p) cc_final: 0.8374 (m) REVERT: F 575 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7115 (mmtt) REVERT: D 49 THR cc_start: 0.7859 (m) cc_final: 0.7465 (p) REVERT: D 50 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6588 (tm-30) REVERT: D 67 ARG cc_start: 0.7451 (mmt-90) cc_final: 0.7203 (mmt-90) REVERT: D 73 MET cc_start: 0.8167 (ptt) cc_final: 0.7745 (ptm) REVERT: D 174 MET cc_start: 0.7745 (mtp) cc_final: 0.7164 (mtp) REVERT: D 256 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7395 (mtm-85) REVERT: D 497 GLN cc_start: 0.6881 (mt0) cc_final: 0.6455 (tt0) REVERT: D 508 ASN cc_start: 0.8117 (p0) cc_final: 0.7654 (p0) REVERT: D 509 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6704 (mm-30) REVERT: E 60 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6654 (tm-30) REVERT: E 95 ASN cc_start: 0.8116 (t0) cc_final: 0.7704 (t0) REVERT: E 142 GLU cc_start: 0.7710 (pt0) cc_final: 0.6770 (pt0) REVERT: E 163 LYS cc_start: 0.7747 (mppt) cc_final: 0.7207 (mppt) REVERT: E 166 ASN cc_start: 0.7403 (m110) cc_final: 0.7165 (m110) REVERT: E 210 TYR cc_start: 0.8517 (p90) cc_final: 0.8129 (p90) REVERT: E 237 ASP cc_start: 0.7416 (t0) cc_final: 0.7083 (t0) REVERT: E 240 ASP cc_start: 0.7232 (m-30) cc_final: 0.6997 (m-30) REVERT: E 247 GLU cc_start: 0.7436 (mp0) cc_final: 0.6967 (mp0) REVERT: E 266 PHE cc_start: 0.8070 (t80) cc_final: 0.7721 (t80) REVERT: E 280 GLN cc_start: 0.5964 (pt0) cc_final: 0.5595 (pt0) REVERT: E 335 GLU cc_start: 0.6557 (tm-30) cc_final: 0.6303 (tm-30) REVERT: E 342 TYR cc_start: 0.7218 (p90) cc_final: 0.6863 (p90) REVERT: E 387 LYS cc_start: 0.8681 (tptm) cc_final: 0.8147 (tptm) REVERT: E 400 TYR cc_start: 0.8128 (t80) cc_final: 0.7306 (t80) REVERT: E 471 ASP cc_start: 0.5905 (t0) cc_final: 0.5538 (t0) REVERT: E 479 LYS cc_start: 0.8280 (mptt) cc_final: 0.7875 (mptt) REVERT: E 483 HIS cc_start: 0.7877 (m170) cc_final: 0.6993 (m90) REVERT: E 501 LYS cc_start: 0.7823 (tttt) cc_final: 0.7190 (tttt) REVERT: E 520 ARG cc_start: 0.7647 (mtp85) cc_final: 0.7018 (mtp85) REVERT: E 530 LYS cc_start: 0.7899 (tmtt) cc_final: 0.7227 (tttt) REVERT: E 532 LYS cc_start: 0.8171 (ttpt) cc_final: 0.7579 (ttpt) REVERT: E 560 ASN cc_start: 0.8235 (m-40) cc_final: 0.8010 (m110) REVERT: I 53 PHE cc_start: 0.8381 (m-80) cc_final: 0.8129 (m-80) REVERT: I 95 ASN cc_start: 0.8296 (m-40) cc_final: 0.8023 (m-40) REVERT: I 96 MET cc_start: 0.4302 (OUTLIER) cc_final: 0.3986 (ptt) REVERT: I 109 TRP cc_start: 0.8654 (m100) cc_final: 0.8444 (m100) REVERT: I 122 ASN cc_start: 0.8064 (p0) cc_final: 0.7798 (p0) REVERT: I 145 ILE cc_start: 0.8767 (mm) cc_final: 0.8469 (mm) REVERT: I 193 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6937 (mp0) REVERT: I 237 ASP cc_start: 0.7096 (t0) cc_final: 0.6643 (t0) REVERT: I 269 ASP cc_start: 0.6839 (p0) cc_final: 0.6554 (p0) REVERT: I 279 TRP cc_start: 0.8880 (p-90) cc_final: 0.8579 (p-90) REVERT: I 293 SER cc_start: 0.8602 (m) cc_final: 0.8034 (p) REVERT: I 314 ARG cc_start: 0.8058 (ptp-170) cc_final: 0.7814 (ptp90) REVERT: I 318 GLN cc_start: 0.8661 (mt0) cc_final: 0.8132 (mm-40) REVERT: I 346 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6622 (mm-30) REVERT: I 408 ARG cc_start: 0.7864 (mmt-90) cc_final: 0.7613 (mmt-90) REVERT: I 511 ASP cc_start: 0.8030 (p0) cc_final: 0.7804 (p0) REVERT: I 529 TRP cc_start: 0.7648 (t60) cc_final: 0.7284 (t60) REVERT: I 565 ASN cc_start: 0.8112 (t0) cc_final: 0.7864 (t0) REVERT: C 67 ARG cc_start: 0.7008 (mmt-90) cc_final: 0.6677 (mmt-90) REVERT: C 77 GLU cc_start: 0.6909 (tp30) cc_final: 0.6229 (tp30) REVERT: C 115 ASN cc_start: 0.7532 (t0) cc_final: 0.6476 (t0) REVERT: C 200 TRP cc_start: 0.8562 (p90) cc_final: 0.8330 (p90) REVERT: C 211 TYR cc_start: 0.6355 (m-80) cc_final: 0.6037 (m-80) REVERT: C 501 LYS cc_start: 0.8269 (tttp) cc_final: 0.7780 (tttm) REVERT: C 509 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6928 (tm-30) REVERT: C 528 TRP cc_start: 0.8534 (m100) cc_final: 0.8212 (m100) REVERT: C 529 TRP cc_start: 0.8837 (t60) cc_final: 0.8424 (t60) REVERT: C 530 LYS cc_start: 0.8475 (ttmt) cc_final: 0.8209 (ttmt) REVERT: B 53 PHE cc_start: 0.8226 (m-80) cc_final: 0.7819 (p90) REVERT: B 80 ARG cc_start: 0.8072 (mmm-85) cc_final: 0.7489 (mmm-85) REVERT: B 125 ASP cc_start: 0.7512 (m-30) cc_final: 0.7112 (m-30) REVERT: B 144 GLU cc_start: 0.7829 (pt0) cc_final: 0.7577 (pt0) REVERT: B 152 THR cc_start: 0.8115 (m) cc_final: 0.7842 (m) REVERT: B 256 ARG cc_start: 0.7804 (mtp180) cc_final: 0.7309 (mtp85) REVERT: B 268 PHE cc_start: 0.8509 (m-10) cc_final: 0.8127 (m-10) REVERT: B 400 TYR cc_start: 0.7807 (t80) cc_final: 0.7437 (t80) REVERT: B 415 ILE cc_start: 0.8314 (mt) cc_final: 0.8033 (mt) REVERT: B 416 GLN cc_start: 0.7924 (tt0) cc_final: 0.7519 (mp10) REVERT: B 417 ASN cc_start: 0.8025 (t0) cc_final: 0.7501 (t0) REVERT: B 430 LEU cc_start: 0.8343 (tp) cc_final: 0.8108 (tp) REVERT: B 463 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7713 (m) REVERT: B 506 LEU cc_start: 0.8335 (mt) cc_final: 0.8112 (mp) REVERT: B 510 TYR cc_start: 0.8846 (t80) cc_final: 0.8519 (t80) REVERT: B 511 ASP cc_start: 0.8152 (t0) cc_final: 0.7667 (t0) REVERT: B 538 LYS cc_start: 0.8418 (tptp) cc_final: 0.7844 (tppt) REVERT: B 549 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: B 565 ASN cc_start: 0.8057 (m110) cc_final: 0.7793 (m110) REVERT: B 569 MET cc_start: 0.7016 (mmm) cc_final: 0.6612 (mmm) REVERT: B 575 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7400 (mmtt) outliers start: 114 outliers final: 70 residues processed: 1549 average time/residue: 0.4482 time to fit residues: 1068.8539 Evaluate side-chains 1591 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1506 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 466 ASN Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 70 HIS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 556 ASP Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 201 LYS Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 497 GLN Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 549 GLN Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 357 optimal weight: 6.9990 chunk 378 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 chunk 339 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 282 ASN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 GLN ** F 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN ** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 GLN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN ** I 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS B 102 HIS B 483 HIS ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 31929 Z= 0.499 Angle : 0.668 11.332 43660 Z= 0.347 Chirality : 0.048 0.181 4764 Planarity : 0.006 0.086 5732 Dihedral : 5.686 68.627 4244 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.16 % Allowed : 23.76 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 3686 helix: -1.26 (0.40), residues: 124 sheet: -0.45 (0.17), residues: 885 loop : -0.45 (0.12), residues: 2677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 279 HIS 0.022 0.001 HIS C 102 PHE 0.038 0.003 PHE G 53 TYR 0.032 0.002 TYR I 464 ARG 0.007 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1725 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1555 time to evaluate : 4.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7570 (tt0) cc_final: 0.7221 (tp30) REVERT: A 79 TYR cc_start: 0.8363 (m-80) cc_final: 0.7691 (m-80) REVERT: A 104 GLN cc_start: 0.7950 (pt0) cc_final: 0.7652 (pt0) REVERT: A 147 ASN cc_start: 0.8208 (t0) cc_final: 0.7898 (t0) REVERT: A 163 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7770 (mtpt) REVERT: A 165 TYR cc_start: 0.7449 (m-80) cc_final: 0.6533 (m-80) REVERT: A 237 ASP cc_start: 0.7779 (t0) cc_final: 0.7229 (t0) REVERT: A 256 ARG cc_start: 0.8119 (mmm-85) cc_final: 0.7818 (mmm-85) REVERT: A 260 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7365 (tt0) REVERT: A 279 TRP cc_start: 0.8866 (p-90) cc_final: 0.8099 (p-90) REVERT: A 312 LYS cc_start: 0.8502 (mtmt) cc_final: 0.8200 (mtmt) REVERT: A 335 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6375 (tm-30) REVERT: A 350 GLN cc_start: 0.7466 (mt0) cc_final: 0.6894 (mp10) REVERT: A 380 PHE cc_start: 0.7665 (p90) cc_final: 0.7374 (p90) REVERT: A 411 GLU cc_start: 0.7928 (mp0) cc_final: 0.7471 (mp0) REVERT: A 413 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6548 (m-30) REVERT: A 414 TRP cc_start: 0.8148 (p90) cc_final: 0.7764 (p90) REVERT: A 426 ASN cc_start: 0.8668 (t0) cc_final: 0.8037 (t0) REVERT: A 427 ASP cc_start: 0.8009 (p0) cc_final: 0.7764 (p0) REVERT: A 464 TYR cc_start: 0.8322 (t80) cc_final: 0.8028 (t80) REVERT: A 473 GLU cc_start: 0.7443 (mm-30) cc_final: 0.6845 (mm-30) REVERT: A 501 LYS cc_start: 0.8582 (ttpp) cc_final: 0.7891 (ttpp) REVERT: A 530 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8114 (tttm) REVERT: A 538 LYS cc_start: 0.8107 (ttmt) cc_final: 0.7664 (ttmt) REVERT: G 50 GLU cc_start: 0.6970 (mp0) cc_final: 0.6557 (mp0) REVERT: G 53 PHE cc_start: 0.5109 (p90) cc_final: 0.4685 (p90) REVERT: G 60 GLU cc_start: 0.7715 (tp30) cc_final: 0.7237 (tp30) REVERT: G 62 THR cc_start: 0.8520 (m) cc_final: 0.8036 (t) REVERT: G 101 ILE cc_start: 0.8261 (mt) cc_final: 0.8013 (mt) REVERT: G 109 TRP cc_start: 0.8385 (m100) cc_final: 0.7847 (m100) REVERT: G 120 TRP cc_start: 0.8642 (m100) cc_final: 0.8032 (m100) REVERT: G 135 GLU cc_start: 0.7528 (tp30) cc_final: 0.6963 (tp30) REVERT: G 144 GLU cc_start: 0.7451 (pm20) cc_final: 0.7159 (pm20) REVERT: G 174 MET cc_start: 0.7703 (mtp) cc_final: 0.7112 (mtp) REVERT: G 193 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: G 213 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7497 (tm-30) REVERT: G 266 PHE cc_start: 0.8304 (t80) cc_final: 0.7783 (t80) REVERT: G 327 GLU cc_start: 0.7436 (mm-30) cc_final: 0.6903 (mm-30) REVERT: G 333 PRO cc_start: 0.9013 (Cg_exo) cc_final: 0.8740 (Cg_endo) REVERT: G 335 GLU cc_start: 0.7327 (tt0) cc_final: 0.6693 (tt0) REVERT: G 342 TYR cc_start: 0.7796 (p90) cc_final: 0.7307 (p90) REVERT: G 345 PHE cc_start: 0.7957 (m-80) cc_final: 0.7281 (m-80) REVERT: G 382 ARG cc_start: 0.5632 (mtm180) cc_final: 0.5375 (mtm180) REVERT: G 398 PHE cc_start: 0.8690 (p90) cc_final: 0.8105 (p90) REVERT: G 442 ILE cc_start: 0.8587 (mm) cc_final: 0.8370 (mm) REVERT: G 475 ASP cc_start: 0.7617 (t0) cc_final: 0.7001 (t0) REVERT: G 479 LYS cc_start: 0.8577 (mmtm) cc_final: 0.8303 (mmtm) REVERT: G 505 ASN cc_start: 0.7586 (t0) cc_final: 0.7003 (t0) REVERT: G 518 MET cc_start: 0.7842 (ptp) cc_final: 0.7504 (ptp) REVERT: G 520 ARG cc_start: 0.8195 (mtm-85) cc_final: 0.7833 (mtm-85) REVERT: G 530 LYS cc_start: 0.8118 (ttpp) cc_final: 0.7386 (ttpp) REVERT: G 560 ASN cc_start: 0.8211 (m-40) cc_final: 0.7897 (m-40) REVERT: F 72 ASN cc_start: 0.8396 (t0) cc_final: 0.8100 (t0) REVERT: F 73 MET cc_start: 0.8079 (ttp) cc_final: 0.7538 (ttp) REVERT: F 80 ARG cc_start: 0.3845 (tpt90) cc_final: 0.1735 (tpt170) REVERT: F 81 ARG cc_start: 0.5375 (ptp-170) cc_final: 0.3880 (ptt-90) REVERT: F 135 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: F 137 HIS cc_start: 0.8198 (m90) cc_final: 0.7926 (m170) REVERT: F 151 LYS cc_start: 0.8213 (mmmm) cc_final: 0.7437 (mmmm) REVERT: F 167 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7797 (m-40) REVERT: F 197 PHE cc_start: 0.8221 (m-10) cc_final: 0.7324 (m-80) REVERT: F 201 LYS cc_start: 0.8157 (mmpt) cc_final: 0.7718 (mmpt) REVERT: F 213 GLN cc_start: 0.7471 (tm-30) cc_final: 0.6750 (tm-30) REVERT: F 237 ASP cc_start: 0.8044 (t0) cc_final: 0.7554 (t0) REVERT: F 280 GLN cc_start: 0.8350 (mt0) cc_final: 0.8036 (mt0) REVERT: F 317 THR cc_start: 0.8275 (p) cc_final: 0.7943 (t) REVERT: F 335 GLU cc_start: 0.7427 (tt0) cc_final: 0.6963 (tt0) REVERT: F 409 TYR cc_start: 0.8390 (t80) cc_final: 0.7914 (t80) REVERT: F 470 TRP cc_start: 0.8039 (p90) cc_final: 0.7727 (p90) REVERT: F 475 ASP cc_start: 0.8089 (t0) cc_final: 0.7544 (t0) REVERT: F 497 GLN cc_start: 0.8359 (mt0) cc_final: 0.7897 (mt0) REVERT: F 518 MET cc_start: 0.7982 (ptp) cc_final: 0.7475 (ptp) REVERT: F 520 ARG cc_start: 0.7933 (mtt90) cc_final: 0.7188 (mtm-85) REVERT: F 532 LYS cc_start: 0.8431 (ttmm) cc_final: 0.7958 (ttmm) REVERT: F 550 GLN cc_start: 0.8220 (mm110) cc_final: 0.7903 (mm110) REVERT: F 551 MET cc_start: 0.7110 (ttt) cc_final: 0.6636 (ttt) REVERT: F 562 VAL cc_start: 0.8585 (p) cc_final: 0.8373 (m) REVERT: F 575 LYS cc_start: 0.7846 (mmtt) cc_final: 0.7243 (mmtt) REVERT: D 46 ASN cc_start: 0.7372 (t0) cc_final: 0.6740 (t0) REVERT: D 49 THR cc_start: 0.8008 (m) cc_final: 0.7562 (p) REVERT: D 50 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6635 (tm-30) REVERT: D 70 HIS cc_start: 0.7945 (t-170) cc_final: 0.7565 (t-170) REVERT: D 73 MET cc_start: 0.8248 (ptt) cc_final: 0.7615 (ptm) REVERT: D 144 GLU cc_start: 0.7013 (pm20) cc_final: 0.6352 (pm20) REVERT: D 174 MET cc_start: 0.7588 (mtp) cc_final: 0.7039 (mtp) REVERT: D 200 TRP cc_start: 0.8772 (p90) cc_final: 0.8215 (p90) REVERT: D 510 TYR cc_start: 0.8345 (t80) cc_final: 0.8065 (t80) REVERT: E 51 PHE cc_start: 0.8493 (m-80) cc_final: 0.8240 (m-80) REVERT: E 80 ARG cc_start: 0.7364 (ttm170) cc_final: 0.7048 (mtm-85) REVERT: E 95 ASN cc_start: 0.8273 (t0) cc_final: 0.7924 (t0) REVERT: E 142 GLU cc_start: 0.7790 (pt0) cc_final: 0.6851 (pt0) REVERT: E 163 LYS cc_start: 0.7962 (mppt) cc_final: 0.7468 (mppt) REVERT: E 170 THR cc_start: 0.8662 (p) cc_final: 0.8307 (t) REVERT: E 237 ASP cc_start: 0.7420 (t0) cc_final: 0.6993 (t0) REVERT: E 240 ASP cc_start: 0.7291 (m-30) cc_final: 0.7052 (m-30) REVERT: E 247 GLU cc_start: 0.7710 (mp0) cc_final: 0.7112 (mp0) REVERT: E 256 ARG cc_start: 0.7789 (mtp180) cc_final: 0.7477 (mtp85) REVERT: E 266 PHE cc_start: 0.8337 (t80) cc_final: 0.8069 (t80) REVERT: E 335 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6064 (tm-30) REVERT: E 342 TYR cc_start: 0.7159 (p90) cc_final: 0.6803 (p90) REVERT: E 386 GLN cc_start: 0.8284 (tt0) cc_final: 0.8056 (tt0) REVERT: E 387 LYS cc_start: 0.8747 (tptm) cc_final: 0.8504 (tptm) REVERT: E 451 TYR cc_start: 0.3590 (OUTLIER) cc_final: 0.3101 (t80) REVERT: E 464 TYR cc_start: 0.7943 (t80) cc_final: 0.7501 (t80) REVERT: E 471 ASP cc_start: 0.6345 (t0) cc_final: 0.6035 (t0) REVERT: E 472 LYS cc_start: 0.3340 (OUTLIER) cc_final: 0.1050 (tmmt) REVERT: E 479 LYS cc_start: 0.8241 (mptt) cc_final: 0.7856 (mptt) REVERT: E 501 LYS cc_start: 0.7962 (tttt) cc_final: 0.7333 (tttt) REVERT: E 520 ARG cc_start: 0.7694 (mtp85) cc_final: 0.7185 (mtp85) REVERT: E 532 LYS cc_start: 0.8311 (ttpt) cc_final: 0.7693 (ttpt) REVERT: E 560 ASN cc_start: 0.8462 (m-40) cc_final: 0.8106 (m110) REVERT: E 582 LYS cc_start: 0.6971 (pmtt) cc_final: 0.6348 (pmtt) REVERT: I 95 ASN cc_start: 0.8332 (m-40) cc_final: 0.7957 (m-40) REVERT: I 109 TRP cc_start: 0.8699 (m100) cc_final: 0.7818 (m100) REVERT: I 122 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7740 (p0) REVERT: I 147 ASN cc_start: 0.7973 (t0) cc_final: 0.7525 (t0) REVERT: I 178 ASP cc_start: 0.6690 (t0) cc_final: 0.6442 (t0) REVERT: I 193 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7094 (mp0) REVERT: I 237 ASP cc_start: 0.7386 (t0) cc_final: 0.6842 (t0) REVERT: I 269 ASP cc_start: 0.6798 (p0) cc_final: 0.6590 (p0) REVERT: I 318 GLN cc_start: 0.8643 (mt0) cc_final: 0.8140 (mm-40) REVERT: I 332 ARG cc_start: 0.8738 (mmt-90) cc_final: 0.8361 (mmt90) REVERT: I 346 GLU cc_start: 0.6743 (mm-30) cc_final: 0.6505 (mm-30) REVERT: I 408 ARG cc_start: 0.7693 (mmt-90) cc_final: 0.7427 (mmt-90) REVERT: I 415 ILE cc_start: 0.8654 (mt) cc_final: 0.8308 (mm) REVERT: I 491 GLN cc_start: 0.7520 (mm-40) cc_final: 0.6841 (mm-40) REVERT: I 538 LYS cc_start: 0.8289 (tppt) cc_final: 0.7984 (tppt) REVERT: I 582 LYS cc_start: 0.8417 (pttm) cc_final: 0.8062 (pttm) REVERT: C 67 ARG cc_start: 0.7015 (mmt-90) cc_final: 0.6606 (mmt-90) REVERT: C 68 LEU cc_start: 0.8242 (tp) cc_final: 0.7577 (tp) REVERT: C 73 MET cc_start: 0.7933 (ptt) cc_final: 0.7547 (ptt) REVERT: C 77 GLU cc_start: 0.7004 (tp30) cc_final: 0.6382 (tp30) REVERT: C 86 ASN cc_start: 0.7794 (p0) cc_final: 0.7533 (p0) REVERT: C 193 GLU cc_start: 0.7173 (tp30) cc_final: 0.6750 (tp30) REVERT: C 509 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: C 520 ARG cc_start: 0.8658 (mpp80) cc_final: 0.8371 (mpp80) REVERT: C 528 TRP cc_start: 0.8535 (m100) cc_final: 0.7734 (m100) REVERT: B 53 PHE cc_start: 0.8410 (m-80) cc_final: 0.7845 (p90) REVERT: B 68 LEU cc_start: 0.8698 (tp) cc_final: 0.8388 (tp) REVERT: B 109 TRP cc_start: 0.8849 (m100) cc_final: 0.8051 (m100) REVERT: B 117 TRP cc_start: 0.7878 (m100) cc_final: 0.7263 (m100) REVERT: B 152 THR cc_start: 0.8231 (m) cc_final: 0.7956 (m) REVERT: B 182 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.8013 (m) REVERT: B 268 PHE cc_start: 0.8501 (m-10) cc_final: 0.8188 (m-10) REVERT: B 424 VAL cc_start: 0.8054 (OUTLIER) cc_final: 0.7803 (m) REVERT: B 463 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.7786 (m) REVERT: B 528 TRP cc_start: 0.8694 (m100) cc_final: 0.8267 (m100) REVERT: B 550 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6932 (mm-40) REVERT: B 551 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.7047 (ttt) REVERT: B 569 MET cc_start: 0.6922 (mmm) cc_final: 0.6639 (mmm) REVERT: B 574 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7244 (mm-30) outliers start: 170 outliers final: 116 residues processed: 1611 average time/residue: 0.4391 time to fit residues: 1102.7830 Evaluate side-chains 1667 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1535 time to evaluate : 3.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain G residue 582 LYS Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 458 ASN Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 451 TYR Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 556 ASP Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 444 TYR Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 497 GLN Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 570 LYS Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 551 MET Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 574 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 282 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 323 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 chunk 340 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 GLN ** F 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN ** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 318 GLN I 446 ASN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN B 137 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 31929 Z= 0.227 Angle : 0.577 10.890 43660 Z= 0.290 Chirality : 0.043 0.172 4764 Planarity : 0.005 0.068 5732 Dihedral : 5.136 71.167 4237 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.67 % Allowed : 26.31 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.13), residues: 3686 helix: -0.96 (0.47), residues: 100 sheet: -0.30 (0.18), residues: 869 loop : -0.37 (0.12), residues: 2717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 279 HIS 0.007 0.001 HIS C 102 PHE 0.030 0.002 PHE G 527 TYR 0.029 0.002 TYR A 561 ARG 0.008 0.001 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1697 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1543 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7490 (tt0) cc_final: 0.7100 (tp30) REVERT: A 67 ARG cc_start: 0.8104 (mmt180) cc_final: 0.7675 (mmt180) REVERT: A 79 TYR cc_start: 0.8223 (m-80) cc_final: 0.7544 (m-80) REVERT: A 96 MET cc_start: 0.6899 (mmt) cc_final: 0.6677 (mmt) REVERT: A 104 GLN cc_start: 0.8080 (pt0) cc_final: 0.7664 (pt0) REVERT: A 147 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7887 (t0) REVERT: A 236 THR cc_start: 0.7996 (p) cc_final: 0.7764 (p) REVERT: A 260 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: A 312 LYS cc_start: 0.8465 (mtmt) cc_final: 0.8192 (mtmt) REVERT: A 335 GLU cc_start: 0.7309 (tt0) cc_final: 0.6345 (tm-30) REVERT: A 350 GLN cc_start: 0.7435 (mt0) cc_final: 0.6815 (mp10) REVERT: A 380 PHE cc_start: 0.7640 (p90) cc_final: 0.7321 (p90) REVERT: A 411 GLU cc_start: 0.7820 (mp0) cc_final: 0.7488 (mp0) REVERT: A 413 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6539 (m-30) REVERT: A 414 TRP cc_start: 0.8182 (p90) cc_final: 0.7668 (p90) REVERT: A 431 LEU cc_start: 0.8546 (mt) cc_final: 0.8311 (mp) REVERT: A 443 ASN cc_start: 0.8141 (p0) cc_final: 0.7897 (p0) REVERT: A 464 TYR cc_start: 0.8253 (t80) cc_final: 0.7953 (t80) REVERT: A 473 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6791 (mm-30) REVERT: A 501 LYS cc_start: 0.8573 (ttpp) cc_final: 0.7906 (ttpp) REVERT: A 528 TRP cc_start: 0.8327 (m100) cc_final: 0.7886 (m100) REVERT: A 530 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7783 (ttpp) REVERT: A 538 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7607 (ttmt) REVERT: A 569 MET cc_start: 0.6929 (mmm) cc_final: 0.6292 (tpp) REVERT: G 48 GLN cc_start: 0.1945 (mm110) cc_final: 0.1352 (mm-40) REVERT: G 50 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6549 (mp0) REVERT: G 53 PHE cc_start: 0.5334 (p90) cc_final: 0.4616 (p90) REVERT: G 60 GLU cc_start: 0.7687 (tp30) cc_final: 0.7212 (tp30) REVERT: G 62 THR cc_start: 0.8462 (m) cc_final: 0.7940 (t) REVERT: G 68 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8010 (tt) REVERT: G 109 TRP cc_start: 0.8432 (m100) cc_final: 0.7907 (m100) REVERT: G 120 TRP cc_start: 0.8544 (m100) cc_final: 0.8130 (m100) REVERT: G 135 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6861 (tp30) REVERT: G 137 HIS cc_start: 0.8293 (m170) cc_final: 0.8028 (m90) REVERT: G 143 GLN cc_start: 0.8266 (mt0) cc_final: 0.7992 (mt0) REVERT: G 144 GLU cc_start: 0.7387 (pm20) cc_final: 0.7172 (pm20) REVERT: G 174 MET cc_start: 0.7605 (mtp) cc_final: 0.7061 (mtp) REVERT: G 213 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7310 (tm-30) REVERT: G 266 PHE cc_start: 0.8201 (t80) cc_final: 0.7738 (t80) REVERT: G 312 LYS cc_start: 0.8409 (mtpp) cc_final: 0.8143 (mtpp) REVERT: G 327 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6736 (mm-30) REVERT: G 335 GLU cc_start: 0.7280 (tt0) cc_final: 0.6685 (tt0) REVERT: G 342 TYR cc_start: 0.7740 (p90) cc_final: 0.7299 (p90) REVERT: G 345 PHE cc_start: 0.7926 (m-80) cc_final: 0.7282 (m-80) REVERT: G 382 ARG cc_start: 0.5318 (mtm180) cc_final: 0.4758 (mtm180) REVERT: G 386 GLN cc_start: 0.7755 (mt0) cc_final: 0.7535 (mt0) REVERT: G 398 PHE cc_start: 0.8698 (p90) cc_final: 0.8294 (p90) REVERT: G 442 ILE cc_start: 0.8547 (mm) cc_final: 0.8241 (mm) REVERT: G 479 LYS cc_start: 0.8626 (mmtm) cc_final: 0.8319 (mmtm) REVERT: G 505 ASN cc_start: 0.7575 (t0) cc_final: 0.6916 (t0) REVERT: G 509 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7554 (mm-30) REVERT: G 518 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7479 (ptp) REVERT: G 528 TRP cc_start: 0.8094 (m100) cc_final: 0.7511 (m100) REVERT: G 530 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7424 (ttpp) REVERT: G 535 PHE cc_start: 0.8218 (m-80) cc_final: 0.7439 (m-80) REVERT: G 560 ASN cc_start: 0.8212 (m-40) cc_final: 0.7890 (m-40) REVERT: G 581 ARG cc_start: 0.7941 (ptt90) cc_final: 0.7408 (ptt90) REVERT: G 582 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8214 (pttm) REVERT: F 65 SER cc_start: 0.8539 (t) cc_final: 0.8116 (p) REVERT: F 67 ARG cc_start: 0.8238 (mmt180) cc_final: 0.7979 (mmt180) REVERT: F 72 ASN cc_start: 0.8407 (t0) cc_final: 0.8113 (t0) REVERT: F 73 MET cc_start: 0.8096 (ttp) cc_final: 0.7283 (ttp) REVERT: F 80 ARG cc_start: 0.3695 (tpt90) cc_final: 0.0890 (tpt170) REVERT: F 81 ARG cc_start: 0.5159 (ptp-170) cc_final: 0.4839 (ptp-170) REVERT: F 109 TRP cc_start: 0.8537 (m100) cc_final: 0.8258 (m100) REVERT: F 120 TRP cc_start: 0.8389 (m100) cc_final: 0.7847 (m100) REVERT: F 135 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: F 151 LYS cc_start: 0.8198 (mmmm) cc_final: 0.7367 (mmmm) REVERT: F 167 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7797 (m-40) REVERT: F 197 PHE cc_start: 0.8301 (m-10) cc_final: 0.7460 (m-80) REVERT: F 201 LYS cc_start: 0.8189 (mmpt) cc_final: 0.7766 (mmpt) REVERT: F 213 GLN cc_start: 0.7415 (tm-30) cc_final: 0.6845 (tm-30) REVERT: F 237 ASP cc_start: 0.8094 (t0) cc_final: 0.7436 (t0) REVERT: F 317 THR cc_start: 0.8148 (p) cc_final: 0.7814 (t) REVERT: F 350 GLN cc_start: 0.7852 (mp10) cc_final: 0.7632 (mp10) REVERT: F 409 TYR cc_start: 0.8325 (t80) cc_final: 0.7969 (t80) REVERT: F 430 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8678 (tt) REVERT: F 475 ASP cc_start: 0.8083 (t0) cc_final: 0.7674 (t0) REVERT: F 518 MET cc_start: 0.7905 (ptp) cc_final: 0.7406 (ptp) REVERT: F 520 ARG cc_start: 0.7940 (mtt90) cc_final: 0.6833 (mtm110) REVERT: F 532 LYS cc_start: 0.8412 (ttmm) cc_final: 0.8003 (ttmm) REVERT: F 551 MET cc_start: 0.7122 (ttt) cc_final: 0.6816 (ttt) REVERT: F 562 VAL cc_start: 0.8609 (p) cc_final: 0.8368 (m) REVERT: F 575 LYS cc_start: 0.7888 (mmtt) cc_final: 0.7334 (mmmt) REVERT: D 46 ASN cc_start: 0.7425 (t0) cc_final: 0.7107 (t0) REVERT: D 49 THR cc_start: 0.8012 (m) cc_final: 0.7553 (p) REVERT: D 50 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6575 (tm-30) REVERT: D 64 ASN cc_start: 0.7913 (m-40) cc_final: 0.7512 (m110) REVERT: D 73 MET cc_start: 0.8259 (ptt) cc_final: 0.7678 (ptm) REVERT: D 174 MET cc_start: 0.7678 (mtp) cc_final: 0.7096 (mtp) REVERT: D 200 TRP cc_start: 0.8765 (p90) cc_final: 0.8243 (p90) REVERT: D 256 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7415 (mtm-85) REVERT: E 51 PHE cc_start: 0.8484 (m-80) cc_final: 0.8241 (m-80) REVERT: E 80 ARG cc_start: 0.7326 (ttm170) cc_final: 0.7001 (mtm-85) REVERT: E 95 ASN cc_start: 0.8216 (t0) cc_final: 0.7841 (t0) REVERT: E 142 GLU cc_start: 0.7674 (pt0) cc_final: 0.6746 (pt0) REVERT: E 163 LYS cc_start: 0.7967 (mppt) cc_final: 0.7482 (mppt) REVERT: E 170 THR cc_start: 0.8655 (p) cc_final: 0.8380 (m) REVERT: E 210 TYR cc_start: 0.8458 (p90) cc_final: 0.8040 (p90) REVERT: E 237 ASP cc_start: 0.7410 (t0) cc_final: 0.7104 (t0) REVERT: E 240 ASP cc_start: 0.7256 (m-30) cc_final: 0.7000 (m-30) REVERT: E 247 GLU cc_start: 0.7628 (mp0) cc_final: 0.7009 (mp0) REVERT: E 266 PHE cc_start: 0.8263 (t80) cc_final: 0.8034 (t80) REVERT: E 335 GLU cc_start: 0.6726 (tm-30) cc_final: 0.6009 (tm-30) REVERT: E 342 TYR cc_start: 0.7092 (p90) cc_final: 0.6762 (p90) REVERT: E 380 PHE cc_start: 0.7839 (p90) cc_final: 0.7621 (p90) REVERT: E 386 GLN cc_start: 0.8257 (tt0) cc_final: 0.7940 (tt0) REVERT: E 387 LYS cc_start: 0.8732 (tptm) cc_final: 0.8476 (tptm) REVERT: E 396 GLU cc_start: 0.7307 (tt0) cc_final: 0.6828 (tt0) REVERT: E 464 TYR cc_start: 0.7864 (t80) cc_final: 0.7366 (t80) REVERT: E 471 ASP cc_start: 0.6376 (t0) cc_final: 0.5968 (t0) REVERT: E 472 LYS cc_start: 0.3215 (OUTLIER) cc_final: 0.0991 (tmmt) REVERT: E 479 LYS cc_start: 0.8248 (mptt) cc_final: 0.7808 (mptt) REVERT: E 483 HIS cc_start: 0.7890 (m170) cc_final: 0.7478 (m170) REVERT: E 501 LYS cc_start: 0.7954 (tttt) cc_final: 0.7294 (tttt) REVERT: E 520 ARG cc_start: 0.7732 (mtp85) cc_final: 0.7271 (mtp85) REVERT: E 530 LYS cc_start: 0.8021 (tmtt) cc_final: 0.7414 (tttt) REVERT: E 532 LYS cc_start: 0.8313 (ttpt) cc_final: 0.7691 (ttpt) REVERT: E 538 LYS cc_start: 0.7248 (ttmm) cc_final: 0.6762 (mtpp) REVERT: E 550 GLN cc_start: 0.7502 (mm-40) cc_final: 0.7056 (mm-40) REVERT: E 560 ASN cc_start: 0.8361 (m-40) cc_final: 0.8054 (m110) REVERT: E 582 LYS cc_start: 0.6851 (pmtt) cc_final: 0.6157 (pmtt) REVERT: I 95 ASN cc_start: 0.8289 (m-40) cc_final: 0.7953 (m-40) REVERT: I 96 MET cc_start: 0.4219 (ptt) cc_final: 0.3986 (ptt) REVERT: I 109 TRP cc_start: 0.8718 (m100) cc_final: 0.7734 (m100) REVERT: I 122 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7743 (p0) REVERT: I 178 ASP cc_start: 0.6720 (t0) cc_final: 0.6392 (t0) REVERT: I 183 MET cc_start: 0.7357 (mmm) cc_final: 0.7151 (mmm) REVERT: I 193 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7015 (mp0) REVERT: I 237 ASP cc_start: 0.7305 (t0) cc_final: 0.6692 (t0) REVERT: I 269 ASP cc_start: 0.6754 (p0) cc_final: 0.6405 (p0) REVERT: I 332 ARG cc_start: 0.8698 (mmt-90) cc_final: 0.8406 (mmt90) REVERT: I 346 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6537 (mm-30) REVERT: I 408 ARG cc_start: 0.7679 (mmt-90) cc_final: 0.7339 (mmt-90) REVERT: I 415 ILE cc_start: 0.8660 (mt) cc_final: 0.8305 (mm) REVERT: I 491 GLN cc_start: 0.7544 (mm-40) cc_final: 0.6744 (mm-40) REVERT: I 528 TRP cc_start: 0.8274 (m100) cc_final: 0.7702 (m100) REVERT: I 582 LYS cc_start: 0.8429 (pttm) cc_final: 0.8085 (pttm) REVERT: C 47 ASN cc_start: 0.7703 (t0) cc_final: 0.7330 (t160) REVERT: C 67 ARG cc_start: 0.6774 (mmt-90) cc_final: 0.6437 (mmt-90) REVERT: C 68 LEU cc_start: 0.8148 (tp) cc_final: 0.7501 (tp) REVERT: C 73 MET cc_start: 0.7986 (ptt) cc_final: 0.7505 (ptt) REVERT: C 147 ASN cc_start: 0.8429 (t0) cc_final: 0.7938 (t0) REVERT: C 193 GLU cc_start: 0.7094 (tp30) cc_final: 0.6712 (tp30) REVERT: C 501 LYS cc_start: 0.8307 (tttp) cc_final: 0.7781 (tttm) REVERT: C 509 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6933 (tm-30) REVERT: C 520 ARG cc_start: 0.8642 (mpp80) cc_final: 0.8179 (mpp80) REVERT: C 528 TRP cc_start: 0.8545 (m100) cc_final: 0.7767 (m100) REVERT: B 53 PHE cc_start: 0.8412 (m-80) cc_final: 0.7912 (p90) REVERT: B 80 ARG cc_start: 0.8103 (mmm-85) cc_final: 0.7633 (mmm-85) REVERT: B 82 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8202 (m) REVERT: B 152 THR cc_start: 0.8231 (m) cc_final: 0.7992 (m) REVERT: B 182 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.8009 (m) REVERT: B 201 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8565 (mmmt) REVERT: B 268 PHE cc_start: 0.8493 (m-10) cc_final: 0.8199 (m-10) REVERT: B 424 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7850 (m) REVERT: B 463 VAL cc_start: 0.8107 (OUTLIER) cc_final: 0.7750 (m) REVERT: B 491 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7023 (mm-40) REVERT: B 551 MET cc_start: 0.7293 (ttt) cc_final: 0.6890 (ttt) REVERT: B 565 ASN cc_start: 0.8045 (m110) cc_final: 0.7757 (m110) REVERT: B 569 MET cc_start: 0.6976 (mmm) cc_final: 0.6666 (mmm) outliers start: 154 outliers final: 102 residues processed: 1591 average time/residue: 0.4510 time to fit residues: 1112.9203 Evaluate side-chains 1649 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1528 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 383 GLN Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 518 MET Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain G residue 582 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 468 GLN Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 318 GLN Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 429 VAL Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 497 GLN Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 518 MET Chi-restraints excluded: chain I residue 521 ILE Chi-restraints excluded: chain I residue 570 LYS Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 10.0000 chunk 341 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 222 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 379 optimal weight: 7.9990 chunk 314 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 199 optimal weight: 1.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 ASN G 231 ASN ** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 GLN ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN ** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 GLN ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 446 ASN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 31929 Z= 0.323 Angle : 0.603 10.277 43660 Z= 0.305 Chirality : 0.045 0.211 4764 Planarity : 0.005 0.069 5732 Dihedral : 5.184 70.211 4237 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.28 % Allowed : 26.43 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 3686 helix: -1.15 (0.42), residues: 124 sheet: -0.26 (0.18), residues: 858 loop : -0.40 (0.12), residues: 2704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 279 HIS 0.005 0.001 HIS A 222 PHE 0.025 0.002 PHE G 527 TYR 0.031 0.002 TYR A 561 ARG 0.007 0.001 ARG G 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1738 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1564 time to evaluate : 3.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7516 (tt0) cc_final: 0.7148 (tp30) REVERT: A 67 ARG cc_start: 0.8140 (mmt180) cc_final: 0.7779 (mmt180) REVERT: A 79 TYR cc_start: 0.8221 (m-80) cc_final: 0.7581 (m-80) REVERT: A 96 MET cc_start: 0.6919 (mmp) cc_final: 0.6661 (mmt) REVERT: A 104 GLN cc_start: 0.7999 (pt0) cc_final: 0.7722 (pt0) REVERT: A 147 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7859 (t0) REVERT: A 165 TYR cc_start: 0.7581 (m-80) cc_final: 0.7275 (m-80) REVERT: A 237 ASP cc_start: 0.7871 (t0) cc_final: 0.7410 (t0) REVERT: A 244 TYR cc_start: 0.7116 (m-80) cc_final: 0.6548 (m-80) REVERT: A 260 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: A 312 LYS cc_start: 0.8463 (mtmt) cc_final: 0.8188 (mtmt) REVERT: A 335 GLU cc_start: 0.7286 (tt0) cc_final: 0.6331 (tm-30) REVERT: A 350 GLN cc_start: 0.7498 (mt0) cc_final: 0.6985 (mp10) REVERT: A 411 GLU cc_start: 0.7832 (mp0) cc_final: 0.7411 (mp0) REVERT: A 413 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6558 (m-30) REVERT: A 414 TRP cc_start: 0.8193 (p90) cc_final: 0.7668 (p90) REVERT: A 443 ASN cc_start: 0.8077 (p0) cc_final: 0.7848 (p0) REVERT: A 464 TYR cc_start: 0.8269 (t80) cc_final: 0.8001 (t80) REVERT: A 473 GLU cc_start: 0.7430 (mm-30) cc_final: 0.6834 (mm-30) REVERT: A 501 LYS cc_start: 0.8570 (ttpp) cc_final: 0.8019 (ttpp) REVERT: A 528 TRP cc_start: 0.8302 (m100) cc_final: 0.7849 (m100) REVERT: A 530 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7844 (ttpp) REVERT: A 538 LYS cc_start: 0.8053 (ttmt) cc_final: 0.7619 (ttmt) REVERT: A 569 MET cc_start: 0.6893 (mmm) cc_final: 0.6382 (tpp) REVERT: G 48 GLN cc_start: 0.1819 (mm110) cc_final: 0.1128 (mm-40) REVERT: G 50 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6575 (mp0) REVERT: G 53 PHE cc_start: 0.5108 (p90) cc_final: 0.4504 (p90) REVERT: G 60 GLU cc_start: 0.7686 (tp30) cc_final: 0.7216 (tp30) REVERT: G 62 THR cc_start: 0.8472 (m) cc_final: 0.7950 (t) REVERT: G 68 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8035 (tt) REVERT: G 104 GLN cc_start: 0.8027 (pt0) cc_final: 0.7513 (pt0) REVERT: G 109 TRP cc_start: 0.8377 (m100) cc_final: 0.7905 (m100) REVERT: G 120 TRP cc_start: 0.8565 (m100) cc_final: 0.8251 (m100) REVERT: G 135 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6950 (tp30) REVERT: G 137 HIS cc_start: 0.8374 (m170) cc_final: 0.8128 (m90) REVERT: G 143 GLN cc_start: 0.8372 (mt0) cc_final: 0.7946 (mt0) REVERT: G 144 GLU cc_start: 0.7327 (pm20) cc_final: 0.7084 (pm20) REVERT: G 145 ILE cc_start: 0.8580 (mp) cc_final: 0.8291 (mp) REVERT: G 174 MET cc_start: 0.7687 (mtp) cc_final: 0.7149 (mtp) REVERT: G 183 MET cc_start: 0.7569 (mmp) cc_final: 0.7365 (mmp) REVERT: G 193 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6599 (mp0) REVERT: G 200 TRP cc_start: 0.8607 (p90) cc_final: 0.8191 (p90) REVERT: G 213 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7415 (tm-30) REVERT: G 245 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7670 (t) REVERT: G 266 PHE cc_start: 0.8241 (t80) cc_final: 0.7775 (t80) REVERT: G 311 ASP cc_start: 0.7751 (p0) cc_final: 0.7224 (p0) REVERT: G 312 LYS cc_start: 0.8440 (mtpp) cc_final: 0.8215 (mtpp) REVERT: G 327 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6783 (mm-30) REVERT: G 331 MET cc_start: 0.7715 (ttm) cc_final: 0.7461 (ttm) REVERT: G 335 GLU cc_start: 0.7301 (tt0) cc_final: 0.6705 (tt0) REVERT: G 342 TYR cc_start: 0.7748 (p90) cc_final: 0.7370 (p90) REVERT: G 345 PHE cc_start: 0.7867 (m-80) cc_final: 0.7208 (m-80) REVERT: G 386 GLN cc_start: 0.7793 (mt0) cc_final: 0.7542 (mt0) REVERT: G 398 PHE cc_start: 0.8623 (p90) cc_final: 0.8171 (p90) REVERT: G 442 ILE cc_start: 0.8531 (mm) cc_final: 0.8263 (mm) REVERT: G 475 ASP cc_start: 0.7556 (t0) cc_final: 0.6866 (t0) REVERT: G 479 LYS cc_start: 0.8629 (mmtm) cc_final: 0.8345 (mmtm) REVERT: G 497 GLN cc_start: 0.8433 (mt0) cc_final: 0.8089 (mt0) REVERT: G 505 ASN cc_start: 0.7598 (t0) cc_final: 0.6883 (t0) REVERT: G 509 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7562 (mm-30) REVERT: G 518 MET cc_start: 0.7781 (ptp) cc_final: 0.7491 (ptp) REVERT: G 528 TRP cc_start: 0.8079 (m100) cc_final: 0.7446 (m100) REVERT: G 530 LYS cc_start: 0.8080 (ttpp) cc_final: 0.7432 (ttpp) REVERT: G 535 PHE cc_start: 0.8224 (m-80) cc_final: 0.7490 (m-80) REVERT: G 582 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8321 (pttm) REVERT: F 65 SER cc_start: 0.8505 (t) cc_final: 0.8031 (p) REVERT: F 67 ARG cc_start: 0.8267 (mmt180) cc_final: 0.7775 (mmt90) REVERT: F 72 ASN cc_start: 0.8447 (t0) cc_final: 0.8167 (t0) REVERT: F 73 MET cc_start: 0.8078 (ttp) cc_final: 0.7716 (ttp) REVERT: F 80 ARG cc_start: 0.3906 (tpt90) cc_final: 0.1323 (mmt180) REVERT: F 81 ARG cc_start: 0.5268 (ptp-170) cc_final: 0.5053 (ptp-170) REVERT: F 101 ILE cc_start: 0.8364 (mt) cc_final: 0.8118 (mt) REVERT: F 120 TRP cc_start: 0.8414 (m100) cc_final: 0.7922 (m100) REVERT: F 135 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: F 151 LYS cc_start: 0.8186 (mmmm) cc_final: 0.7365 (mmmm) REVERT: F 167 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7776 (m-40) REVERT: F 197 PHE cc_start: 0.8262 (m-10) cc_final: 0.7391 (m-80) REVERT: F 201 LYS cc_start: 0.8209 (mmpt) cc_final: 0.7801 (mmpt) REVERT: F 213 GLN cc_start: 0.7408 (tm-30) cc_final: 0.6908 (tm-30) REVERT: F 237 ASP cc_start: 0.8120 (t0) cc_final: 0.7440 (t0) REVERT: F 242 GLN cc_start: 0.7594 (pt0) cc_final: 0.7249 (pp30) REVERT: F 279 TRP cc_start: 0.8259 (p-90) cc_final: 0.8052 (p-90) REVERT: F 317 THR cc_start: 0.8192 (p) cc_final: 0.7809 (t) REVERT: F 350 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7516 (mp10) REVERT: F 409 TYR cc_start: 0.8349 (t80) cc_final: 0.7945 (t80) REVERT: F 473 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7152 (tm-30) REVERT: F 475 ASP cc_start: 0.8071 (t0) cc_final: 0.7141 (t0) REVERT: F 497 GLN cc_start: 0.8259 (mt0) cc_final: 0.7745 (mt0) REVERT: F 499 PHE cc_start: 0.8507 (m-80) cc_final: 0.8058 (m-80) REVERT: F 518 MET cc_start: 0.7926 (ptp) cc_final: 0.7383 (ptp) REVERT: F 532 LYS cc_start: 0.8394 (ttmm) cc_final: 0.7961 (ttmm) REVERT: F 551 MET cc_start: 0.7052 (ttt) cc_final: 0.6750 (ttt) REVERT: F 562 VAL cc_start: 0.8613 (p) cc_final: 0.8403 (m) REVERT: D 46 ASN cc_start: 0.7446 (t0) cc_final: 0.7095 (t0) REVERT: D 50 GLU cc_start: 0.7427 (mm-30) cc_final: 0.6595 (tm-30) REVERT: D 70 HIS cc_start: 0.7889 (t-170) cc_final: 0.7400 (t-170) REVERT: D 73 MET cc_start: 0.8274 (ptt) cc_final: 0.7660 (ptm) REVERT: D 107 THR cc_start: 0.8365 (m) cc_final: 0.7757 (p) REVERT: D 174 MET cc_start: 0.7622 (mtp) cc_final: 0.7120 (mtp) REVERT: D 200 TRP cc_start: 0.8753 (p90) cc_final: 0.8236 (p90) REVERT: D 256 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7668 (mtm-85) REVERT: E 51 PHE cc_start: 0.8485 (m-80) cc_final: 0.8261 (m-80) REVERT: E 95 ASN cc_start: 0.8258 (t0) cc_final: 0.7902 (t0) REVERT: E 142 GLU cc_start: 0.7657 (pt0) cc_final: 0.6485 (pt0) REVERT: E 163 LYS cc_start: 0.8017 (mppt) cc_final: 0.7542 (mppt) REVERT: E 170 THR cc_start: 0.8616 (p) cc_final: 0.8399 (m) REVERT: E 210 TYR cc_start: 0.8505 (p90) cc_final: 0.8212 (p90) REVERT: E 213 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7671 (tm-30) REVERT: E 237 ASP cc_start: 0.7387 (t0) cc_final: 0.6999 (t0) REVERT: E 240 ASP cc_start: 0.7199 (m-30) cc_final: 0.6991 (m-30) REVERT: E 247 GLU cc_start: 0.7660 (mp0) cc_final: 0.7027 (mp0) REVERT: E 266 PHE cc_start: 0.8292 (t80) cc_final: 0.8045 (t80) REVERT: E 335 GLU cc_start: 0.6795 (tm-30) cc_final: 0.6040 (tm-30) REVERT: E 342 TYR cc_start: 0.7094 (p90) cc_final: 0.6765 (p90) REVERT: E 380 PHE cc_start: 0.7810 (p90) cc_final: 0.7531 (p90) REVERT: E 386 GLN cc_start: 0.8254 (tt0) cc_final: 0.7998 (tt0) REVERT: E 387 LYS cc_start: 0.8748 (tptm) cc_final: 0.8519 (tptm) REVERT: E 396 GLU cc_start: 0.7317 (tt0) cc_final: 0.6970 (tt0) REVERT: E 430 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7522 (tt) REVERT: E 451 TYR cc_start: 0.3440 (OUTLIER) cc_final: 0.3035 (t80) REVERT: E 464 TYR cc_start: 0.7946 (t80) cc_final: 0.7591 (t80) REVERT: E 472 LYS cc_start: 0.3407 (OUTLIER) cc_final: 0.1219 (tmmt) REVERT: E 479 LYS cc_start: 0.8240 (mptt) cc_final: 0.7795 (mptt) REVERT: E 501 LYS cc_start: 0.7979 (tttt) cc_final: 0.7746 (tttt) REVERT: E 520 ARG cc_start: 0.7714 (mtp85) cc_final: 0.7292 (mtp85) REVERT: E 530 LYS cc_start: 0.8052 (tmtt) cc_final: 0.7476 (tttt) REVERT: E 532 LYS cc_start: 0.8314 (ttpt) cc_final: 0.7541 (ttpt) REVERT: E 538 LYS cc_start: 0.7341 (ttmm) cc_final: 0.6910 (mtpp) REVERT: E 550 GLN cc_start: 0.7393 (mm-40) cc_final: 0.7134 (mm-40) REVERT: E 560 ASN cc_start: 0.8379 (m-40) cc_final: 0.8075 (m110) REVERT: E 582 LYS cc_start: 0.6890 (pmtt) cc_final: 0.6181 (pmtt) REVERT: I 95 ASN cc_start: 0.8308 (m-40) cc_final: 0.7931 (m-40) REVERT: I 109 TRP cc_start: 0.8666 (m100) cc_final: 0.7733 (m100) REVERT: I 122 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7744 (p0) REVERT: I 178 ASP cc_start: 0.6767 (t0) cc_final: 0.6421 (t0) REVERT: I 185 PHE cc_start: 0.8274 (t80) cc_final: 0.7956 (t80) REVERT: I 193 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7060 (mp0) REVERT: I 214 TRP cc_start: -0.1715 (OUTLIER) cc_final: -0.4049 (p90) REVERT: I 237 ASP cc_start: 0.7347 (t0) cc_final: 0.6706 (t0) REVERT: I 269 ASP cc_start: 0.6758 (p0) cc_final: 0.6347 (p0) REVERT: I 318 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8311 (mm110) REVERT: I 332 ARG cc_start: 0.8705 (mmt-90) cc_final: 0.8402 (mmt90) REVERT: I 346 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6533 (mm-30) REVERT: I 386 GLN cc_start: 0.7666 (tt0) cc_final: 0.7200 (tt0) REVERT: I 408 ARG cc_start: 0.7690 (mmt-90) cc_final: 0.7482 (mmt-90) REVERT: I 415 ILE cc_start: 0.8642 (mt) cc_final: 0.8304 (mm) REVERT: I 491 GLN cc_start: 0.7556 (mm-40) cc_final: 0.6684 (mm-40) REVERT: I 528 TRP cc_start: 0.8320 (m100) cc_final: 0.7753 (m100) REVERT: I 532 LYS cc_start: 0.8461 (ttmm) cc_final: 0.8205 (ttpp) REVERT: I 582 LYS cc_start: 0.8398 (pttm) cc_final: 0.8090 (pttm) REVERT: C 47 ASN cc_start: 0.7746 (t0) cc_final: 0.7416 (t160) REVERT: C 67 ARG cc_start: 0.6725 (mmt-90) cc_final: 0.6338 (mmt-90) REVERT: C 68 LEU cc_start: 0.8181 (tp) cc_final: 0.7543 (tp) REVERT: C 73 MET cc_start: 0.7912 (ptt) cc_final: 0.7397 (ptt) REVERT: C 147 ASN cc_start: 0.8362 (t0) cc_final: 0.7968 (t0) REVERT: C 193 GLU cc_start: 0.7174 (tp30) cc_final: 0.6736 (tp30) REVERT: C 501 LYS cc_start: 0.8315 (tttp) cc_final: 0.7807 (tttm) REVERT: C 509 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: C 520 ARG cc_start: 0.8627 (mpp80) cc_final: 0.8023 (mpp80) REVERT: C 528 TRP cc_start: 0.8534 (m100) cc_final: 0.7718 (m100) REVERT: B 53 PHE cc_start: 0.8405 (m-80) cc_final: 0.7879 (p90) REVERT: B 68 LEU cc_start: 0.8599 (tp) cc_final: 0.8323 (tp) REVERT: B 82 VAL cc_start: 0.8453 (OUTLIER) cc_final: 0.8210 (m) REVERT: B 142 GLU cc_start: 0.7743 (pp20) cc_final: 0.7268 (pp20) REVERT: B 152 THR cc_start: 0.8255 (m) cc_final: 0.7988 (m) REVERT: B 182 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8047 (m) REVERT: B 268 PHE cc_start: 0.8500 (m-10) cc_final: 0.8204 (m-10) REVERT: B 424 VAL cc_start: 0.8163 (OUTLIER) cc_final: 0.7891 (m) REVERT: B 430 LEU cc_start: 0.8456 (tp) cc_final: 0.8088 (tp) REVERT: B 463 VAL cc_start: 0.8114 (OUTLIER) cc_final: 0.7740 (m) REVERT: B 491 GLN cc_start: 0.7508 (mm-40) cc_final: 0.7080 (mm-40) REVERT: B 528 TRP cc_start: 0.8646 (m100) cc_final: 0.8094 (m100) REVERT: B 551 MET cc_start: 0.7286 (ttt) cc_final: 0.7024 (ttt) REVERT: B 569 MET cc_start: 0.6987 (mmm) cc_final: 0.6695 (mmm) outliers start: 174 outliers final: 122 residues processed: 1623 average time/residue: 0.4401 time to fit residues: 1104.4487 Evaluate side-chains 1687 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1542 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 78 ASN Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain G residue 582 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 458 ASN Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 451 TYR Chi-restraints excluded: chain E residue 468 GLN Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 214 TRP Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 429 VAL Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 497 GLN Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 518 MET Chi-restraints excluded: chain I residue 521 ILE Chi-restraints excluded: chain I residue 551 MET Chi-restraints excluded: chain I residue 570 LYS Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 chunk 276 optimal weight: 9.9990 chunk 214 optimal weight: 5.9990 chunk 319 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 chunk 377 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 230 optimal weight: 20.0000 chunk 174 optimal weight: 4.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 282 ASN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN A 549 GLN A 558 GLN G 231 ASN ** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 GLN ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN ** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN I 318 GLN I 446 ASN ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS B 446 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 31929 Z= 0.446 Angle : 0.660 12.532 43660 Z= 0.338 Chirality : 0.047 0.208 4764 Planarity : 0.006 0.072 5732 Dihedral : 5.441 71.333 4237 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.64 % Allowed : 27.22 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3686 helix: -1.19 (0.42), residues: 124 sheet: -0.36 (0.18), residues: 881 loop : -0.52 (0.12), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 279 HIS 0.006 0.001 HIS A 222 PHE 0.035 0.002 PHE A 266 TYR 0.035 0.002 TYR A 561 ARG 0.011 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1706 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1520 time to evaluate : 3.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7544 (tt0) cc_final: 0.7156 (tp30) REVERT: A 67 ARG cc_start: 0.8168 (mmt180) cc_final: 0.7620 (mmt180) REVERT: A 96 MET cc_start: 0.6935 (mmp) cc_final: 0.6676 (mmt) REVERT: A 104 GLN cc_start: 0.8048 (pt0) cc_final: 0.7720 (pt0) REVERT: A 147 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7855 (t0) REVERT: A 237 ASP cc_start: 0.7881 (t0) cc_final: 0.7261 (t0) REVERT: A 244 TYR cc_start: 0.7265 (m-80) cc_final: 0.6615 (m-80) REVERT: A 260 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: A 282 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7890 (m110) REVERT: A 291 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8181 (mp) REVERT: A 312 LYS cc_start: 0.8465 (mtmt) cc_final: 0.8177 (mtmt) REVERT: A 335 GLU cc_start: 0.7246 (tt0) cc_final: 0.6267 (tm-30) REVERT: A 350 GLN cc_start: 0.7404 (mt0) cc_final: 0.7001 (mp10) REVERT: A 411 GLU cc_start: 0.7897 (mp0) cc_final: 0.7442 (mp0) REVERT: A 413 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6650 (m-30) REVERT: A 414 TRP cc_start: 0.8184 (p90) cc_final: 0.7779 (p90) REVERT: A 443 ASN cc_start: 0.8084 (p0) cc_final: 0.7868 (p0) REVERT: A 473 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6839 (mm-30) REVERT: A 495 PRO cc_start: 0.7341 (Cg_exo) cc_final: 0.7064 (Cg_endo) REVERT: A 501 LYS cc_start: 0.8601 (ttpp) cc_final: 0.8130 (ttpp) REVERT: A 528 TRP cc_start: 0.8328 (m100) cc_final: 0.7860 (m100) REVERT: A 530 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7873 (ttpp) REVERT: G 50 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6631 (mp0) REVERT: G 60 GLU cc_start: 0.7662 (tp30) cc_final: 0.7256 (tp30) REVERT: G 62 THR cc_start: 0.8467 (m) cc_final: 0.8008 (t) REVERT: G 90 THR cc_start: 0.8619 (p) cc_final: 0.8372 (t) REVERT: G 104 GLN cc_start: 0.8017 (pt0) cc_final: 0.7623 (pt0) REVERT: G 109 TRP cc_start: 0.8447 (m100) cc_final: 0.7951 (m100) REVERT: G 120 TRP cc_start: 0.8614 (m100) cc_final: 0.8209 (m100) REVERT: G 135 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7025 (tp30) REVERT: G 137 HIS cc_start: 0.8415 (m170) cc_final: 0.8189 (m90) REVERT: G 143 GLN cc_start: 0.8382 (mt0) cc_final: 0.7862 (mt0) REVERT: G 145 ILE cc_start: 0.8546 (mp) cc_final: 0.8233 (mp) REVERT: G 174 MET cc_start: 0.7683 (mtp) cc_final: 0.7131 (mtp) REVERT: G 193 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: G 200 TRP cc_start: 0.8613 (p90) cc_final: 0.8181 (p90) REVERT: G 213 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7477 (tm-30) REVERT: G 245 THR cc_start: 0.7941 (OUTLIER) cc_final: 0.7739 (t) REVERT: G 266 PHE cc_start: 0.8278 (t80) cc_final: 0.7766 (t80) REVERT: G 312 LYS cc_start: 0.8499 (mtpp) cc_final: 0.8233 (mtpp) REVERT: G 327 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6912 (mm-30) REVERT: G 335 GLU cc_start: 0.7328 (tt0) cc_final: 0.6710 (tt0) REVERT: G 345 PHE cc_start: 0.7837 (m-80) cc_final: 0.7222 (m-80) REVERT: G 382 ARG cc_start: 0.5473 (mtm180) cc_final: 0.4799 (mtm180) REVERT: G 386 GLN cc_start: 0.7898 (mt0) cc_final: 0.7651 (mt0) REVERT: G 398 PHE cc_start: 0.8586 (p90) cc_final: 0.8196 (p90) REVERT: G 434 ASP cc_start: 0.7669 (m-30) cc_final: 0.7367 (t0) REVERT: G 442 ILE cc_start: 0.8562 (mm) cc_final: 0.8321 (mm) REVERT: G 475 ASP cc_start: 0.7632 (t0) cc_final: 0.7003 (t0) REVERT: G 479 LYS cc_start: 0.8643 (mmtm) cc_final: 0.8394 (mmtm) REVERT: G 497 GLN cc_start: 0.8423 (mt0) cc_final: 0.8115 (mt0) REVERT: G 505 ASN cc_start: 0.7639 (t0) cc_final: 0.6861 (t0) REVERT: G 509 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7570 (mm-30) REVERT: G 518 MET cc_start: 0.7818 (ptp) cc_final: 0.7543 (ptp) REVERT: G 530 LYS cc_start: 0.8066 (ttpp) cc_final: 0.7647 (ttpp) REVERT: G 535 PHE cc_start: 0.8272 (m-80) cc_final: 0.7539 (m-80) REVERT: G 544 THR cc_start: 0.7821 (OUTLIER) cc_final: 0.7604 (t) REVERT: G 582 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8299 (pttm) REVERT: F 65 SER cc_start: 0.8445 (t) cc_final: 0.8103 (p) REVERT: F 72 ASN cc_start: 0.8453 (t0) cc_final: 0.8163 (t0) REVERT: F 73 MET cc_start: 0.8139 (ttp) cc_final: 0.7651 (ttp) REVERT: F 80 ARG cc_start: 0.4054 (tpt90) cc_final: 0.1461 (mmt180) REVERT: F 81 ARG cc_start: 0.5349 (ptp-170) cc_final: 0.4927 (ptp-170) REVERT: F 120 TRP cc_start: 0.8423 (m100) cc_final: 0.7933 (m100) REVERT: F 135 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: F 151 LYS cc_start: 0.8178 (mmmm) cc_final: 0.7601 (mmmm) REVERT: F 195 LEU cc_start: 0.7529 (mt) cc_final: 0.7152 (mt) REVERT: F 197 PHE cc_start: 0.8198 (m-10) cc_final: 0.7378 (m-80) REVERT: F 201 LYS cc_start: 0.8209 (mmpt) cc_final: 0.7786 (mmpt) REVERT: F 213 GLN cc_start: 0.7441 (tm-30) cc_final: 0.6881 (tm-30) REVERT: F 237 ASP cc_start: 0.8089 (t0) cc_final: 0.7421 (t0) REVERT: F 242 GLN cc_start: 0.7698 (pt0) cc_final: 0.7339 (pp30) REVERT: F 279 TRP cc_start: 0.8327 (p-90) cc_final: 0.8078 (p-90) REVERT: F 409 TYR cc_start: 0.8383 (t80) cc_final: 0.7940 (t80) REVERT: F 426 ASN cc_start: 0.6320 (OUTLIER) cc_final: 0.3668 (t0) REVERT: F 439 LYS cc_start: 0.8102 (mmtp) cc_final: 0.7427 (mmtp) REVERT: F 468 GLN cc_start: 0.7097 (tt0) cc_final: 0.6813 (mt0) REVERT: F 473 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7188 (tm-30) REVERT: F 497 GLN cc_start: 0.8233 (mt0) cc_final: 0.7769 (mt0) REVERT: F 501 LYS cc_start: 0.8030 (ttpp) cc_final: 0.7511 (ttpp) REVERT: F 518 MET cc_start: 0.7892 (ptp) cc_final: 0.7394 (ptp) REVERT: F 532 LYS cc_start: 0.8426 (ttmm) cc_final: 0.7941 (ttmm) REVERT: F 551 MET cc_start: 0.7053 (ttt) cc_final: 0.6803 (ttt) REVERT: F 562 VAL cc_start: 0.8612 (p) cc_final: 0.8402 (m) REVERT: F 575 LYS cc_start: 0.8310 (mmmt) cc_final: 0.7998 (mmmt) REVERT: D 46 ASN cc_start: 0.7420 (t0) cc_final: 0.6758 (t0) REVERT: D 50 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6598 (tm-30) REVERT: D 70 HIS cc_start: 0.7916 (t-170) cc_final: 0.7383 (t-170) REVERT: D 107 THR cc_start: 0.8363 (m) cc_final: 0.7702 (p) REVERT: D 142 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7402 (pm20) REVERT: D 174 MET cc_start: 0.7594 (mtp) cc_final: 0.7068 (mtp) REVERT: D 190 MET cc_start: 0.7873 (mmm) cc_final: 0.7618 (mmm) REVERT: D 200 TRP cc_start: 0.8724 (p90) cc_final: 0.8220 (p90) REVERT: D 208 TRP cc_start: 0.8227 (t60) cc_final: 0.7547 (t60) REVERT: D 569 MET cc_start: 0.7069 (mmp) cc_final: 0.6866 (mmp) REVERT: E 51 PHE cc_start: 0.8490 (m-80) cc_final: 0.8207 (m-80) REVERT: E 95 ASN cc_start: 0.8300 (t0) cc_final: 0.7958 (t0) REVERT: E 142 GLU cc_start: 0.7773 (pt0) cc_final: 0.6636 (pt0) REVERT: E 163 LYS cc_start: 0.8057 (mppt) cc_final: 0.7577 (mppt) REVERT: E 209 ARG cc_start: 0.5225 (OUTLIER) cc_final: 0.4373 (ptt180) REVERT: E 237 ASP cc_start: 0.7410 (t0) cc_final: 0.7145 (t0) REVERT: E 247 GLU cc_start: 0.7648 (mp0) cc_final: 0.7065 (mp0) REVERT: E 266 PHE cc_start: 0.8291 (t80) cc_final: 0.8016 (t80) REVERT: E 335 GLU cc_start: 0.6835 (tm-30) cc_final: 0.6077 (tm-30) REVERT: E 342 TYR cc_start: 0.7055 (p90) cc_final: 0.6702 (p90) REVERT: E 380 PHE cc_start: 0.7809 (p90) cc_final: 0.7515 (p90) REVERT: E 386 GLN cc_start: 0.8246 (tt0) cc_final: 0.8021 (tt0) REVERT: E 387 LYS cc_start: 0.8770 (tptm) cc_final: 0.8518 (tptm) REVERT: E 396 GLU cc_start: 0.7313 (tt0) cc_final: 0.6910 (tt0) REVERT: E 400 TYR cc_start: 0.7999 (t80) cc_final: 0.7289 (t80) REVERT: E 404 GLN cc_start: 0.8085 (pt0) cc_final: 0.7421 (pt0) REVERT: E 430 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7592 (tt) REVERT: E 451 TYR cc_start: 0.3464 (OUTLIER) cc_final: 0.3067 (t80) REVERT: E 464 TYR cc_start: 0.8000 (t80) cc_final: 0.7727 (t80) REVERT: E 472 LYS cc_start: 0.3432 (OUTLIER) cc_final: 0.1255 (tmmt) REVERT: E 501 LYS cc_start: 0.8032 (tttt) cc_final: 0.7612 (tttt) REVERT: E 526 ASP cc_start: 0.6699 (p0) cc_final: 0.6215 (p0) REVERT: E 530 LYS cc_start: 0.8016 (tmtt) cc_final: 0.7479 (tttt) REVERT: E 532 LYS cc_start: 0.8322 (ttpt) cc_final: 0.7586 (ttpt) REVERT: E 538 LYS cc_start: 0.7473 (ttmm) cc_final: 0.7047 (mtpp) REVERT: E 550 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7049 (mm-40) REVERT: E 560 ASN cc_start: 0.8431 (m-40) cc_final: 0.8094 (m110) REVERT: E 582 LYS cc_start: 0.6966 (pmtt) cc_final: 0.6264 (pmtt) REVERT: I 67 ARG cc_start: 0.8000 (mmt-90) cc_final: 0.7787 (mmt90) REVERT: I 95 ASN cc_start: 0.8353 (m-40) cc_final: 0.7994 (m-40) REVERT: I 109 TRP cc_start: 0.8597 (m100) cc_final: 0.7774 (m100) REVERT: I 122 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7723 (p0) REVERT: I 178 ASP cc_start: 0.6618 (t0) cc_final: 0.6358 (t0) REVERT: I 193 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7234 (mp0) REVERT: I 214 TRP cc_start: -0.1372 (OUTLIER) cc_final: -0.3741 (p90) REVERT: I 237 ASP cc_start: 0.7335 (t0) cc_final: 0.6674 (t0) REVERT: I 269 ASP cc_start: 0.6733 (p0) cc_final: 0.6457 (p0) REVERT: I 332 ARG cc_start: 0.8700 (mmt-90) cc_final: 0.8367 (mmt90) REVERT: I 346 GLU cc_start: 0.6795 (mm-30) cc_final: 0.6541 (mm-30) REVERT: I 386 GLN cc_start: 0.7661 (tt0) cc_final: 0.7170 (tt0) REVERT: I 415 ILE cc_start: 0.8623 (mt) cc_final: 0.8279 (mm) REVERT: I 479 LYS cc_start: 0.8458 (mmtt) cc_final: 0.7851 (mmtt) REVERT: I 491 GLN cc_start: 0.7489 (mm-40) cc_final: 0.6839 (mm-40) REVERT: I 528 TRP cc_start: 0.8365 (m100) cc_final: 0.7705 (m100) REVERT: I 532 LYS cc_start: 0.8455 (ttmm) cc_final: 0.8114 (ttpp) REVERT: I 577 GLN cc_start: 0.8320 (mt0) cc_final: 0.8030 (mt0) REVERT: I 582 LYS cc_start: 0.8334 (pttm) cc_final: 0.7998 (pttm) REVERT: C 47 ASN cc_start: 0.7775 (t0) cc_final: 0.7420 (t160) REVERT: C 67 ARG cc_start: 0.6824 (mmt-90) cc_final: 0.6316 (mmt-90) REVERT: C 68 LEU cc_start: 0.8155 (tp) cc_final: 0.7535 (tp) REVERT: C 73 MET cc_start: 0.7833 (ptt) cc_final: 0.7300 (ptt) REVERT: C 164 VAL cc_start: 0.8603 (p) cc_final: 0.8355 (m) REVERT: C 193 GLU cc_start: 0.7289 (tp30) cc_final: 0.6820 (tp30) REVERT: C 378 TYR cc_start: 0.2195 (OUTLIER) cc_final: 0.0412 (m-80) REVERT: C 509 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6997 (tm-30) REVERT: C 520 ARG cc_start: 0.8657 (mpp80) cc_final: 0.8005 (mpp80) REVERT: C 528 TRP cc_start: 0.8529 (m100) cc_final: 0.7650 (m100) REVERT: B 52 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7848 (ttmm) REVERT: B 53 PHE cc_start: 0.8409 (m-80) cc_final: 0.7858 (p90) REVERT: B 68 LEU cc_start: 0.8639 (tp) cc_final: 0.8377 (tp) REVERT: B 82 VAL cc_start: 0.8470 (OUTLIER) cc_final: 0.8254 (m) REVERT: B 109 TRP cc_start: 0.8733 (m100) cc_final: 0.7869 (m100) REVERT: B 142 GLU cc_start: 0.7736 (pp20) cc_final: 0.7264 (pp20) REVERT: B 201 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8588 (mtmt) REVERT: B 344 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8576 (p) REVERT: B 396 GLU cc_start: 0.7776 (tt0) cc_final: 0.7520 (tt0) REVERT: B 430 LEU cc_start: 0.8445 (tp) cc_final: 0.8125 (tp) REVERT: B 463 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7795 (m) REVERT: B 491 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7063 (mm-40) REVERT: B 528 TRP cc_start: 0.8619 (m100) cc_final: 0.8133 (m100) REVERT: B 551 MET cc_start: 0.7253 (ttt) cc_final: 0.6955 (ttt) REVERT: B 569 MET cc_start: 0.6992 (mmm) cc_final: 0.6688 (mmm) REVERT: B 575 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7359 (mmtt) outliers start: 186 outliers final: 140 residues processed: 1581 average time/residue: 0.4809 time to fit residues: 1197.0259 Evaluate side-chains 1683 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1517 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 558 GLN Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 147 ASN Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 444 TYR Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain G residue 551 MET Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain G residue 582 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 426 ASN Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 458 ASN Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 451 TYR Chi-restraints excluded: chain E residue 468 GLN Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain E residue 556 ASP Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 214 TRP Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 318 GLN Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 429 VAL Chi-restraints excluded: chain I residue 466 ASN Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 497 GLN Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 518 MET Chi-restraints excluded: chain I residue 521 ILE Chi-restraints excluded: chain I residue 551 MET Chi-restraints excluded: chain I residue 570 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 497 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 240 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 296 optimal weight: 0.0870 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN A 558 GLN G 127 GLN G 181 ASN ** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 GLN ** G 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN ** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 HIS ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN I 318 GLN ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS B 446 ASN B 468 GLN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 31929 Z= 0.229 Angle : 0.609 14.601 43660 Z= 0.303 Chirality : 0.044 0.195 4764 Planarity : 0.005 0.066 5732 Dihedral : 5.141 71.545 4237 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.07 % Allowed : 28.44 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3686 helix: -0.97 (0.48), residues: 100 sheet: -0.26 (0.18), residues: 869 loop : -0.43 (0.12), residues: 2717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 470 HIS 0.008 0.001 HIS C 102 PHE 0.027 0.002 PHE G 303 TYR 0.030 0.002 TYR A 561 ARG 0.008 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1676 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1509 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7469 (tt0) cc_final: 0.7078 (tp30) REVERT: A 67 ARG cc_start: 0.8109 (mmt180) cc_final: 0.7658 (mmt180) REVERT: A 96 MET cc_start: 0.6866 (mmp) cc_final: 0.6598 (mmt) REVERT: A 104 GLN cc_start: 0.8089 (pt0) cc_final: 0.7731 (pt0) REVERT: A 183 MET cc_start: 0.8068 (mmm) cc_final: 0.7823 (mmm) REVERT: A 237 ASP cc_start: 0.7756 (t0) cc_final: 0.7318 (t0) REVERT: A 244 TYR cc_start: 0.7174 (m-80) cc_final: 0.6548 (m-80) REVERT: A 260 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: A 312 LYS cc_start: 0.8484 (mtmt) cc_final: 0.8054 (mtmt) REVERT: A 335 GLU cc_start: 0.7184 (tt0) cc_final: 0.6232 (tm-30) REVERT: A 350 GLN cc_start: 0.7400 (mt0) cc_final: 0.6979 (mp10) REVERT: A 380 PHE cc_start: 0.7670 (p90) cc_final: 0.7350 (p90) REVERT: A 411 GLU cc_start: 0.7836 (mp0) cc_final: 0.7485 (mp0) REVERT: A 413 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6607 (m-30) REVERT: A 414 TRP cc_start: 0.8222 (p90) cc_final: 0.7717 (p90) REVERT: A 443 ASN cc_start: 0.8043 (p0) cc_final: 0.7337 (p0) REVERT: A 446 ASN cc_start: 0.8039 (m110) cc_final: 0.7671 (m110) REVERT: A 471 ASP cc_start: 0.5834 (OUTLIER) cc_final: 0.5534 (m-30) REVERT: A 473 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6780 (mm-30) REVERT: A 495 PRO cc_start: 0.7291 (Cg_exo) cc_final: 0.6921 (Cg_endo) REVERT: A 501 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8036 (ttpp) REVERT: A 528 TRP cc_start: 0.8277 (m100) cc_final: 0.7820 (m100) REVERT: A 530 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7816 (ttpp) REVERT: G 50 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6631 (mp0) REVERT: G 53 PHE cc_start: 0.5341 (p90) cc_final: 0.4580 (p90) REVERT: G 60 GLU cc_start: 0.7656 (tp30) cc_final: 0.7234 (tp30) REVERT: G 62 THR cc_start: 0.8460 (m) cc_final: 0.7955 (t) REVERT: G 68 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8030 (tt) REVERT: G 90 THR cc_start: 0.8528 (p) cc_final: 0.8327 (t) REVERT: G 104 GLN cc_start: 0.8022 (pt0) cc_final: 0.7700 (pt0) REVERT: G 109 TRP cc_start: 0.8424 (m100) cc_final: 0.8115 (m100) REVERT: G 120 TRP cc_start: 0.8523 (m100) cc_final: 0.8295 (m100) REVERT: G 135 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6959 (tp30) REVERT: G 136 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7998 (tp) REVERT: G 137 HIS cc_start: 0.8372 (m170) cc_final: 0.7978 (m90) REVERT: G 143 GLN cc_start: 0.8282 (mt0) cc_final: 0.8002 (mt0) REVERT: G 174 MET cc_start: 0.7711 (mtp) cc_final: 0.7209 (mtp) REVERT: G 193 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6558 (mp0) REVERT: G 200 TRP cc_start: 0.8598 (p90) cc_final: 0.8125 (p90) REVERT: G 213 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7318 (tm-30) REVERT: G 245 THR cc_start: 0.7913 (OUTLIER) cc_final: 0.7689 (t) REVERT: G 266 PHE cc_start: 0.8176 (t80) cc_final: 0.7729 (t80) REVERT: G 312 LYS cc_start: 0.8475 (mtpp) cc_final: 0.8210 (mtpp) REVERT: G 327 GLU cc_start: 0.7466 (mm-30) cc_final: 0.6811 (mm-30) REVERT: G 335 GLU cc_start: 0.7279 (tt0) cc_final: 0.6675 (tt0) REVERT: G 345 PHE cc_start: 0.7830 (m-80) cc_final: 0.7276 (m-80) REVERT: G 382 ARG cc_start: 0.5122 (mtm180) cc_final: 0.4318 (mtm180) REVERT: G 398 PHE cc_start: 0.8563 (p90) cc_final: 0.8191 (p90) REVERT: G 434 ASP cc_start: 0.7721 (m-30) cc_final: 0.7419 (t0) REVERT: G 442 ILE cc_start: 0.8469 (mm) cc_final: 0.8242 (mm) REVERT: G 468 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7522 (tt0) REVERT: G 475 ASP cc_start: 0.7585 (t0) cc_final: 0.6958 (t0) REVERT: G 479 LYS cc_start: 0.8596 (mmtm) cc_final: 0.8301 (mmtm) REVERT: G 497 GLN cc_start: 0.8332 (mt0) cc_final: 0.8013 (mt0) REVERT: G 505 ASN cc_start: 0.7592 (t0) cc_final: 0.6810 (t0) REVERT: G 509 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7549 (mm-30) REVERT: G 518 MET cc_start: 0.7770 (ptp) cc_final: 0.7493 (ptp) REVERT: G 528 TRP cc_start: 0.8092 (m100) cc_final: 0.7468 (m100) REVERT: G 530 LYS cc_start: 0.7930 (ttpp) cc_final: 0.7414 (ttpp) REVERT: G 535 PHE cc_start: 0.8230 (m-80) cc_final: 0.7423 (m-80) REVERT: G 582 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8316 (pttm) REVERT: F 65 SER cc_start: 0.8398 (t) cc_final: 0.7911 (p) REVERT: F 72 ASN cc_start: 0.8454 (t0) cc_final: 0.8161 (t0) REVERT: F 73 MET cc_start: 0.8150 (ttp) cc_final: 0.7641 (ttp) REVERT: F 80 ARG cc_start: 0.4107 (tpt90) cc_final: 0.1396 (mmt180) REVERT: F 81 ARG cc_start: 0.5283 (ptp-170) cc_final: 0.5045 (ptp-170) REVERT: F 120 TRP cc_start: 0.8358 (m100) cc_final: 0.7875 (m100) REVERT: F 135 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: F 151 LYS cc_start: 0.8166 (mmmm) cc_final: 0.7562 (mmmm) REVERT: F 201 LYS cc_start: 0.8192 (mmpt) cc_final: 0.7763 (mmpt) REVERT: F 213 GLN cc_start: 0.7380 (tm-30) cc_final: 0.6838 (tm-30) REVERT: F 242 GLN cc_start: 0.7687 (pt0) cc_final: 0.7323 (pp30) REVERT: F 279 TRP cc_start: 0.8287 (p-90) cc_final: 0.7945 (p-90) REVERT: F 409 TYR cc_start: 0.8317 (t80) cc_final: 0.7925 (t80) REVERT: F 439 LYS cc_start: 0.8118 (mmtp) cc_final: 0.7562 (mmtp) REVERT: F 473 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7134 (tm-30) REVERT: F 497 GLN cc_start: 0.8204 (mt0) cc_final: 0.7723 (mt0) REVERT: F 501 LYS cc_start: 0.8126 (ttpp) cc_final: 0.7854 (ttpt) REVERT: F 518 MET cc_start: 0.7888 (ptp) cc_final: 0.7362 (ptp) REVERT: F 532 LYS cc_start: 0.8359 (ttmm) cc_final: 0.7893 (ttmm) REVERT: F 551 MET cc_start: 0.6963 (ttt) cc_final: 0.6730 (ttt) REVERT: F 562 VAL cc_start: 0.8616 (p) cc_final: 0.8408 (m) REVERT: F 575 LYS cc_start: 0.8305 (mmmt) cc_final: 0.8075 (mmmt) REVERT: D 46 ASN cc_start: 0.7474 (t0) cc_final: 0.6806 (t0) REVERT: D 50 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6535 (tm-30) REVERT: D 70 HIS cc_start: 0.7824 (t-170) cc_final: 0.7319 (t-170) REVERT: D 73 MET cc_start: 0.8274 (ptt) cc_final: 0.7651 (ptm) REVERT: D 107 THR cc_start: 0.8328 (m) cc_final: 0.7675 (p) REVERT: D 142 GLU cc_start: 0.8004 (pt0) cc_final: 0.7407 (pm20) REVERT: D 174 MET cc_start: 0.7630 (mtp) cc_final: 0.7204 (mtp) REVERT: D 190 MET cc_start: 0.7842 (mmm) cc_final: 0.7581 (mmm) REVERT: D 200 TRP cc_start: 0.8728 (p90) cc_final: 0.8201 (p90) REVERT: D 208 TRP cc_start: 0.8266 (t60) cc_final: 0.7534 (t60) REVERT: D 256 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7594 (tpp80) REVERT: E 51 PHE cc_start: 0.8475 (m-80) cc_final: 0.8183 (m-80) REVERT: E 95 ASN cc_start: 0.8247 (t0) cc_final: 0.7891 (t0) REVERT: E 142 GLU cc_start: 0.7628 (pt0) cc_final: 0.6467 (pt0) REVERT: E 163 LYS cc_start: 0.8049 (mppt) cc_final: 0.7595 (mppt) REVERT: E 209 ARG cc_start: 0.5080 (OUTLIER) cc_final: 0.4309 (ptt180) REVERT: E 210 TYR cc_start: 0.8468 (p90) cc_final: 0.8163 (p90) REVERT: E 237 ASP cc_start: 0.7383 (t0) cc_final: 0.7071 (t0) REVERT: E 240 ASP cc_start: 0.7206 (m-30) cc_final: 0.6959 (m-30) REVERT: E 247 GLU cc_start: 0.7674 (mp0) cc_final: 0.7033 (mp0) REVERT: E 266 PHE cc_start: 0.8241 (t80) cc_final: 0.7959 (t80) REVERT: E 335 GLU cc_start: 0.6854 (tm-30) cc_final: 0.6048 (tm-30) REVERT: E 342 TYR cc_start: 0.7056 (p90) cc_final: 0.6692 (p90) REVERT: E 377 ARG cc_start: 0.5271 (mtt180) cc_final: 0.4885 (mtt180) REVERT: E 380 PHE cc_start: 0.7793 (p90) cc_final: 0.7492 (p90) REVERT: E 386 GLN cc_start: 0.8239 (tt0) cc_final: 0.7971 (tt0) REVERT: E 387 LYS cc_start: 0.8749 (tptm) cc_final: 0.8499 (tptm) REVERT: E 396 GLU cc_start: 0.7290 (tt0) cc_final: 0.6893 (tt0) REVERT: E 404 GLN cc_start: 0.8061 (pt0) cc_final: 0.7387 (pt0) REVERT: E 430 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7547 (tt) REVERT: E 464 TYR cc_start: 0.7931 (t80) cc_final: 0.7564 (t80) REVERT: E 472 LYS cc_start: 0.3198 (OUTLIER) cc_final: 0.1120 (tmmt) REVERT: E 479 LYS cc_start: 0.8309 (mptt) cc_final: 0.7903 (mptt) REVERT: E 501 LYS cc_start: 0.7962 (tttt) cc_final: 0.7535 (tttt) REVERT: E 526 ASP cc_start: 0.6637 (p0) cc_final: 0.6160 (p0) REVERT: E 530 LYS cc_start: 0.7946 (tmtt) cc_final: 0.7419 (tttt) REVERT: E 532 LYS cc_start: 0.8320 (ttpt) cc_final: 0.7583 (ttpt) REVERT: E 550 GLN cc_start: 0.7460 (mm-40) cc_final: 0.7062 (mm-40) REVERT: E 560 ASN cc_start: 0.8394 (m-40) cc_final: 0.8094 (m110) REVERT: E 582 LYS cc_start: 0.6869 (pmtt) cc_final: 0.6173 (pmtt) REVERT: I 67 ARG cc_start: 0.7975 (mmt-90) cc_final: 0.7706 (mmt90) REVERT: I 95 ASN cc_start: 0.8335 (m-40) cc_final: 0.7942 (m-40) REVERT: I 109 TRP cc_start: 0.8616 (m100) cc_final: 0.7920 (m100) REVERT: I 122 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7720 (p0) REVERT: I 178 ASP cc_start: 0.6696 (t0) cc_final: 0.6356 (t0) REVERT: I 193 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7198 (mp0) REVERT: I 214 TRP cc_start: -0.1713 (OUTLIER) cc_final: -0.3961 (p90) REVERT: I 237 ASP cc_start: 0.7223 (t0) cc_final: 0.6574 (t0) REVERT: I 269 ASP cc_start: 0.6728 (p0) cc_final: 0.6351 (p0) REVERT: I 332 ARG cc_start: 0.8669 (mmt-90) cc_final: 0.8366 (mmt90) REVERT: I 346 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6601 (mm-30) REVERT: I 386 GLN cc_start: 0.7661 (tt0) cc_final: 0.7179 (tt0) REVERT: I 415 ILE cc_start: 0.8644 (mt) cc_final: 0.8286 (mm) REVERT: I 491 GLN cc_start: 0.7474 (mm-40) cc_final: 0.7046 (mm-40) REVERT: I 532 LYS cc_start: 0.8471 (ttmm) cc_final: 0.8125 (ttpp) REVERT: I 577 GLN cc_start: 0.8229 (mt0) cc_final: 0.7982 (mt0) REVERT: I 582 LYS cc_start: 0.8402 (pttm) cc_final: 0.8152 (pttm) REVERT: C 47 ASN cc_start: 0.7736 (t0) cc_final: 0.7274 (t160) REVERT: C 67 ARG cc_start: 0.6705 (mmt-90) cc_final: 0.6189 (mmt-90) REVERT: C 73 MET cc_start: 0.7734 (ptt) cc_final: 0.7209 (ptt) REVERT: C 164 VAL cc_start: 0.8616 (p) cc_final: 0.8363 (m) REVERT: C 193 GLU cc_start: 0.7217 (tp30) cc_final: 0.6745 (tp30) REVERT: C 378 TYR cc_start: 0.2300 (OUTLIER) cc_final: 0.0529 (m-80) REVERT: C 501 LYS cc_start: 0.8300 (tttp) cc_final: 0.7775 (tttm) REVERT: C 509 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6914 (tm-30) REVERT: C 520 ARG cc_start: 0.8656 (mpp80) cc_final: 0.7997 (mpp80) REVERT: B 52 LYS cc_start: 0.8181 (ttmm) cc_final: 0.7861 (ttmm) REVERT: B 53 PHE cc_start: 0.8386 (m-80) cc_final: 0.7894 (p90) REVERT: B 80 ARG cc_start: 0.8045 (mmm-85) cc_final: 0.7674 (mmm-85) REVERT: B 109 TRP cc_start: 0.8735 (m100) cc_final: 0.7890 (m100) REVERT: B 131 ASN cc_start: 0.7640 (t0) cc_final: 0.7396 (t0) REVERT: B 142 GLU cc_start: 0.7684 (pp20) cc_final: 0.7245 (pp20) REVERT: B 151 LYS cc_start: 0.8481 (mttm) cc_final: 0.8100 (mttm) REVERT: B 178 ASP cc_start: 0.6844 (t0) cc_final: 0.6628 (t0) REVERT: B 256 ARG cc_start: 0.7729 (mtp180) cc_final: 0.7528 (mtp180) REVERT: B 344 SER cc_start: 0.8812 (OUTLIER) cc_final: 0.8574 (p) REVERT: B 396 GLU cc_start: 0.7767 (tt0) cc_final: 0.7510 (tt0) REVERT: B 430 LEU cc_start: 0.8436 (tp) cc_final: 0.8104 (tp) REVERT: B 491 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7077 (mm-40) REVERT: B 528 TRP cc_start: 0.8627 (m100) cc_final: 0.8116 (m100) REVERT: B 551 MET cc_start: 0.7302 (ttt) cc_final: 0.7073 (ttt) REVERT: B 565 ASN cc_start: 0.8067 (m110) cc_final: 0.7776 (m110) REVERT: B 569 MET cc_start: 0.6969 (mmm) cc_final: 0.6675 (mmm) REVERT: B 575 LYS cc_start: 0.8131 (mmtt) cc_final: 0.7467 (mmtt) outliers start: 167 outliers final: 113 residues processed: 1561 average time/residue: 0.4373 time to fit residues: 1057.2636 Evaluate side-chains 1632 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1498 time to evaluate : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 270 CYS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 551 MET Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain G residue 582 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 458 ASN Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 468 GLN Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 214 TRP Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 318 GLN Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 429 VAL Chi-restraints excluded: chain I residue 466 ASN Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 497 GLN Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 518 MET Chi-restraints excluded: chain I residue 521 ILE Chi-restraints excluded: chain I residue 551 MET Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 8.9990 chunk 361 optimal weight: 10.0000 chunk 330 optimal weight: 20.0000 chunk 352 optimal weight: 8.9990 chunk 211 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 276 optimal weight: 0.0870 chunk 108 optimal weight: 4.9990 chunk 318 optimal weight: 9.9990 chunk 332 optimal weight: 9.9990 chunk 350 optimal weight: 1.9990 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 GLN G 181 ASN ** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 386 GLN ** G 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 HIS F 421 ASN ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 318 GLN I 446 ASN ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 31929 Z= 0.419 Angle : 0.668 13.820 43660 Z= 0.338 Chirality : 0.047 0.218 4764 Planarity : 0.006 0.077 5732 Dihedral : 5.384 71.462 4237 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.98 % Allowed : 28.95 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3686 helix: -1.23 (0.41), residues: 124 sheet: -0.34 (0.18), residues: 871 loop : -0.54 (0.12), residues: 2691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP F 470 HIS 0.020 0.001 HIS C 102 PHE 0.037 0.002 PHE A 266 TYR 0.030 0.002 TYR A 561 ARG 0.009 0.001 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1693 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1529 time to evaluate : 3.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7546 (tt0) cc_final: 0.7148 (tp30) REVERT: A 67 ARG cc_start: 0.8142 (mmt180) cc_final: 0.7729 (mmt180) REVERT: A 96 MET cc_start: 0.6960 (mmp) cc_final: 0.6687 (mmt) REVERT: A 104 GLN cc_start: 0.8073 (pt0) cc_final: 0.7750 (pt0) REVERT: A 135 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7205 (mt-10) REVERT: A 175 VAL cc_start: 0.8649 (t) cc_final: 0.8238 (p) REVERT: A 183 MET cc_start: 0.8029 (mmm) cc_final: 0.7778 (mmm) REVERT: A 230 THR cc_start: 0.8544 (p) cc_final: 0.8291 (t) REVERT: A 237 ASP cc_start: 0.7751 (t0) cc_final: 0.7241 (t0) REVERT: A 244 TYR cc_start: 0.7282 (m-80) cc_final: 0.6658 (m-80) REVERT: A 260 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: A 291 LEU cc_start: 0.8420 (mp) cc_final: 0.8194 (mt) REVERT: A 312 LYS cc_start: 0.8481 (mtmt) cc_final: 0.8143 (mtmt) REVERT: A 335 GLU cc_start: 0.7294 (tt0) cc_final: 0.6328 (tm-30) REVERT: A 350 GLN cc_start: 0.7390 (mt0) cc_final: 0.6975 (mp10) REVERT: A 411 GLU cc_start: 0.7921 (mp0) cc_final: 0.7462 (mp0) REVERT: A 413 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6596 (m-30) REVERT: A 414 TRP cc_start: 0.8181 (p90) cc_final: 0.7747 (p90) REVERT: A 468 GLN cc_start: 0.7627 (tt0) cc_final: 0.7088 (tt0) REVERT: A 471 ASP cc_start: 0.5917 (OUTLIER) cc_final: 0.5385 (m-30) REVERT: A 473 GLU cc_start: 0.7430 (mm-30) cc_final: 0.6822 (mm-30) REVERT: A 495 PRO cc_start: 0.7437 (Cg_exo) cc_final: 0.7060 (Cg_endo) REVERT: A 501 LYS cc_start: 0.8576 (ttpp) cc_final: 0.8042 (ttpp) REVERT: A 530 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7882 (ttpp) REVERT: A 538 LYS cc_start: 0.8006 (ttmt) cc_final: 0.7591 (ttmt) REVERT: A 565 ASN cc_start: 0.8599 (m-40) cc_final: 0.8088 (m-40) REVERT: G 50 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6660 (mp0) REVERT: G 53 PHE cc_start: 0.5088 (p90) cc_final: 0.4419 (p90) REVERT: G 60 GLU cc_start: 0.7671 (tp30) cc_final: 0.7197 (tp30) REVERT: G 62 THR cc_start: 0.8448 (m) cc_final: 0.7974 (t) REVERT: G 104 GLN cc_start: 0.8044 (pt0) cc_final: 0.7829 (pt0) REVERT: G 109 TRP cc_start: 0.8420 (m100) cc_final: 0.7947 (m100) REVERT: G 120 TRP cc_start: 0.8582 (m100) cc_final: 0.8210 (m100) REVERT: G 135 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7037 (tp30) REVERT: G 136 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8087 (tp) REVERT: G 137 HIS cc_start: 0.8482 (m170) cc_final: 0.8119 (m90) REVERT: G 143 GLN cc_start: 0.8418 (mt0) cc_final: 0.8211 (mt0) REVERT: G 144 GLU cc_start: 0.7209 (pm20) cc_final: 0.6644 (pm20) REVERT: G 145 ILE cc_start: 0.8487 (mp) cc_final: 0.8252 (mp) REVERT: G 174 MET cc_start: 0.7700 (mtp) cc_final: 0.7132 (mtp) REVERT: G 193 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: G 200 TRP cc_start: 0.8625 (p90) cc_final: 0.8141 (p90) REVERT: G 213 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7510 (tm-30) REVERT: G 237 ASP cc_start: 0.7556 (t0) cc_final: 0.7072 (t0) REVERT: G 245 THR cc_start: 0.7955 (OUTLIER) cc_final: 0.7738 (t) REVERT: G 266 PHE cc_start: 0.8281 (t80) cc_final: 0.7739 (t80) REVERT: G 312 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8279 (mtpp) REVERT: G 327 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6866 (mm-30) REVERT: G 335 GLU cc_start: 0.7265 (tt0) cc_final: 0.6646 (tt0) REVERT: G 345 PHE cc_start: 0.7862 (m-80) cc_final: 0.7193 (m-80) REVERT: G 382 ARG cc_start: 0.5224 (mtm180) cc_final: 0.4532 (mtm180) REVERT: G 386 GLN cc_start: 0.7697 (mt0) cc_final: 0.7431 (mm-40) REVERT: G 398 PHE cc_start: 0.8572 (p90) cc_final: 0.8229 (p90) REVERT: G 434 ASP cc_start: 0.7692 (m-30) cc_final: 0.7471 (t0) REVERT: G 442 ILE cc_start: 0.8461 (mm) cc_final: 0.8247 (mm) REVERT: G 475 ASP cc_start: 0.7643 (t0) cc_final: 0.7024 (t0) REVERT: G 479 LYS cc_start: 0.8619 (mmtm) cc_final: 0.8358 (mmtm) REVERT: G 497 GLN cc_start: 0.8348 (mt0) cc_final: 0.8008 (mt0) REVERT: G 505 ASN cc_start: 0.7636 (t0) cc_final: 0.6826 (t0) REVERT: G 509 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7576 (mm-30) REVERT: G 518 MET cc_start: 0.7817 (ptp) cc_final: 0.7545 (ptp) REVERT: G 530 LYS cc_start: 0.7844 (ttpp) cc_final: 0.7357 (ttpp) REVERT: G 535 PHE cc_start: 0.8274 (m-80) cc_final: 0.7521 (m-80) REVERT: G 582 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8339 (pttm) REVERT: F 65 SER cc_start: 0.8412 (t) cc_final: 0.7941 (p) REVERT: F 72 ASN cc_start: 0.8453 (t0) cc_final: 0.8182 (t0) REVERT: F 73 MET cc_start: 0.8179 (ttp) cc_final: 0.7701 (ttp) REVERT: F 80 ARG cc_start: 0.4035 (tpt90) cc_final: 0.3372 (tpt90) REVERT: F 81 ARG cc_start: 0.5392 (ptp-170) cc_final: 0.4689 (ptp-170) REVERT: F 86 ASN cc_start: 0.7932 (p0) cc_final: 0.7561 (p0) REVERT: F 109 TRP cc_start: 0.8427 (m100) cc_final: 0.7655 (m100) REVERT: F 120 TRP cc_start: 0.8407 (m100) cc_final: 0.7963 (m100) REVERT: F 135 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: F 151 LYS cc_start: 0.8176 (mmmm) cc_final: 0.7580 (mmmm) REVERT: F 191 ARG cc_start: 0.8337 (mtp85) cc_final: 0.8131 (mmm-85) REVERT: F 195 LEU cc_start: 0.7547 (mt) cc_final: 0.7225 (mt) REVERT: F 197 PHE cc_start: 0.8159 (m-10) cc_final: 0.7452 (m-80) REVERT: F 201 LYS cc_start: 0.8217 (mmpt) cc_final: 0.7785 (mmpt) REVERT: F 213 GLN cc_start: 0.7418 (tm-30) cc_final: 0.6844 (tm-30) REVERT: F 237 ASP cc_start: 0.8021 (t0) cc_final: 0.7398 (t0) REVERT: F 242 GLN cc_start: 0.7682 (pt0) cc_final: 0.7328 (pp30) REVERT: F 279 TRP cc_start: 0.8299 (p-90) cc_final: 0.7963 (p-90) REVERT: F 312 LYS cc_start: 0.8672 (mptt) cc_final: 0.7887 (mptt) REVERT: F 327 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7388 (mm-30) REVERT: F 346 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6482 (mt-10) REVERT: F 409 TYR cc_start: 0.8366 (t80) cc_final: 0.7950 (t80) REVERT: F 439 LYS cc_start: 0.8244 (mmtp) cc_final: 0.7753 (mmtp) REVERT: F 468 GLN cc_start: 0.7109 (tt0) cc_final: 0.6893 (mt0) REVERT: F 473 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7219 (tm-30) REVERT: F 475 ASP cc_start: 0.8126 (t0) cc_final: 0.7347 (t0) REVERT: F 497 GLN cc_start: 0.8223 (mt0) cc_final: 0.7776 (mt0) REVERT: F 501 LYS cc_start: 0.8076 (ttpp) cc_final: 0.7135 (ttpp) REVERT: F 518 MET cc_start: 0.7858 (ptp) cc_final: 0.7360 (ptp) REVERT: F 532 LYS cc_start: 0.8378 (ttmm) cc_final: 0.7893 (ttmm) REVERT: F 551 MET cc_start: 0.7021 (ttt) cc_final: 0.6770 (ttt) REVERT: F 562 VAL cc_start: 0.8616 (p) cc_final: 0.8412 (m) REVERT: F 575 LYS cc_start: 0.8329 (mmmt) cc_final: 0.8027 (mmmt) REVERT: D 46 ASN cc_start: 0.7481 (t0) cc_final: 0.6832 (t0) REVERT: D 50 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6574 (tm-30) REVERT: D 70 HIS cc_start: 0.7824 (t-170) cc_final: 0.7292 (t-170) REVERT: D 107 THR cc_start: 0.8279 (m) cc_final: 0.7633 (p) REVERT: D 142 GLU cc_start: 0.7981 (pt0) cc_final: 0.7476 (pm20) REVERT: D 174 MET cc_start: 0.7651 (mtp) cc_final: 0.6984 (mtp) REVERT: D 190 MET cc_start: 0.7869 (mmm) cc_final: 0.7614 (mmm) REVERT: D 208 TRP cc_start: 0.8307 (t60) cc_final: 0.7522 (t60) REVERT: D 256 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7910 (mtm-85) REVERT: E 45 PHE cc_start: 0.8230 (t80) cc_final: 0.7719 (t80) REVERT: E 95 ASN cc_start: 0.8292 (t0) cc_final: 0.7950 (t0) REVERT: E 142 GLU cc_start: 0.7751 (pt0) cc_final: 0.6601 (pt0) REVERT: E 163 LYS cc_start: 0.8066 (mppt) cc_final: 0.7603 (mppt) REVERT: E 183 MET cc_start: 0.7281 (mmm) cc_final: 0.7013 (mmm) REVERT: E 209 ARG cc_start: 0.4912 (OUTLIER) cc_final: 0.4076 (ptt180) REVERT: E 210 TYR cc_start: 0.8467 (p90) cc_final: 0.8164 (p90) REVERT: E 213 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7566 (tm-30) REVERT: E 247 GLU cc_start: 0.7728 (mp0) cc_final: 0.7118 (mp0) REVERT: E 266 PHE cc_start: 0.8292 (t80) cc_final: 0.8013 (t80) REVERT: E 335 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6130 (tm-30) REVERT: E 342 TYR cc_start: 0.7026 (p90) cc_final: 0.6703 (p90) REVERT: E 380 PHE cc_start: 0.7785 (p90) cc_final: 0.7461 (p90) REVERT: E 386 GLN cc_start: 0.8237 (tt0) cc_final: 0.8013 (tt0) REVERT: E 387 LYS cc_start: 0.8788 (tptm) cc_final: 0.8532 (tptm) REVERT: E 396 GLU cc_start: 0.7273 (tt0) cc_final: 0.6854 (tt0) REVERT: E 400 TYR cc_start: 0.8012 (t80) cc_final: 0.7315 (t80) REVERT: E 404 GLN cc_start: 0.8092 (pt0) cc_final: 0.7411 (pt0) REVERT: E 430 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7587 (tt) REVERT: E 451 TYR cc_start: 0.3566 (OUTLIER) cc_final: 0.3213 (t80) REVERT: E 464 TYR cc_start: 0.8016 (t80) cc_final: 0.7728 (t80) REVERT: E 472 LYS cc_start: 0.3363 (OUTLIER) cc_final: 0.1245 (tmmt) REVERT: E 501 LYS cc_start: 0.8027 (tttt) cc_final: 0.7657 (tttt) REVERT: E 526 ASP cc_start: 0.6652 (p0) cc_final: 0.6190 (p0) REVERT: E 530 LYS cc_start: 0.8014 (tmtt) cc_final: 0.7459 (tttt) REVERT: E 532 LYS cc_start: 0.8329 (ttpt) cc_final: 0.7567 (ttpt) REVERT: E 538 LYS cc_start: 0.7324 (ttmm) cc_final: 0.6785 (mtpp) REVERT: E 550 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7006 (mm-40) REVERT: E 551 MET cc_start: 0.7088 (ttt) cc_final: 0.6830 (ttt) REVERT: E 560 ASN cc_start: 0.8416 (m-40) cc_final: 0.8087 (m110) REVERT: I 95 ASN cc_start: 0.8360 (m-40) cc_final: 0.7942 (m-40) REVERT: I 109 TRP cc_start: 0.8550 (m100) cc_final: 0.7847 (m100) REVERT: I 122 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7695 (p0) REVERT: I 178 ASP cc_start: 0.6638 (t0) cc_final: 0.6330 (t0) REVERT: I 193 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7252 (mp0) REVERT: I 214 TRP cc_start: -0.1681 (OUTLIER) cc_final: -0.3830 (p90) REVERT: I 237 ASP cc_start: 0.7344 (t0) cc_final: 0.6738 (t0) REVERT: I 269 ASP cc_start: 0.6752 (p0) cc_final: 0.6405 (p0) REVERT: I 332 ARG cc_start: 0.8691 (mmt-90) cc_final: 0.8374 (mmt90) REVERT: I 346 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6528 (mm-30) REVERT: I 386 GLN cc_start: 0.7732 (tt0) cc_final: 0.7237 (tt0) REVERT: I 415 ILE cc_start: 0.8626 (mt) cc_final: 0.8291 (mm) REVERT: I 479 LYS cc_start: 0.8441 (mmtt) cc_final: 0.7853 (mmtt) REVERT: I 491 GLN cc_start: 0.7458 (mm-40) cc_final: 0.7036 (mm-40) REVERT: I 532 LYS cc_start: 0.8434 (ttmm) cc_final: 0.8067 (ttpp) REVERT: I 577 GLN cc_start: 0.8296 (mt0) cc_final: 0.8019 (mt0) REVERT: I 582 LYS cc_start: 0.8341 (pttm) cc_final: 0.8009 (pttm) REVERT: C 47 ASN cc_start: 0.7793 (t0) cc_final: 0.7538 (t160) REVERT: C 67 ARG cc_start: 0.6867 (mmt-90) cc_final: 0.6153 (mmt-90) REVERT: C 73 MET cc_start: 0.7721 (ptt) cc_final: 0.7192 (ptt) REVERT: C 86 ASN cc_start: 0.7817 (p0) cc_final: 0.7532 (p0) REVERT: C 193 GLU cc_start: 0.7315 (tp30) cc_final: 0.6823 (tp30) REVERT: C 378 TYR cc_start: 0.2258 (OUTLIER) cc_final: 0.0495 (m-80) REVERT: C 509 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: C 520 ARG cc_start: 0.8715 (mpp80) cc_final: 0.7936 (mpp80) REVERT: B 52 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7877 (ttmm) REVERT: B 53 PHE cc_start: 0.8421 (m-80) cc_final: 0.7938 (p90) REVERT: B 58 TRP cc_start: 0.8202 (m100) cc_final: 0.7599 (m100) REVERT: B 80 ARG cc_start: 0.8015 (mmm-85) cc_final: 0.7552 (mmm-85) REVERT: B 82 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8150 (m) REVERT: B 109 TRP cc_start: 0.8646 (m100) cc_final: 0.7831 (m100) REVERT: B 131 ASN cc_start: 0.7750 (t0) cc_final: 0.7469 (t0) REVERT: B 142 GLU cc_start: 0.7629 (pp20) cc_final: 0.7266 (pp20) REVERT: B 151 LYS cc_start: 0.8487 (mttm) cc_final: 0.8165 (mttm) REVERT: B 178 ASP cc_start: 0.6915 (t0) cc_final: 0.6667 (t0) REVERT: B 201 LYS cc_start: 0.8834 (mmmt) cc_final: 0.8611 (mtmt) REVERT: B 344 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8559 (p) REVERT: B 396 GLU cc_start: 0.7781 (tt0) cc_final: 0.7555 (tt0) REVERT: B 430 LEU cc_start: 0.8415 (tp) cc_final: 0.8107 (tp) REVERT: B 470 TRP cc_start: 0.8415 (p90) cc_final: 0.7825 (p90) REVERT: B 491 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7104 (mm-40) REVERT: B 551 MET cc_start: 0.7323 (ttt) cc_final: 0.7086 (ttt) REVERT: B 565 ASN cc_start: 0.8091 (m110) cc_final: 0.7791 (m110) REVERT: B 569 MET cc_start: 0.6968 (mmm) cc_final: 0.6679 (mmm) REVERT: B 575 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7488 (mmtt) outliers start: 164 outliers final: 131 residues processed: 1585 average time/residue: 0.4393 time to fit residues: 1080.6156 Evaluate side-chains 1679 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1527 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 270 CYS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 416 GLN Chi-restraints excluded: chain G residue 551 MET Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain G residue 582 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 222 HIS Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 458 ASN Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 451 TYR Chi-restraints excluded: chain E residue 468 GLN Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 214 TRP Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 318 GLN Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 429 VAL Chi-restraints excluded: chain I residue 466 ASN Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 497 GLN Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 518 MET Chi-restraints excluded: chain I residue 521 ILE Chi-restraints excluded: chain I residue 551 MET Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 497 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 5.9990 chunk 372 optimal weight: 8.9990 chunk 227 optimal weight: 0.5980 chunk 176 optimal weight: 2.9990 chunk 258 optimal weight: 6.9990 chunk 390 optimal weight: 3.9990 chunk 359 optimal weight: 0.9980 chunk 310 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 240 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN G 127 GLN ** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN F 143 GLN ** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 HIS ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN E 127 GLN ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 31929 Z= 0.259 Angle : 0.630 14.862 43660 Z= 0.314 Chirality : 0.044 0.218 4764 Planarity : 0.005 0.069 5732 Dihedral : 5.201 72.760 4237 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.43 % Allowed : 30.05 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3686 helix: -1.01 (0.48), residues: 100 sheet: -0.28 (0.18), residues: 868 loop : -0.48 (0.12), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP F 470 HIS 0.020 0.001 HIS C 102 PHE 0.033 0.002 PHE A 266 TYR 0.028 0.002 TYR A 561 ARG 0.008 0.001 ARG G 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1677 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1531 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7472 (tt0) cc_final: 0.7086 (tp30) REVERT: A 67 ARG cc_start: 0.8087 (mmt180) cc_final: 0.7629 (mmt180) REVERT: A 96 MET cc_start: 0.6934 (mmp) cc_final: 0.6639 (mmt) REVERT: A 104 GLN cc_start: 0.8090 (pt0) cc_final: 0.7745 (pt0) REVERT: A 135 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7186 (mt-10) REVERT: A 175 VAL cc_start: 0.8655 (t) cc_final: 0.8254 (p) REVERT: A 183 MET cc_start: 0.8034 (mmm) cc_final: 0.7802 (mmm) REVERT: A 230 THR cc_start: 0.8515 (p) cc_final: 0.8264 (t) REVERT: A 237 ASP cc_start: 0.7672 (t0) cc_final: 0.7171 (t0) REVERT: A 244 TYR cc_start: 0.7244 (m-80) cc_final: 0.6666 (m-80) REVERT: A 260 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7292 (tt0) REVERT: A 291 LEU cc_start: 0.8476 (mp) cc_final: 0.8256 (mt) REVERT: A 312 LYS cc_start: 0.8475 (mtmt) cc_final: 0.8224 (mtmt) REVERT: A 335 GLU cc_start: 0.7274 (tt0) cc_final: 0.6302 (tm-30) REVERT: A 350 GLN cc_start: 0.7413 (mt0) cc_final: 0.6964 (mp10) REVERT: A 411 GLU cc_start: 0.7887 (mp0) cc_final: 0.7510 (mp0) REVERT: A 413 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6562 (m-30) REVERT: A 414 TRP cc_start: 0.8183 (p90) cc_final: 0.7711 (p90) REVERT: A 429 VAL cc_start: 0.8478 (p) cc_final: 0.8258 (t) REVERT: A 446 ASN cc_start: 0.8007 (m110) cc_final: 0.7674 (m110) REVERT: A 471 ASP cc_start: 0.5785 (OUTLIER) cc_final: 0.5556 (m-30) REVERT: A 473 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6799 (mm-30) REVERT: A 495 PRO cc_start: 0.7320 (Cg_exo) cc_final: 0.6951 (Cg_endo) REVERT: A 501 LYS cc_start: 0.8549 (ttpp) cc_final: 0.7882 (ttpp) REVERT: A 528 TRP cc_start: 0.8306 (m100) cc_final: 0.7822 (m100) REVERT: A 530 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7807 (ttpp) REVERT: A 538 LYS cc_start: 0.8004 (ttmt) cc_final: 0.7580 (ttmt) REVERT: A 565 ASN cc_start: 0.8596 (m-40) cc_final: 0.8144 (m-40) REVERT: G 50 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6642 (mp0) REVERT: G 53 PHE cc_start: 0.5348 (p90) cc_final: 0.4549 (p90) REVERT: G 60 GLU cc_start: 0.7568 (tp30) cc_final: 0.7126 (tp30) REVERT: G 62 THR cc_start: 0.8380 (m) cc_final: 0.7761 (t) REVERT: G 68 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8031 (tt) REVERT: G 83 VAL cc_start: 0.8739 (t) cc_final: 0.8351 (m) REVERT: G 104 GLN cc_start: 0.8040 (pt0) cc_final: 0.7797 (pt0) REVERT: G 109 TRP cc_start: 0.8412 (m100) cc_final: 0.8096 (m100) REVERT: G 120 TRP cc_start: 0.8510 (m100) cc_final: 0.8261 (m100) REVERT: G 135 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6977 (tp30) REVERT: G 136 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7966 (tp) REVERT: G 143 GLN cc_start: 0.8297 (mt0) cc_final: 0.8076 (mt0) REVERT: G 144 GLU cc_start: 0.7210 (pm20) cc_final: 0.6586 (pm20) REVERT: G 174 MET cc_start: 0.7741 (mtp) cc_final: 0.7238 (mtp) REVERT: G 193 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6567 (mp0) REVERT: G 213 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7241 (tm-30) REVERT: G 237 ASP cc_start: 0.7484 (t0) cc_final: 0.7001 (t0) REVERT: G 245 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7714 (t) REVERT: G 266 PHE cc_start: 0.8190 (t80) cc_final: 0.7747 (t80) REVERT: G 312 LYS cc_start: 0.8537 (mtpp) cc_final: 0.8278 (mtpp) REVERT: G 327 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6764 (mm-30) REVERT: G 335 GLU cc_start: 0.7261 (tt0) cc_final: 0.6630 (tt0) REVERT: G 345 PHE cc_start: 0.7795 (m-80) cc_final: 0.7172 (m-80) REVERT: G 382 ARG cc_start: 0.5273 (mtm180) cc_final: 0.4377 (mtm110) REVERT: G 386 GLN cc_start: 0.7706 (mt0) cc_final: 0.7489 (mm-40) REVERT: G 398 PHE cc_start: 0.8551 (p90) cc_final: 0.8194 (p90) REVERT: G 468 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7756 (tp40) REVERT: G 475 ASP cc_start: 0.7596 (t0) cc_final: 0.6983 (t0) REVERT: G 479 LYS cc_start: 0.8620 (mmtm) cc_final: 0.8344 (mmtm) REVERT: G 497 GLN cc_start: 0.8309 (mt0) cc_final: 0.7961 (mt0) REVERT: G 505 ASN cc_start: 0.7593 (t0) cc_final: 0.6797 (t0) REVERT: G 509 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7569 (mm-30) REVERT: G 518 MET cc_start: 0.7781 (ptp) cc_final: 0.7505 (ptp) REVERT: G 528 TRP cc_start: 0.8101 (m100) cc_final: 0.7480 (m100) REVERT: G 530 LYS cc_start: 0.7833 (ttpp) cc_final: 0.7162 (ttpp) REVERT: G 532 LYS cc_start: 0.8158 (ttmm) cc_final: 0.7956 (ttmm) REVERT: G 535 PHE cc_start: 0.8250 (m-80) cc_final: 0.7475 (m-80) REVERT: G 582 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8343 (pttm) REVERT: F 65 SER cc_start: 0.8396 (t) cc_final: 0.7845 (p) REVERT: F 72 ASN cc_start: 0.8453 (t0) cc_final: 0.8171 (t0) REVERT: F 73 MET cc_start: 0.8177 (ttp) cc_final: 0.7693 (ttp) REVERT: F 80 ARG cc_start: 0.4027 (tpt90) cc_final: 0.0989 (tpt170) REVERT: F 81 ARG cc_start: 0.5321 (ptp-170) cc_final: 0.4942 (ptp-170) REVERT: F 109 TRP cc_start: 0.8398 (m100) cc_final: 0.7797 (m100) REVERT: F 120 TRP cc_start: 0.8345 (m100) cc_final: 0.7939 (m100) REVERT: F 135 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: F 151 LYS cc_start: 0.8154 (mmmm) cc_final: 0.7564 (mmmm) REVERT: F 195 LEU cc_start: 0.7569 (mt) cc_final: 0.7334 (mt) REVERT: F 201 LYS cc_start: 0.8195 (mmpt) cc_final: 0.7772 (mmpt) REVERT: F 213 GLN cc_start: 0.7390 (tm-30) cc_final: 0.6818 (tm-30) REVERT: F 237 ASP cc_start: 0.8017 (t0) cc_final: 0.7387 (t0) REVERT: F 242 GLN cc_start: 0.7697 (pt0) cc_final: 0.7338 (pp30) REVERT: F 279 TRP cc_start: 0.8273 (p-90) cc_final: 0.7924 (p-90) REVERT: F 346 GLU cc_start: 0.6527 (mt-10) cc_final: 0.6266 (mt-10) REVERT: F 409 TYR cc_start: 0.8314 (t80) cc_final: 0.7947 (t80) REVERT: F 439 LYS cc_start: 0.8122 (mmtp) cc_final: 0.7674 (mmtp) REVERT: F 459 ASN cc_start: 0.8055 (m-40) cc_final: 0.7674 (m110) REVERT: F 473 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7201 (tm-30) REVERT: F 475 ASP cc_start: 0.8080 (t0) cc_final: 0.7279 (t0) REVERT: F 497 GLN cc_start: 0.8216 (mt0) cc_final: 0.7755 (mt0) REVERT: F 518 MET cc_start: 0.7855 (ptp) cc_final: 0.7335 (ptp) REVERT: F 532 LYS cc_start: 0.8340 (ttmm) cc_final: 0.7870 (ttmm) REVERT: F 551 MET cc_start: 0.6985 (ttt) cc_final: 0.6755 (ttt) REVERT: F 562 VAL cc_start: 0.8616 (p) cc_final: 0.8405 (m) REVERT: F 575 LYS cc_start: 0.8334 (mmmt) cc_final: 0.8089 (mmmt) REVERT: D 50 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6542 (tm-30) REVERT: D 70 HIS cc_start: 0.7804 (t-170) cc_final: 0.7299 (t-170) REVERT: D 73 MET cc_start: 0.8274 (ptt) cc_final: 0.7657 (ptm) REVERT: D 107 THR cc_start: 0.8274 (m) cc_final: 0.7578 (p) REVERT: D 142 GLU cc_start: 0.7978 (pt0) cc_final: 0.7475 (pm20) REVERT: D 174 MET cc_start: 0.7727 (mtp) cc_final: 0.7087 (mtp) REVERT: D 190 MET cc_start: 0.7852 (mmm) cc_final: 0.7596 (mmm) REVERT: D 208 TRP cc_start: 0.8315 (t60) cc_final: 0.7395 (t60) REVERT: D 256 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7695 (tpp80) REVERT: E 60 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7062 (tm-30) REVERT: E 86 ASN cc_start: 0.7464 (p0) cc_final: 0.7152 (p0) REVERT: E 95 ASN cc_start: 0.8240 (t0) cc_final: 0.7883 (t0) REVERT: E 142 GLU cc_start: 0.7746 (pt0) cc_final: 0.6582 (pt0) REVERT: E 163 LYS cc_start: 0.8061 (mppt) cc_final: 0.7601 (mppt) REVERT: E 183 MET cc_start: 0.7284 (mmm) cc_final: 0.7040 (mmm) REVERT: E 209 ARG cc_start: 0.4820 (OUTLIER) cc_final: 0.4324 (ptt180) REVERT: E 210 TYR cc_start: 0.8389 (p90) cc_final: 0.8110 (p90) REVERT: E 247 GLU cc_start: 0.7667 (mp0) cc_final: 0.7023 (mp0) REVERT: E 266 PHE cc_start: 0.8255 (t80) cc_final: 0.7968 (t80) REVERT: E 335 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6237 (tm-30) REVERT: E 342 TYR cc_start: 0.7023 (p90) cc_final: 0.6695 (p90) REVERT: E 377 ARG cc_start: 0.5158 (mtt180) cc_final: 0.4760 (mtt180) REVERT: E 380 PHE cc_start: 0.7769 (p90) cc_final: 0.7335 (p90) REVERT: E 386 GLN cc_start: 0.8236 (tt0) cc_final: 0.7980 (tt0) REVERT: E 387 LYS cc_start: 0.8782 (tptm) cc_final: 0.8514 (tptm) REVERT: E 396 GLU cc_start: 0.7305 (tt0) cc_final: 0.6825 (tt0) REVERT: E 400 TYR cc_start: 0.7979 (t80) cc_final: 0.7285 (t80) REVERT: E 404 GLN cc_start: 0.8083 (pt0) cc_final: 0.7374 (pt0) REVERT: E 430 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7573 (tt) REVERT: E 464 TYR cc_start: 0.7935 (t80) cc_final: 0.7560 (t80) REVERT: E 472 LYS cc_start: 0.3160 (OUTLIER) cc_final: 0.1225 (tmmt) REVERT: E 479 LYS cc_start: 0.8325 (mptt) cc_final: 0.7927 (mptt) REVERT: E 501 LYS cc_start: 0.7973 (tttt) cc_final: 0.7629 (tttt) REVERT: E 526 ASP cc_start: 0.6619 (p0) cc_final: 0.6165 (p0) REVERT: E 530 LYS cc_start: 0.7940 (tmtt) cc_final: 0.7432 (tttt) REVERT: E 532 LYS cc_start: 0.8324 (ttpt) cc_final: 0.7576 (ttpt) REVERT: E 538 LYS cc_start: 0.7244 (ttmm) cc_final: 0.6525 (mtpp) REVERT: E 551 MET cc_start: 0.7081 (ttt) cc_final: 0.6853 (ttt) REVERT: E 560 ASN cc_start: 0.8404 (m-40) cc_final: 0.8113 (m110) REVERT: E 581 ARG cc_start: 0.8193 (ttp-170) cc_final: 0.7941 (ttp-170) REVERT: I 67 ARG cc_start: 0.7973 (mmt-90) cc_final: 0.7735 (mmt90) REVERT: I 95 ASN cc_start: 0.8344 (m-40) cc_final: 0.7912 (m-40) REVERT: I 109 TRP cc_start: 0.8560 (m100) cc_final: 0.7837 (m100) REVERT: I 122 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7720 (p0) REVERT: I 178 ASP cc_start: 0.6438 (t0) cc_final: 0.6200 (t0) REVERT: I 193 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7189 (mp0) REVERT: I 214 TRP cc_start: -0.1873 (OUTLIER) cc_final: -0.3993 (p90) REVERT: I 237 ASP cc_start: 0.7294 (t0) cc_final: 0.6675 (t0) REVERT: I 266 PHE cc_start: 0.7952 (t80) cc_final: 0.7729 (t80) REVERT: I 269 ASP cc_start: 0.6687 (p0) cc_final: 0.6322 (p0) REVERT: I 318 GLN cc_start: 0.8615 (mt0) cc_final: 0.8300 (mm110) REVERT: I 332 ARG cc_start: 0.8670 (mmt-90) cc_final: 0.8359 (mmt90) REVERT: I 346 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6557 (mm-30) REVERT: I 386 GLN cc_start: 0.7682 (tt0) cc_final: 0.7187 (tt0) REVERT: I 415 ILE cc_start: 0.8621 (mt) cc_final: 0.8249 (mm) REVERT: I 491 GLN cc_start: 0.7429 (mm-40) cc_final: 0.6952 (mm-40) REVERT: I 532 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8198 (ttmm) REVERT: I 538 LYS cc_start: 0.8257 (tppt) cc_final: 0.7266 (tppt) REVERT: I 577 GLN cc_start: 0.8237 (mt0) cc_final: 0.7968 (mt0) REVERT: I 582 LYS cc_start: 0.8385 (pttm) cc_final: 0.8139 (pttm) REVERT: C 45 PHE cc_start: 0.7958 (t80) cc_final: 0.7757 (t80) REVERT: C 67 ARG cc_start: 0.6678 (mmt-90) cc_final: 0.6043 (mmt-90) REVERT: C 73 MET cc_start: 0.7707 (ptt) cc_final: 0.7172 (ptt) REVERT: C 86 ASN cc_start: 0.7798 (p0) cc_final: 0.7472 (p0) REVERT: C 164 VAL cc_start: 0.8637 (p) cc_final: 0.8385 (m) REVERT: C 193 GLU cc_start: 0.7265 (tp30) cc_final: 0.6793 (tp30) REVERT: C 266 PHE cc_start: 0.8524 (t80) cc_final: 0.8087 (t80) REVERT: C 378 TYR cc_start: 0.2230 (OUTLIER) cc_final: 0.0509 (m-80) REVERT: C 509 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6929 (tm-30) REVERT: C 520 ARG cc_start: 0.8710 (mpp80) cc_final: 0.7954 (mpp80) REVERT: B 52 LYS cc_start: 0.8212 (ttmm) cc_final: 0.7886 (ttmm) REVERT: B 53 PHE cc_start: 0.8357 (m-80) cc_final: 0.7880 (p90) REVERT: B 58 TRP cc_start: 0.8138 (m100) cc_final: 0.7575 (m100) REVERT: B 80 ARG cc_start: 0.8010 (mmm-85) cc_final: 0.7499 (mmm-85) REVERT: B 95 ASN cc_start: 0.8185 (t0) cc_final: 0.7787 (m110) REVERT: B 109 TRP cc_start: 0.8665 (m100) cc_final: 0.7849 (m100) REVERT: B 125 ASP cc_start: 0.7692 (m-30) cc_final: 0.7301 (m-30) REVERT: B 142 GLU cc_start: 0.7641 (pp20) cc_final: 0.7334 (pp20) REVERT: B 151 LYS cc_start: 0.8513 (mttm) cc_final: 0.8175 (mttm) REVERT: B 178 ASP cc_start: 0.6840 (t0) cc_final: 0.6637 (t0) REVERT: B 201 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8593 (mtmt) REVERT: B 211 TYR cc_start: 0.7795 (m-80) cc_final: 0.7469 (m-10) REVERT: B 256 ARG cc_start: 0.7652 (mtp180) cc_final: 0.7337 (mtp-110) REVERT: B 261 PHE cc_start: 0.8366 (t80) cc_final: 0.8028 (t80) REVERT: B 396 GLU cc_start: 0.7674 (tt0) cc_final: 0.7408 (tt0) REVERT: B 430 LEU cc_start: 0.8418 (tp) cc_final: 0.8098 (tp) REVERT: B 491 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7047 (mm-40) REVERT: B 528 TRP cc_start: 0.8663 (m100) cc_final: 0.8458 (m100) REVERT: B 551 MET cc_start: 0.7314 (ttt) cc_final: 0.7057 (ttt) REVERT: B 565 ASN cc_start: 0.8060 (m110) cc_final: 0.7778 (m110) REVERT: B 569 MET cc_start: 0.6953 (mmm) cc_final: 0.6638 (mmm) REVERT: B 575 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7493 (mmtt) outliers start: 146 outliers final: 112 residues processed: 1582 average time/residue: 0.4507 time to fit residues: 1107.6989 Evaluate side-chains 1661 residues out of total 3295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1529 time to evaluate : 3.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 416 GLN Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 551 MET Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain G residue 582 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 222 HIS Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 458 ASN Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 214 TRP Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 429 VAL Chi-restraints excluded: chain I residue 466 ASN Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 497 GLN Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 518 MET Chi-restraints excluded: chain I residue 521 ILE Chi-restraints excluded: chain I residue 551 MET Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 549 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 0.6980 chunk 331 optimal weight: 20.0000 chunk 95 optimal weight: 7.9990 chunk 286 optimal weight: 4.9990 chunk 45 optimal weight: 0.0470 chunk 86 optimal weight: 8.9990 chunk 311 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 319 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 overall best weight: 1.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN G 127 GLN ** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN F 143 GLN ** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN ** F 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 HIS ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN I 147 ASN ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.125127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.107178 restraints weight = 52454.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111469 restraints weight = 24289.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114219 restraints weight = 13592.651| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 31929 Z= 0.202 Angle : 0.621 17.351 43660 Z= 0.306 Chirality : 0.044 0.368 4764 Planarity : 0.005 0.063 5732 Dihedral : 5.003 72.396 4237 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.10 % Allowed : 30.62 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3686 helix: -0.78 (0.50), residues: 94 sheet: -0.22 (0.18), residues: 885 loop : -0.43 (0.12), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 528 HIS 0.027 0.001 HIS C 102 PHE 0.032 0.002 PHE A 266 TYR 0.025 0.001 TYR A 561 ARG 0.008 0.001 ARG B 332 =============================================================================== Job complete usr+sys time: 14011.59 seconds wall clock time: 245 minutes 25.92 seconds (14725.92 seconds total)