Starting phenix.real_space_refine on Fri Jul 26 11:41:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utu_26789/07_2024/7utu_26789.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utu_26789/07_2024/7utu_26789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utu_26789/07_2024/7utu_26789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utu_26789/07_2024/7utu_26789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utu_26789/07_2024/7utu_26789.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utu_26789/07_2024/7utu_26789.cif" } resolution = 3.0 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= 0.008 sd= 0.057 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 124 5.16 5 C 20993 2.51 5 N 5652 2.21 5 O 6235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 239": "OD1" <-> "OD2" Residue "A TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 155": "OE1" <-> "OE2" 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 PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 305": "OD1" <-> "OD2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 471": "OD1" <-> "OD2" Residue "B PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 327": "OE1" <-> "OE2" Residue "I TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 556": "OD1" <-> "OD2" Residue "I TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 240": "OD1" <-> "OD2" Residue "E PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 471": "OD1" <-> "OD2" Residue "E TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "G GLU 193": "OE1" <-> "OE2" Residue "G TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 240": "OD1" <-> "OD2" Residue "G TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 434": "OD1" <-> "OD2" Residue "G TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 193": "OE1" <-> "OE2" 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 TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 298": "OE1" <-> "OE2" Residue "F ASP 305": "OD1" <-> "OD2" Residue "F ASP 311": "OD1" <-> "OD2" Residue "F TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 346": "OE1" <-> "OE2" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 396": "OE1" <-> "OE2" Residue "F PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 405": "OD1" <-> "OD2" Residue "F TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 33004 Number of models: 1 Model: "" Number of chains: 10 Chain: "L" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 480 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'TRANS': 95} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'UNK:plan-1': 96} Unresolved non-hydrogen planarities: 96 Chain: "H" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 570 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'TRANS': 113} Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'UNK:plan-1': 114} Unresolved non-hydrogen planarities: 114 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: "D" Number of atoms: 3444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3444 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 397} Chain breaks: 4 Chain: "B" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4150 Classifications: {'peptide': 519} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 480} Chain breaks: 4 Chain: "I" Number of atoms: 4178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4178 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 485} Chain breaks: 3 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: "C" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3243 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 376} Chain breaks: 5 Chain: "G" Number of atoms: 4225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4225 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 490} Chain breaks: 3 Chain: "F" 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 Time building chain proxies: 17.42, per 1000 atoms: 0.53 Number of scatterers: 33004 At special positions: 0 Unit cell: (192.5, 198, 144.1, 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 124 16.00 O 6235 8.00 N 5652 7.00 C 20993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 494 " distance=2.04 Simple disulfide: pdb=" SG CYS D 490 " - pdb=" SG CYS D 494 " distance=2.04 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 494 " distance=2.04 Simple disulfide: pdb=" SG CYS I 490 " - pdb=" SG CYS I 494 " distance=2.03 Simple disulfide: pdb=" SG CYS E 490 " - pdb=" SG CYS E 494 " distance=2.04 Simple disulfide: pdb=" SG CYS C 490 " - pdb=" SG CYS C 494 " distance=2.03 Simple disulfide: pdb=" SG CYS G 490 " - pdb=" SG CYS G 494 " distance=2.03 Simple disulfide: pdb=" SG CYS F 490 " - pdb=" SG CYS F 494 " distance=2.04 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: 12.09 Conformation dependent library (CDL) restraints added in 5.6 seconds 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7888 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 59 sheets defined 12.0% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'H' and resid 25 through 29 removed outlier: 3.859A pdb=" N UNK H 29 " --> pdb=" O UNK H 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 116 through 121 removed outlier: 4.182A pdb=" N TRP A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 132 removed outlier: 3.719A pdb=" N THR A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.004A pdb=" N MET A 190 " --> pdb=" O PRO A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.504A pdb=" N ASP A 240 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 309 through 313 removed outlier: 3.851A pdb=" N ARG A 313 " --> pdb=" O GLN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 557 through 561 removed outlier: 3.638A pdb=" N ASN A 560 " --> pdb=" O ASN A 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 245 through 250 Processing helix chain 'D' and resid 381 through 385 removed outlier: 4.133A pdb=" N GLY D 385 " --> pdb=" O ARG D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 562 removed outlier: 3.720A pdb=" N VAL D 562 " --> pdb=" O PHE D 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 92 removed outlier: 4.350A pdb=" N VAL B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 4.105A pdb=" N TRP B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.600A pdb=" N ASP B 240 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL B 241 " --> pdb=" O PRO B 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 237 through 241' Processing helix chain 'B' and resid 245 through 250 Processing helix chain 'B' and resid 281 through 285 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.666A pdb=" N ASP B 413 " --> pdb=" O PRO B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'I' and resid 86 through 92 removed outlier: 4.431A pdb=" N VAL I 92 " --> pdb=" O ASP I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 121 removed outlier: 4.190A pdb=" N TRP I 120 " --> pdb=" O ALA I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 132 removed outlier: 3.745A pdb=" N THR I 132 " --> pdb=" O LEU I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 192 removed outlier: 3.537A pdb=" N MET I 190 " --> pdb=" O PRO I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 241 removed outlier: 3.574A pdb=" N VAL I 241 " --> pdb=" O PRO I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 285 removed outlier: 3.791A pdb=" N LEU I 285 " --> pdb=" O ASN I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 309 through 313 removed outlier: 3.618A pdb=" N ARG I 313 " --> pdb=" O GLN I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 385 removed outlier: 3.623A pdb=" N GLY I 385 " --> pdb=" O ARG I 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 409 through 413 Processing helix chain 'I' and resid 425 through 427 No H-bonds generated for 'chain 'I' and resid 425 through 427' Processing helix chain 'I' and resid 443 through 448 removed outlier: 3.565A pdb=" N ILE I 447 " --> pdb=" O TYR I 444 " (cutoff:3.500A) Processing helix chain 'I' and resid 558 through 562 removed outlier: 3.610A pdb=" N TYR I 561 " --> pdb=" O GLN I 558 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL I 562 " --> pdb=" O PHE I 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 558 through 562' Processing helix chain 'E' and resid 86 through 92 removed outlier: 3.825A pdb=" N VAL E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 237 through 241 removed outlier: 3.721A pdb=" N ASP E 240 " --> pdb=" O ASP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 250 Processing helix chain 'E' and resid 281 through 285 Processing helix chain 'E' and resid 309 through 313 removed outlier: 3.575A pdb=" N ARG E 313 " --> pdb=" O GLN E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 427 No H-bonds generated for 'chain 'E' and resid 425 through 427' Processing helix chain 'E' and resid 443 through 447 Processing helix chain 'E' and resid 557 through 562 removed outlier: 3.818A pdb=" N VAL E 562 " --> pdb=" O PHE E 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 237 through 241 Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.962A pdb=" N GLY C 385 " --> pdb=" O ARG C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 562 removed outlier: 4.029A pdb=" N VAL C 562 " --> pdb=" O PHE C 559 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 91 Processing helix chain 'G' and resid 95 through 99 removed outlier: 3.537A pdb=" N ASP G 99 " --> pdb=" O MET G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 120 Processing helix chain 'G' and resid 122 through 132 Processing helix chain 'G' and resid 237 through 241 removed outlier: 3.550A pdb=" N ASP G 240 " --> pdb=" O ASP G 237 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL G 241 " --> pdb=" O PRO G 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 237 through 241' Processing helix chain 'G' and resid 245 through 250 Processing helix chain 'G' and resid 281 through 285 Processing helix chain 'G' and resid 309 through 313 removed outlier: 3.860A pdb=" N ARG G 313 " --> pdb=" O GLN G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 413 removed outlier: 3.516A pdb=" N ASP G 413 " --> pdb=" O PRO G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 427 No H-bonds generated for 'chain 'G' and resid 425 through 427' Processing helix chain 'G' and resid 435 through 439 removed outlier: 3.869A pdb=" N GLY G 438 " --> pdb=" O PRO G 435 " (cutoff:3.500A) Processing helix chain 'G' and resid 443 through 448 removed outlier: 3.599A pdb=" N PHE G 448 " --> pdb=" O THR G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 562 removed outlier: 4.269A pdb=" N TYR G 561 " --> pdb=" O ASN G 557 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL G 562 " --> pdb=" O GLN G 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 557 through 562' Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 95 through 99 Processing helix chain 'F' and resid 116 through 120 Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 245 through 250 Processing helix chain 'F' and resid 281 through 285 removed outlier: 3.663A pdb=" N LEU F 285 " --> pdb=" O ASN F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 313 removed outlier: 3.596A pdb=" N ARG F 313 " --> pdb=" O GLN F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 385 removed outlier: 3.860A pdb=" N GLY F 385 " --> pdb=" O ARG F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 413 removed outlier: 3.715A pdb=" N ASP F 413 " --> pdb=" O PRO F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 427 No H-bonds generated for 'chain 'F' and resid 425 through 427' Processing helix chain 'F' and resid 443 through 447 Processing helix chain 'F' and resid 557 through 561 removed outlier: 3.602A pdb=" N ASN F 560 " --> pdb=" O ASN F 557 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR F 561 " --> pdb=" O GLN F 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 557 through 561' Processing sheet with id=AA1, first strand: chain 'L' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'L' and resid 41 through 42 removed outlier: 3.673A pdb=" N UNK L 74 " --> pdb=" O UNK L 35 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N UNK L 77 " --> pdb=" O UNK L 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 55 through 57 removed outlier: 3.507A pdb=" N UNK L 55 " --> pdb=" O UNK L 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.585A pdb=" N UNK H 4 " --> pdb=" O UNK H 20 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N UNK H 18 " --> pdb=" O UNK H 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 42 through 47 removed outlier: 6.882A pdb=" N UNK H 33 " --> pdb=" O UNK H 44 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N UNK H 46 " --> pdb=" O UNK H 31 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N UNK H 31 " --> pdb=" O UNK H 46 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N UNK H 88 " --> pdb=" O UNK H 105 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N UNK H 105 " --> pdb=" O UNK H 88 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N UNK H 90 " --> pdb=" O UNK H 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 44 through 45 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 44 through 45 current: chain 'B' and resid 102 through 112 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 49 through 54 removed outlier: 4.046A pdb=" N TRP A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) 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=AA8, first strand: chain 'A' and resid 80 through 84 Processing sheet with id=AA9, first strand: chain 'A' and resid 215 through 218 removed outlier: 3.823A pdb=" N GLY A 235 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N THR A 217 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N TYR A 233 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 276 through 277 Processing sheet with id=AB2, first strand: chain 'A' and resid 315 through 317 removed outlier: 3.604A pdb=" N PHE G 398 " --> pdb=" O TYR G 378 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 335 through 336 removed outlier: 6.792A pdb=" N GLU A 335 " --> pdb=" O ALA A 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 351 through 354 removed outlier: 3.616A pdb=" N SER A 348 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 396 through 399 removed outlier: 6.813A pdb=" N ASN A 375 " --> pdb=" O MET F 319 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET F 319 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 429 through 430 removed outlier: 3.653A pdb=" N SER G 348 " --> pdb=" O GLY G 351 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 470 through 472 removed outlier: 7.036A pdb=" N ASP A 471 " --> pdb=" O CYS A 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, 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 111 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 58 through 72 current: chain 'D' and resid 164 through 167 Processing sheet with id=AC1, first strand: chain 'D' and resid 80 through 84 Processing sheet with id=AC2, first strand: chain 'D' and resid 215 through 218 removed outlier: 7.255A pdb=" N THR D 217 " --> pdb=" O TYR D 233 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TYR D 233 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 276 through 278 Processing sheet with id=AC4, first strand: chain 'D' and resid 345 through 348 Processing sheet with id=AC5, first strand: chain 'D' and resid 377 through 380 Processing sheet with id=AC6, first strand: chain 'B' and resid 44 through 45 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 44 through 45 current: chain 'C' and resid 102 through 112 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 49 through 53 removed outlier: 3.608A pdb=" N LYS B 52 " --> pdb=" O GLU B 60 " (cutoff:3.500A) 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=AC8, first strand: chain 'B' and resid 215 through 218 removed outlier: 6.246A pdb=" N ASP B 215 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 217 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 276 through 278 Processing sheet with id=AD1, first strand: chain 'B' and resid 335 through 336 removed outlier: 6.728A pdb=" N GLU B 335 " --> pdb=" O ALA B 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 351 through 354 removed outlier: 3.636A pdb=" N SER B 348 " --> pdb=" O GLY B 351 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 396 through 399 removed outlier: 3.506A pdb=" N GLU B 396 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN B 375 " --> pdb=" O MET I 319 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET I 319 " --> pdb=" O ASN B 375 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 415 through 416 Processing sheet with id=AD5, first strand: chain 'I' and resid 44 through 45 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 44 through 45 current: chain 'G' and resid 102 through 112 No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, 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=AD7, first strand: chain 'I' and resid 80 through 84 Processing sheet with id=AD8, first strand: chain 'I' and resid 276 through 278 Processing sheet with id=AD9, first strand: chain 'I' and resid 379 through 380 Processing sheet with id=AE1, first strand: chain 'E' and resid 49 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=AE2, first strand: chain 'E' and resid 215 through 218 removed outlier: 6.574A pdb=" N ASP E 215 " --> pdb=" O HIS E 234 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR E 217 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE E 232 " --> pdb=" O THR E 217 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 276 through 278 Processing sheet with id=AE4, first strand: chain 'E' and resid 335 through 336 removed outlier: 6.800A pdb=" N GLU E 335 " --> pdb=" O ALA E 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 345 through 348 removed outlier: 3.652A pdb=" N SER E 348 " --> pdb=" O GLY E 351 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 377 through 380 Processing sheet with id=AE7, first strand: chain 'E' and resid 415 through 416 Processing sheet with id=AE8, first strand: chain 'C' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 58 through 72 current: chain 'C' and resid 164 through 167 Processing sheet with id=AE9, first strand: chain 'C' and resid 215 through 218 removed outlier: 3.552A pdb=" N GLY C 235 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N THR C 217 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N TYR C 233 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 345 through 348 Processing sheet with id=AF2, first strand: chain 'C' and resid 377 through 380 Processing sheet with id=AF3, first strand: chain 'C' and resid 463 through 464 removed outlier: 4.028A pdb=" N TYR C 464 " --> pdb=" O GLU C 574 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU C 574 " --> pdb=" O TYR C 464 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'G' and resid 49 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=AF5, first strand: chain 'G' and resid 215 through 218 removed outlier: 3.625A pdb=" N GLY G 235 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR G 217 " --> pdb=" O TYR G 233 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TYR G 233 " --> pdb=" O THR G 217 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 276 through 278 Processing sheet with id=AF7, first strand: chain 'G' and resid 315 through 319 removed outlier: 3.977A pdb=" N MET G 319 " --> pdb=" O ASN F 375 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN F 375 " --> pdb=" O MET G 319 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 335 through 336 removed outlier: 6.713A pdb=" N GLU G 335 " --> pdb=" O ALA G 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'G' and resid 429 through 430 Processing sheet with id=AG1, first strand: chain 'F' and resid 49 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=AG2, first strand: chain 'F' and resid 80 through 84 Processing sheet with id=AG3, first strand: chain 'F' and resid 216 through 218 removed outlier: 3.544A pdb=" N THR F 217 " --> pdb=" O ILE F 232 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 276 through 278 removed outlier: 5.990A pdb=" N HIS F 277 " --> pdb=" O ARG F 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'F' and resid 335 through 336 removed outlier: 6.818A pdb=" N GLU F 335 " --> pdb=" O ALA F 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 355 hydrogen bonds defined for protein. 714 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: 9.07 Time building geometry restraints manager: 13.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10784 1.34 - 1.47: 9069 1.47 - 1.60: 13875 1.60 - 1.73: 0 1.73 - 1.86: 216 Bond restraints: 33944 Sorted by residual: bond pdb=" CA GLN E 404 " pdb=" C GLN E 404 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.72e-02 3.38e+03 1.17e+01 bond pdb=" C CYS I 494 " pdb=" N PRO I 495 " ideal model delta sigma weight residual 1.330 1.368 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" CA ASP B 168 " pdb=" CB ASP B 168 " ideal model delta sigma weight residual 1.526 1.579 -0.053 1.70e-02 3.46e+03 9.77e+00 bond pdb=" C THR G 107 " pdb=" N PRO G 108 " ideal model delta sigma weight residual 1.331 1.356 -0.025 7.90e-03 1.60e+04 9.77e+00 bond pdb=" N GLY I 37 " pdb=" CA GLY I 37 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.41e+00 ... (remaining 33939 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.81: 1460 106.81 - 113.93: 17940 113.93 - 121.06: 15710 121.06 - 128.18: 10732 128.18 - 135.30: 581 Bond angle restraints: 46423 Sorted by residual: angle pdb=" C ASN E 493 " pdb=" CA ASN E 493 " pdb=" CB ASN E 493 " ideal model delta sigma weight residual 109.99 118.44 -8.45 1.61e+00 3.86e-01 2.76e+01 angle pdb=" CA GLU B 411 " pdb=" CB GLU B 411 " pdb=" CG GLU B 411 " ideal model delta sigma weight residual 114.10 123.11 -9.01 2.00e+00 2.50e-01 2.03e+01 angle pdb=" CA GLU B 60 " pdb=" CB GLU B 60 " pdb=" CG GLU B 60 " ideal model delta sigma weight residual 114.10 123.10 -9.00 2.00e+00 2.50e-01 2.03e+01 angle pdb=" CA VAL E 250 " pdb=" C VAL E 250 " pdb=" N PRO E 251 " ideal model delta sigma weight residual 116.57 120.97 -4.40 9.80e-01 1.04e+00 2.02e+01 angle pdb=" CA VAL D 250 " pdb=" C VAL D 250 " pdb=" N PRO D 251 " ideal model delta sigma weight residual 116.57 120.87 -4.30 9.80e-01 1.04e+00 1.93e+01 ... (remaining 46418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 17815 17.88 - 35.77: 1560 35.77 - 53.65: 392 53.65 - 71.54: 72 71.54 - 89.42: 46 Dihedral angle restraints: 19885 sinusoidal: 7654 harmonic: 12231 Sorted by residual: dihedral pdb=" CA CYS I 494 " pdb=" C CYS I 494 " pdb=" N PRO I 495 " pdb=" CA PRO I 495 " ideal model delta harmonic sigma weight residual 180.00 -147.37 -32.63 0 5.00e+00 4.00e-02 4.26e+01 dihedral pdb=" CA THR B 425 " pdb=" C THR B 425 " pdb=" N ASN B 426 " pdb=" CA ASN B 426 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA CYS F 494 " pdb=" C CYS F 494 " pdb=" N PRO F 495 " pdb=" CA PRO F 495 " ideal model delta harmonic sigma weight residual -180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 19882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3987 0.058 - 0.117: 849 0.117 - 0.175: 203 0.175 - 0.233: 13 0.233 - 0.291: 1 Chirality restraints: 5053 Sorted by residual: chirality pdb=" CB VAL A 130 " pdb=" CA VAL A 130 " pdb=" CG1 VAL A 130 " pdb=" CG2 VAL A 130 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA ILE B 219 " pdb=" N ILE B 219 " pdb=" C ILE B 219 " pdb=" CB ILE B 219 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE D 219 " pdb=" N ILE D 219 " pdb=" C ILE D 219 " pdb=" CB ILE D 219 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 5050 not shown) Planarity restraints: 6105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 141 " 0.023 2.00e-02 2.50e+03 3.16e-02 1.75e+01 pdb=" CG PHE I 141 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 PHE I 141 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE I 141 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE I 141 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE I 141 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE I 141 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 45 " 0.016 2.00e-02 2.50e+03 2.52e-02 1.11e+01 pdb=" CG PHE C 45 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE C 45 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE C 45 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE C 45 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 45 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 45 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 237 " 0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO D 238 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO D 238 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 238 " 0.045 5.00e-02 4.00e+02 ... (remaining 6102 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 441 2.63 - 3.20: 29446 3.20 - 3.77: 49383 3.77 - 4.33: 70875 4.33 - 4.90: 117163 Nonbonded interactions: 267308 Sorted by model distance: nonbonded pdb=" OG1 THR A 326 " pdb=" OD1 ASP G 100 " model vdw 2.067 2.440 nonbonded pdb=" OE1 GLN I 558 " pdb=" OG1 THR G 236 " model vdw 2.081 2.440 nonbonded pdb=" OG SER I 339 " pdb=" OG1 THR I 450 " model vdw 2.114 2.440 nonbonded pdb=" OD1 ASN B 443 " pdb=" OG1 THR B 445 " model vdw 2.116 2.440 nonbonded pdb=" OD1 ASN E 443 " pdb=" OG1 THR E 445 " model vdw 2.116 2.440 ... (remaining 267303 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 37 through 290 or resid 302 through 306 or resid 309 throu \ gh 391 or resid 394 through 508 or resid 517 through 584)) selection = (chain 'B' and (resid 37 through 391 or resid 394 through 508 or resid 517 throu \ gh 584)) selection = (chain 'E' and (resid 37 through 290 or resid 302 through 306 or resid 309 throu \ gh 391 or resid 394 through 508 or resid 517 through 584)) selection = (chain 'F' and (resid 37 through 290 or resid 302 through 306 or resid 309 throu \ gh 391 or resid 394 through 508 or resid 517 through 584)) selection = (chain 'G' and (resid 37 through 290 or resid 302 through 306 or resid 309 throu \ gh 508 or resid 517 through 584)) selection = (chain 'I' and (resid 37 through 290 or resid 302 through 306 or resid 309 throu \ gh 391 or resid 394 through 584)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 37 through 277 or resid 340 through 404 or resid 457 throu \ gh 540 or resid 549 through 579)) } 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 individual isotropic 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: 0.620 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: 0.030 Extract box with map and model: 1.360 Check model and map are aligned: 0.250 Set scattering table: 0.300 Process input model: 81.670 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.150 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:11.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 : 0.006 0.084 33944 Z= 0.425 Angle : 0.990 11.821 46423 Z= 0.526 Chirality : 0.052 0.291 5053 Planarity : 0.007 0.121 6105 Dihedral : 15.291 89.423 11973 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.26 % Allowed : 16.90 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.34 % 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: -1.20 (0.12), residues: 3937 helix: -0.22 (0.44), residues: 93 sheet: -0.87 (0.15), residues: 1000 loop : -0.80 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP I 214 HIS 0.018 0.002 HIS A 234 PHE 0.072 0.003 PHE I 141 TYR 0.048 0.002 TYR C 464 ARG 0.026 0.001 ARG B 520 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1181 time to evaluate : 3.884 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: A 380 PHE cc_start: 0.8652 (p90) cc_final: 0.8387 (p90) REVERT: A 444 TYR cc_start: 0.8305 (p90) cc_final: 0.7797 (p90) REVERT: A 558 GLN cc_start: 0.7893 (tt0) cc_final: 0.7677 (tt0) REVERT: A 576 SER cc_start: 0.8603 (t) cc_final: 0.8172 (m) REVERT: D 60 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6902 (tm-30) REVERT: D 145 ILE cc_start: 0.8680 (mt) cc_final: 0.8462 (mp) REVERT: D 185 PHE cc_start: 0.8786 (t80) cc_final: 0.8518 (t80) REVERT: D 209 ARG cc_start: 0.8031 (pmt170) cc_final: 0.5507 (pmt-80) REVERT: D 214 TRP cc_start: 0.7890 (p90) cc_final: 0.7549 (p90) REVERT: D 246 ILE cc_start: 0.8087 (mm) cc_final: 0.7866 (mp) REVERT: D 274 ARG cc_start: 0.8338 (mmm-85) cc_final: 0.7479 (mmm-85) REVERT: D 377 ARG cc_start: 0.8428 (ttt-90) cc_final: 0.8212 (ttm-80) REVERT: D 383 GLN cc_start: 0.8076 (mt0) cc_final: 0.7865 (mt0) REVERT: D 488 PHE cc_start: 0.8217 (m-80) cc_final: 0.7787 (m-80) REVERT: D 566 ILE cc_start: 0.8010 (pt) cc_final: 0.7711 (pp) REVERT: D 581 ARG cc_start: 0.7927 (ttp80) cc_final: 0.7373 (ttp80) REVERT: B 167 ASN cc_start: 0.7978 (m-40) cc_final: 0.7767 (m-40) REVERT: B 277 HIS cc_start: 0.8296 (p-80) cc_final: 0.8064 (p90) REVERT: B 329 THR cc_start: 0.8304 (p) cc_final: 0.8034 (t) REVERT: B 378 TYR cc_start: 0.8354 (m-80) cc_final: 0.7948 (m-80) REVERT: B 396 GLU cc_start: 0.7767 (tt0) cc_final: 0.7356 (tt0) REVERT: B 397 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7844 (mtt180) REVERT: I 67 ARG cc_start: 0.7591 (mmt-90) cc_final: 0.6996 (mmt180) REVERT: I 73 MET cc_start: 0.7127 (ptt) cc_final: 0.6567 (ptt) REVERT: I 104 GLN cc_start: 0.7745 (pt0) cc_final: 0.7267 (pp30) REVERT: I 107 THR cc_start: 0.8506 (m) cc_final: 0.8264 (t) REVERT: I 151 LYS cc_start: 0.7795 (mmmt) cc_final: 0.7312 (mmmt) REVERT: I 198 TYR cc_start: 0.8345 (m-80) cc_final: 0.7977 (m-80) REVERT: I 213 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7576 (tm-30) REVERT: I 283 ARG cc_start: 0.8106 (mmm-85) cc_final: 0.7888 (mmm160) REVERT: I 311 ASP cc_start: 0.7876 (p0) cc_final: 0.7580 (p0) REVERT: I 380 PHE cc_start: 0.8260 (p90) cc_final: 0.7811 (p90) REVERT: I 382 ARG cc_start: 0.8073 (mtt90) cc_final: 0.7844 (mtt90) REVERT: I 443 ASN cc_start: 0.7997 (p0) cc_final: 0.7776 (p0) REVERT: I 472 LYS cc_start: 0.8244 (tptm) cc_final: 0.7991 (mmtp) REVERT: I 528 TRP cc_start: 0.8247 (m100) cc_final: 0.7682 (m100) REVERT: E 216 ARG cc_start: 0.7654 (ttt90) cc_final: 0.7284 (ttt180) REVERT: E 309 GLN cc_start: 0.7557 (mt0) cc_final: 0.6876 (mt0) REVERT: E 312 LYS cc_start: 0.8538 (mttt) cc_final: 0.7436 (mttt) REVERT: E 417 ASN cc_start: 0.8475 (t0) cc_final: 0.7710 (t0) REVERT: E 419 ASN cc_start: 0.8573 (m-40) cc_final: 0.8067 (p0) REVERT: E 428 ASN cc_start: 0.8359 (m-40) cc_final: 0.7909 (t0) REVERT: E 479 LYS cc_start: 0.8699 (mttp) cc_final: 0.8370 (mttp) REVERT: E 582 LYS cc_start: 0.8072 (ttmt) cc_final: 0.7843 (tttt) REVERT: C 54 LEU cc_start: 0.8466 (mt) cc_final: 0.8230 (mm) REVERT: C 77 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7045 (mm-30) REVERT: C 128 LEU cc_start: 0.7961 (tp) cc_final: 0.7730 (tm) REVERT: C 143 GLN cc_start: 0.8085 (mt0) cc_final: 0.7783 (mt0) REVERT: C 183 MET cc_start: 0.7115 (mmm) cc_final: 0.6880 (mmm) REVERT: C 209 ARG cc_start: 0.6973 (pmt170) cc_final: 0.6729 (pmt-80) REVERT: C 387 LYS cc_start: 0.8313 (tttt) cc_final: 0.8082 (tttm) REVERT: C 464 TYR cc_start: 0.7574 (t80) cc_final: 0.7171 (t80) REVERT: C 522 VAL cc_start: 0.8636 (t) cc_final: 0.8309 (m) REVERT: C 538 LYS cc_start: 0.8213 (tptp) cc_final: 0.7659 (tptp) REVERT: G 128 LEU cc_start: 0.8477 (tp) cc_final: 0.8238 (tm) REVERT: G 135 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7106 (mp0) REVERT: G 144 GLU cc_start: 0.7566 (pt0) cc_final: 0.7223 (pt0) REVERT: G 177 LEU cc_start: 0.7989 (tp) cc_final: 0.7696 (tm) REVERT: G 190 MET cc_start: 0.7562 (mmm) cc_final: 0.6831 (mmm) REVERT: G 204 ILE cc_start: 0.8594 (pt) cc_final: 0.8255 (pp) REVERT: G 213 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7939 (tm-30) REVERT: G 266 PHE cc_start: 0.8271 (t80) cc_final: 0.8054 (t80) REVERT: G 276 THR cc_start: 0.8344 (p) cc_final: 0.8119 (t) REVERT: G 469 ILE cc_start: 0.8600 (mt) cc_final: 0.8382 (mm) REVERT: G 527 PHE cc_start: 0.7921 (p90) cc_final: 0.7698 (p90) REVERT: G 536 LYS cc_start: 0.8320 (ttpp) cc_final: 0.8093 (ttpp) REVERT: G 577 GLN cc_start: 0.8486 (mt0) cc_final: 0.8245 (mt0) REVERT: F 73 MET cc_start: 0.7766 (ptt) cc_final: 0.7542 (ptt) REVERT: F 81 ARG cc_start: 0.7448 (ttp-170) cc_final: 0.7146 (pmt170) REVERT: F 115 ASN cc_start: 0.8444 (t0) cc_final: 0.8217 (t0) REVERT: F 177 LEU cc_start: 0.8128 (tp) cc_final: 0.7886 (tt) REVERT: F 186 THR cc_start: 0.8460 (p) cc_final: 0.8180 (p) REVERT: F 254 LEU cc_start: 0.8366 (mt) cc_final: 0.8137 (mt) REVERT: F 380 PHE cc_start: 0.8391 (p90) cc_final: 0.8095 (p90) REVERT: F 532 LYS cc_start: 0.8709 (ptmm) cc_final: 0.8313 (ptmm) outliers start: 9 outliers final: 5 residues processed: 1182 average time/residue: 1.3490 time to fit residues: 1912.1647 Evaluate side-chains 1130 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1125 time to evaluate : 3.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 558 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 352 optimal weight: 8.9990 chunk 316 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 326 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 198 optimal weight: 9.9990 chunk 243 optimal weight: 6.9990 chunk 378 optimal weight: 0.1980 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 321 ASN A 428 ASN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 ASN D 104 GLN D 213 GLN ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 HIS B 72 ASN B 242 GLN B 560 ASN I 48 GLN E 48 GLN E 147 ASN E 222 HIS E 234 HIS E 280 GLN C 104 GLN C 167 ASN C 386 GLN C 491 GLN C 549 GLN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN F 85 ASN F 102 HIS F 222 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 33944 Z= 0.373 Angle : 0.607 8.361 46423 Z= 0.309 Chirality : 0.046 0.165 5053 Planarity : 0.005 0.061 6105 Dihedral : 5.794 56.396 4518 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.42 % Allowed : 16.85 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % 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: -0.92 (0.12), residues: 3937 helix: 0.32 (0.45), residues: 94 sheet: -0.61 (0.15), residues: 1020 loop : -0.64 (0.11), residues: 2823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 109 HIS 0.006 0.001 HIS B 277 PHE 0.028 0.002 PHE F 448 TYR 0.028 0.002 TYR C 464 ARG 0.005 0.001 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1280 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1160 time to evaluate : 3.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 GLU cc_start: 0.7545 (tt0) cc_final: 0.7316 (tm-30) REVERT: D 60 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6947 (tm-30) REVERT: D 79 TYR cc_start: 0.8758 (m-80) cc_final: 0.8466 (m-80) REVERT: D 104 GLN cc_start: 0.8420 (pt0) cc_final: 0.8181 (pt0) REVERT: D 177 LEU cc_start: 0.8561 (tp) cc_final: 0.8358 (tp) REVERT: D 209 ARG cc_start: 0.8167 (pmt170) cc_final: 0.5499 (pmt-80) REVERT: D 214 TRP cc_start: 0.7999 (p90) cc_final: 0.7742 (p90) REVERT: D 237 ASP cc_start: 0.7441 (t0) cc_final: 0.7152 (t0) REVERT: D 241 VAL cc_start: 0.7990 (t) cc_final: 0.7777 (t) REVERT: D 246 ILE cc_start: 0.7983 (mm) cc_final: 0.7779 (mp) REVERT: D 269 ASP cc_start: 0.7096 (p0) cc_final: 0.6818 (p0) REVERT: D 544 THR cc_start: 0.8121 (m) cc_final: 0.7639 (t) REVERT: D 573 TYR cc_start: 0.7810 (p90) cc_final: 0.7552 (p90) REVERT: B 89 LYS cc_start: 0.8417 (tptt) cc_final: 0.8087 (tptm) REVERT: B 133 MET cc_start: 0.7438 (mmt) cc_final: 0.7123 (mmt) REVERT: B 151 LYS cc_start: 0.8697 (mtpp) cc_final: 0.8384 (mttm) REVERT: B 166 ASN cc_start: 0.7999 (m-40) cc_final: 0.7709 (p0) REVERT: B 167 ASN cc_start: 0.8031 (m-40) cc_final: 0.7557 (m-40) REVERT: B 213 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7805 (tm-30) REVERT: B 230 THR cc_start: 0.8534 (m) cc_final: 0.8279 (t) REVERT: B 378 TYR cc_start: 0.8314 (m-80) cc_final: 0.7521 (m-80) REVERT: B 394 THR cc_start: 0.8699 (t) cc_final: 0.8400 (p) REVERT: B 396 GLU cc_start: 0.7735 (tt0) cc_final: 0.7353 (tt0) REVERT: B 397 ARG cc_start: 0.8248 (mtt90) cc_final: 0.7919 (mtt180) REVERT: B 408 ARG cc_start: 0.7660 (mmt-90) cc_final: 0.6854 (mpt180) REVERT: B 464 TYR cc_start: 0.8089 (t80) cc_final: 0.7700 (t80) REVERT: B 473 GLU cc_start: 0.7411 (mm-30) cc_final: 0.6927 (mm-30) REVERT: B 476 THR cc_start: 0.8032 (p) cc_final: 0.7772 (p) REVERT: I 71 LEU cc_start: 0.8354 (tp) cc_final: 0.8099 (tm) REVERT: I 73 MET cc_start: 0.7130 (ptt) cc_final: 0.6586 (ptt) REVERT: I 107 THR cc_start: 0.8620 (m) cc_final: 0.8292 (t) REVERT: I 151 LYS cc_start: 0.7805 (mmmt) cc_final: 0.7323 (mmmt) REVERT: I 209 ARG cc_start: 0.5382 (OUTLIER) cc_final: 0.4697 (ppt170) REVERT: I 311 ASP cc_start: 0.7972 (p0) cc_final: 0.7763 (p0) REVERT: I 319 MET cc_start: 0.7790 (mtp) cc_final: 0.7557 (mtp) REVERT: I 338 TYR cc_start: 0.8298 (p90) cc_final: 0.7235 (p90) REVERT: I 408 ARG cc_start: 0.8428 (tpp80) cc_final: 0.8147 (tpp-160) REVERT: I 443 ASN cc_start: 0.7967 (p0) cc_final: 0.7747 (p0) REVERT: I 466 ASN cc_start: 0.8108 (m-40) cc_final: 0.7884 (m-40) REVERT: I 572 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8468 (m) REVERT: E 242 GLN cc_start: 0.8418 (mt0) cc_final: 0.8071 (mt0) REVERT: E 309 GLN cc_start: 0.7536 (mt0) cc_final: 0.6850 (mt0) REVERT: E 312 LYS cc_start: 0.8529 (mttt) cc_final: 0.7474 (mttt) REVERT: E 411 GLU cc_start: 0.7487 (mp0) cc_final: 0.6953 (mp0) REVERT: E 479 LYS cc_start: 0.8492 (mttp) cc_final: 0.8174 (mtpp) REVERT: C 54 LEU cc_start: 0.8576 (mt) cc_final: 0.8358 (mm) REVERT: C 77 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7016 (mm-30) REVERT: C 128 LEU cc_start: 0.7975 (tp) cc_final: 0.7697 (tm) REVERT: C 143 GLN cc_start: 0.8125 (mt0) cc_final: 0.7866 (mt0) REVERT: C 183 MET cc_start: 0.7223 (mmm) cc_final: 0.7020 (mmm) REVERT: C 237 ASP cc_start: 0.7482 (t0) cc_final: 0.7248 (t0) REVERT: C 387 LYS cc_start: 0.8301 (tttt) cc_final: 0.7988 (ttpp) REVERT: C 397 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7403 (pmm-80) REVERT: C 464 TYR cc_start: 0.7617 (t80) cc_final: 0.7320 (t80) REVERT: C 522 VAL cc_start: 0.8785 (OUTLIER) cc_final: 0.8469 (m) REVERT: C 538 LYS cc_start: 0.8238 (tptp) cc_final: 0.7706 (tptp) REVERT: G 52 LYS cc_start: 0.7921 (ttmm) cc_final: 0.7539 (ttmm) REVERT: G 77 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7541 (mm-30) REVERT: G 89 LYS cc_start: 0.8473 (tptt) cc_final: 0.8263 (tptt) REVERT: G 135 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7192 (mp0) REVERT: G 190 MET cc_start: 0.7535 (mmm) cc_final: 0.6856 (mmm) REVERT: G 204 ILE cc_start: 0.8622 (pt) cc_final: 0.8301 (pp) REVERT: G 213 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7952 (tm-30) REVERT: G 276 THR cc_start: 0.8385 (p) cc_final: 0.8121 (t) REVERT: G 344 SER cc_start: 0.8746 (OUTLIER) cc_final: 0.8411 (p) REVERT: G 527 PHE cc_start: 0.8069 (p90) cc_final: 0.7845 (p90) REVERT: G 530 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8193 (ttmt) REVERT: F 73 MET cc_start: 0.7759 (ptt) cc_final: 0.7532 (ptt) REVERT: F 80 ARG cc_start: 0.5488 (tpt90) cc_final: 0.5105 (tpt170) REVERT: F 177 LEU cc_start: 0.8080 (tp) cc_final: 0.7839 (tt) REVERT: F 214 TRP cc_start: 0.8576 (p90) cc_final: 0.8033 (p90) REVERT: F 216 ARG cc_start: 0.7702 (ttt90) cc_final: 0.7197 (ttt-90) REVERT: F 326 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8240 (t) REVERT: F 472 LYS cc_start: 0.8191 (tttt) cc_final: 0.7946 (tttt) REVERT: F 479 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7453 (mmtp) outliers start: 120 outliers final: 65 residues processed: 1198 average time/residue: 1.2900 time to fit residues: 1865.1366 Evaluate side-chains 1196 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1124 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 209 ARG Chi-restraints excluded: chain I residue 401 ILE Chi-restraints excluded: chain I residue 413 ASP Chi-restraints excluded: chain I residue 415 ILE Chi-restraints excluded: chain I residue 490 CYS Chi-restraints excluded: chain I residue 556 ASP Chi-restraints excluded: chain I residue 564 SER Chi-restraints excluded: chain I residue 572 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain E residue 442 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 538 LYS Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 570 LYS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 466 ASN Chi-restraints excluded: chain G residue 511 ASP Chi-restraints excluded: chain G residue 530 LYS Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 479 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 210 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 315 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 379 optimal weight: 8.9990 chunk 409 optimal weight: 10.0000 chunk 337 optimal weight: 8.9990 chunk 376 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 304 optimal weight: 0.2980 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 426 ASN A 558 GLN B 48 GLN B 70 HIS B 137 HIS B 242 GLN I 167 ASN E 48 GLN E 222 HIS E 280 GLN E 404 GLN ** C 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 GLN F 147 ASN ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 GLN F 549 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 33944 Z= 0.556 Angle : 0.658 8.964 46423 Z= 0.338 Chirality : 0.048 0.191 5053 Planarity : 0.006 0.081 6105 Dihedral : 5.710 56.077 4509 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.68 % Allowed : 17.70 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % 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: -1.00 (0.12), residues: 3937 helix: 0.40 (0.47), residues: 94 sheet: -0.74 (0.16), residues: 1016 loop : -0.67 (0.11), residues: 2827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 545 HIS 0.026 0.002 HIS E 222 PHE 0.034 0.002 PHE D 45 TYR 0.033 0.002 TYR F 342 ARG 0.009 0.001 ARG I 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1372 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1208 time to evaluate : 3.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 TYR cc_start: 0.8655 (t80) cc_final: 0.8033 (t80) REVERT: D 56 ASN cc_start: 0.7961 (m-40) cc_final: 0.7759 (m-40) REVERT: D 77 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6789 (mm-30) REVERT: D 79 TYR cc_start: 0.8807 (m-80) cc_final: 0.8560 (m-80) REVERT: D 104 GLN cc_start: 0.8311 (pt0) cc_final: 0.7870 (pt0) REVERT: D 106 VAL cc_start: 0.8298 (t) cc_final: 0.7864 (m) REVERT: D 209 ARG cc_start: 0.8257 (pmt170) cc_final: 0.5812 (ptm160) REVERT: D 214 TRP cc_start: 0.8078 (p90) cc_final: 0.7654 (p90) REVERT: D 237 ASP cc_start: 0.7599 (t0) cc_final: 0.7336 (t0) REVERT: D 241 VAL cc_start: 0.8052 (t) cc_final: 0.7832 (t) REVERT: D 246 ILE cc_start: 0.7969 (mm) cc_final: 0.7768 (mp) REVERT: D 269 ASP cc_start: 0.7158 (p0) cc_final: 0.6838 (p0) REVERT: D 398 PHE cc_start: 0.8566 (p90) cc_final: 0.8301 (p90) REVERT: D 510 TYR cc_start: 0.8573 (t80) cc_final: 0.8319 (t80) REVERT: D 544 THR cc_start: 0.8132 (m) cc_final: 0.7635 (t) REVERT: D 550 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8254 (mm-40) REVERT: D 573 TYR cc_start: 0.7843 (p90) cc_final: 0.7124 (p90) REVERT: D 574 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6871 (mm-30) REVERT: B 60 GLU cc_start: 0.7379 (tp30) cc_final: 0.7122 (tp30) REVERT: B 89 LYS cc_start: 0.8469 (tptt) cc_final: 0.8213 (tptm) REVERT: B 96 MET cc_start: 0.8022 (ptp) cc_final: 0.7802 (ptp) REVERT: B 133 MET cc_start: 0.7398 (mmt) cc_final: 0.7014 (mmt) REVERT: B 151 LYS cc_start: 0.8698 (mtpp) cc_final: 0.8412 (mttp) REVERT: B 166 ASN cc_start: 0.8056 (m-40) cc_final: 0.7780 (p0) REVERT: B 167 ASN cc_start: 0.8062 (m-40) cc_final: 0.7624 (m-40) REVERT: B 213 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8038 (tm-30) REVERT: B 378 TYR cc_start: 0.8272 (m-80) cc_final: 0.7590 (m-80) REVERT: B 394 THR cc_start: 0.8721 (t) cc_final: 0.8440 (p) REVERT: B 396 GLU cc_start: 0.7764 (tt0) cc_final: 0.7361 (tt0) REVERT: B 397 ARG cc_start: 0.8253 (mtt90) cc_final: 0.7875 (mtt180) REVERT: B 408 ARG cc_start: 0.7753 (mmt-90) cc_final: 0.7078 (mpt180) REVERT: B 435 PRO cc_start: 0.8660 (Cg_endo) cc_final: 0.8424 (Cg_exo) REVERT: B 473 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6876 (mm-30) REVERT: B 476 THR cc_start: 0.8102 (p) cc_final: 0.7801 (p) REVERT: B 511 ASP cc_start: 0.7409 (p0) cc_final: 0.7192 (p0) REVERT: B 535 PHE cc_start: 0.8330 (m-80) cc_final: 0.7798 (m-10) REVERT: I 71 LEU cc_start: 0.8385 (tp) cc_final: 0.8148 (tm) REVERT: I 73 MET cc_start: 0.7095 (ptt) cc_final: 0.6670 (ptt) REVERT: I 87 MET cc_start: 0.8465 (tpt) cc_final: 0.8011 (tpt) REVERT: I 107 THR cc_start: 0.8612 (m) cc_final: 0.8386 (t) REVERT: I 151 LYS cc_start: 0.7757 (mmmt) cc_final: 0.7265 (mmmt) REVERT: I 209 ARG cc_start: 0.5413 (OUTLIER) cc_final: 0.4642 (ppt170) REVERT: I 213 GLN cc_start: 0.7966 (tp-100) cc_final: 0.7679 (tp-100) REVERT: I 283 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8071 (mmm160) REVERT: I 311 ASP cc_start: 0.8043 (p0) cc_final: 0.7839 (p0) REVERT: I 314 ARG cc_start: 0.8062 (ttm-80) cc_final: 0.7783 (ttm110) REVERT: I 319 MET cc_start: 0.7798 (mtp) cc_final: 0.7456 (mtp) REVERT: I 443 ASN cc_start: 0.7795 (p0) cc_final: 0.7580 (p0) REVERT: I 466 ASN cc_start: 0.8106 (m-40) cc_final: 0.7849 (m-40) REVERT: I 572 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8276 (m) REVERT: I 574 GLU cc_start: 0.7258 (mm-30) cc_final: 0.7026 (mm-30) REVERT: E 133 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7745 (mmm) REVERT: E 168 ASP cc_start: 0.7266 (t0) cc_final: 0.6803 (t0) REVERT: E 182 THR cc_start: 0.8014 (t) cc_final: 0.7744 (p) REVERT: E 221 SER cc_start: 0.8795 (p) cc_final: 0.8558 (p) REVERT: E 244 TYR cc_start: 0.8506 (m-80) cc_final: 0.8228 (m-80) REVERT: E 257 THR cc_start: 0.8478 (p) cc_final: 0.8206 (t) REVERT: E 309 GLN cc_start: 0.7541 (mt0) cc_final: 0.6807 (mt0) REVERT: E 312 LYS cc_start: 0.8521 (mttt) cc_final: 0.7502 (mttt) REVERT: E 349 THR cc_start: 0.8328 (p) cc_final: 0.7727 (p) REVERT: E 350 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7238 (mp10) REVERT: E 411 GLU cc_start: 0.7489 (mp0) cc_final: 0.6944 (mp0) REVERT: E 416 GLN cc_start: 0.8511 (pt0) cc_final: 0.8054 (pt0) REVERT: E 444 TYR cc_start: 0.7822 (p90) cc_final: 0.7614 (p90) REVERT: E 447 ILE cc_start: 0.7974 (pt) cc_final: 0.7625 (mm) REVERT: E 475 ASP cc_start: 0.7587 (t0) cc_final: 0.7371 (t0) REVERT: E 479 LYS cc_start: 0.8516 (mttp) cc_final: 0.8239 (mttp) REVERT: C 128 LEU cc_start: 0.7979 (tp) cc_final: 0.7745 (tm) REVERT: C 177 LEU cc_start: 0.7832 (tp) cc_final: 0.7405 (tm) REVERT: C 183 MET cc_start: 0.7406 (mmm) cc_final: 0.7174 (mmm) REVERT: C 222 HIS cc_start: 0.3353 (OUTLIER) cc_final: 0.2725 (t-170) REVERT: C 237 ASP cc_start: 0.7514 (t0) cc_final: 0.7164 (t0) REVERT: C 247 GLU cc_start: 0.7626 (mp0) cc_final: 0.7266 (mp0) REVERT: C 387 LYS cc_start: 0.8296 (tttt) cc_final: 0.8018 (tttt) REVERT: C 397 ARG cc_start: 0.7758 (mtt180) cc_final: 0.7401 (pmm-80) REVERT: C 464 TYR cc_start: 0.7679 (t80) cc_final: 0.7193 (t80) REVERT: C 522 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8470 (p) REVERT: C 538 LYS cc_start: 0.8268 (tptp) cc_final: 0.7669 (tptp) REVERT: C 575 LYS cc_start: 0.7585 (mmtm) cc_final: 0.7269 (mmtm) REVERT: G 68 LEU cc_start: 0.8158 (tp) cc_final: 0.7748 (tm) REVERT: G 77 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7595 (mm-30) REVERT: G 81 ARG cc_start: 0.8415 (ttp80) cc_final: 0.8080 (ttm110) REVERT: G 121 PHE cc_start: 0.8126 (m-80) cc_final: 0.7913 (m-80) REVERT: G 190 MET cc_start: 0.7514 (mmm) cc_final: 0.6821 (mmm) REVERT: G 204 ILE cc_start: 0.8664 (pt) cc_final: 0.8335 (pp) REVERT: G 213 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7823 (tm-30) REVERT: G 276 THR cc_start: 0.8343 (p) cc_final: 0.8093 (p) REVERT: G 344 SER cc_start: 0.8744 (OUTLIER) cc_final: 0.8423 (p) REVERT: G 408 ARG cc_start: 0.8207 (mmt-90) cc_final: 0.7744 (mmt90) REVERT: G 434 ASP cc_start: 0.7486 (m-30) cc_final: 0.7109 (m-30) REVERT: G 439 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7458 (mmtm) REVERT: G 440 THR cc_start: 0.8379 (p) cc_final: 0.8108 (t) REVERT: G 469 ILE cc_start: 0.8669 (mt) cc_final: 0.8459 (mm) REVERT: G 538 LYS cc_start: 0.8330 (tptp) cc_final: 0.8104 (tptp) REVERT: F 80 ARG cc_start: 0.5003 (tpt90) cc_final: 0.4722 (tpt170) REVERT: F 126 TRP cc_start: 0.8453 (t-100) cc_final: 0.8172 (t-100) REVERT: F 214 TRP cc_start: 0.8607 (p90) cc_final: 0.8061 (p90) REVERT: F 216 ARG cc_start: 0.7768 (ttt90) cc_final: 0.7230 (ttt-90) REVERT: F 254 LEU cc_start: 0.8313 (mt) cc_final: 0.8070 (mt) REVERT: F 263 THR cc_start: 0.8294 (m) cc_final: 0.8025 (m) REVERT: F 326 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8304 (t) REVERT: F 425 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8338 (p) REVERT: F 473 GLU cc_start: 0.6660 (tm-30) cc_final: 0.6102 (tm-30) REVERT: F 475 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.6939 (t0) REVERT: F 491 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7593 (mm-40) REVERT: F 528 TRP cc_start: 0.8296 (m100) cc_final: 0.7847 (m100) outliers start: 164 outliers final: 96 residues processed: 1255 average time/residue: 1.3377 time to fit residues: 2027.0248 Evaluate side-chains 1283 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1177 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 444 TYR Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 209 ARG Chi-restraints excluded: chain I residue 316 VAL Chi-restraints excluded: chain I residue 401 ILE Chi-restraints excluded: chain I residue 413 ASP Chi-restraints excluded: chain I residue 415 ILE Chi-restraints excluded: chain I residue 476 THR Chi-restraints excluded: chain I residue 481 ARG Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 490 CYS Chi-restraints excluded: chain I residue 564 SER Chi-restraints excluded: chain I residue 572 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 442 ILE Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 538 LYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 582 LYS Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain C residue 519 SER Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 570 LYS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 280 GLN Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 466 ASN Chi-restraints excluded: chain G residue 511 ASP Chi-restraints excluded: chain G residue 574 GLU Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 475 ASP Chi-restraints excluded: chain F residue 497 GLN Chi-restraints excluded: chain F residue 536 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 374 optimal weight: 3.9990 chunk 285 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 chunk 254 optimal weight: 0.9980 chunk 380 optimal weight: 7.9990 chunk 403 optimal weight: 1.9990 chunk 198 optimal weight: 9.9990 chunk 360 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 558 GLN D 383 GLN D 558 GLN B 137 HIS ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 ASN E 48 GLN E 280 GLN E 302 ASN E 404 GLN C 127 GLN C 549 GLN C 560 ASN G 85 ASN G 403 HIS G 416 GLN F 147 ASN F 309 GLN F 468 GLN F 549 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33944 Z= 0.154 Angle : 0.527 8.756 46423 Z= 0.266 Chirality : 0.042 0.151 5053 Planarity : 0.004 0.058 6105 Dihedral : 5.039 56.892 4509 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.39 % Allowed : 21.38 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % 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: -0.73 (0.13), residues: 3937 helix: 0.49 (0.47), residues: 95 sheet: -0.53 (0.16), residues: 986 loop : -0.48 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 214 HIS 0.006 0.001 HIS B 277 PHE 0.032 0.001 PHE C 53 TYR 0.022 0.001 TYR B 524 ARG 0.006 0.000 ARG I 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1293 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1174 time to evaluate : 3.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 TYR cc_start: 0.8566 (t80) cc_final: 0.7999 (t80) REVERT: D 77 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6771 (mm-30) REVERT: D 79 TYR cc_start: 0.8789 (m-80) cc_final: 0.8562 (m-80) REVERT: D 209 ARG cc_start: 0.8158 (pmt170) cc_final: 0.5826 (ptm160) REVERT: D 214 TRP cc_start: 0.8062 (p90) cc_final: 0.7739 (p90) REVERT: D 237 ASP cc_start: 0.7512 (t0) cc_final: 0.7271 (t0) REVERT: D 241 VAL cc_start: 0.8017 (t) cc_final: 0.7786 (t) REVERT: D 246 ILE cc_start: 0.7924 (mm) cc_final: 0.7719 (mp) REVERT: D 269 ASP cc_start: 0.6978 (p0) cc_final: 0.6625 (p0) REVERT: D 544 THR cc_start: 0.8121 (m) cc_final: 0.7630 (t) REVERT: D 573 TYR cc_start: 0.7877 (p90) cc_final: 0.7225 (p90) REVERT: D 574 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6844 (mm-30) REVERT: B 60 GLU cc_start: 0.7441 (tp30) cc_final: 0.7089 (tp30) REVERT: B 89 LYS cc_start: 0.8453 (tptt) cc_final: 0.8176 (tptm) REVERT: B 96 MET cc_start: 0.7983 (ptp) cc_final: 0.7654 (ptp) REVERT: B 133 MET cc_start: 0.7331 (mmt) cc_final: 0.6963 (mmt) REVERT: B 151 LYS cc_start: 0.8735 (mtpp) cc_final: 0.8528 (mttm) REVERT: B 166 ASN cc_start: 0.8018 (m-40) cc_final: 0.7775 (p0) REVERT: B 167 ASN cc_start: 0.8049 (m-40) cc_final: 0.7778 (m-40) REVERT: B 378 TYR cc_start: 0.8261 (m-80) cc_final: 0.7506 (m-80) REVERT: B 394 THR cc_start: 0.8712 (t) cc_final: 0.8439 (p) REVERT: B 396 GLU cc_start: 0.7768 (tt0) cc_final: 0.7254 (tt0) REVERT: B 397 ARG cc_start: 0.8187 (mtt90) cc_final: 0.7777 (mtt180) REVERT: B 408 ARG cc_start: 0.7788 (mmt-90) cc_final: 0.7089 (mpt180) REVERT: B 435 PRO cc_start: 0.8629 (Cg_endo) cc_final: 0.8371 (Cg_exo) REVERT: B 473 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6873 (mm-30) REVERT: B 476 THR cc_start: 0.8132 (p) cc_final: 0.7850 (p) REVERT: B 509 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7090 (mm-30) REVERT: B 511 ASP cc_start: 0.7392 (p0) cc_final: 0.7147 (p0) REVERT: B 535 PHE cc_start: 0.8012 (m-80) cc_final: 0.7565 (m-80) REVERT: I 71 LEU cc_start: 0.8425 (tp) cc_final: 0.8181 (tm) REVERT: I 73 MET cc_start: 0.7199 (ptt) cc_final: 0.6749 (ptt) REVERT: I 87 MET cc_start: 0.8397 (tpt) cc_final: 0.7980 (tpt) REVERT: I 96 MET cc_start: 0.4571 (ttp) cc_final: 0.3965 (tmm) REVERT: I 107 THR cc_start: 0.8580 (m) cc_final: 0.8308 (t) REVERT: I 151 LYS cc_start: 0.7702 (mmmt) cc_final: 0.7222 (mmmt) REVERT: I 213 GLN cc_start: 0.7880 (tp-100) cc_final: 0.7597 (tp-100) REVERT: I 311 ASP cc_start: 0.8003 (p0) cc_final: 0.7758 (p0) REVERT: I 319 MET cc_start: 0.7548 (mtp) cc_final: 0.7238 (mtp) REVERT: I 466 ASN cc_start: 0.8070 (m-40) cc_final: 0.7805 (m-40) REVERT: I 572 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8227 (m) REVERT: I 574 GLU cc_start: 0.7268 (mm-30) cc_final: 0.7026 (mm-30) REVERT: E 125 ASP cc_start: 0.7813 (m-30) cc_final: 0.7609 (m-30) REVERT: E 164 VAL cc_start: 0.8767 (m) cc_final: 0.8453 (p) REVERT: E 168 ASP cc_start: 0.7221 (t0) cc_final: 0.6729 (t0) REVERT: E 190 MET cc_start: 0.8278 (tpp) cc_final: 0.7803 (ttp) REVERT: E 244 TYR cc_start: 0.8519 (m-80) cc_final: 0.8221 (m-80) REVERT: E 257 THR cc_start: 0.8428 (p) cc_final: 0.8187 (t) REVERT: E 302 ASN cc_start: 0.7448 (t160) cc_final: 0.7190 (t0) REVERT: E 309 GLN cc_start: 0.7432 (mt0) cc_final: 0.6758 (mt0) REVERT: E 312 LYS cc_start: 0.8490 (mttt) cc_final: 0.7502 (mttt) REVERT: E 411 GLU cc_start: 0.7466 (mp0) cc_final: 0.6918 (mp0) REVERT: E 416 GLN cc_start: 0.8379 (pt0) cc_final: 0.8009 (pt0) REVERT: E 419 ASN cc_start: 0.8588 (m-40) cc_final: 0.8155 (p0) REVERT: E 447 ILE cc_start: 0.8011 (pt) cc_final: 0.7668 (mm) REVERT: E 475 ASP cc_start: 0.7553 (t0) cc_final: 0.7341 (t0) REVERT: E 479 LYS cc_start: 0.8507 (mttp) cc_final: 0.8237 (mttp) REVERT: C 54 LEU cc_start: 0.8523 (mt) cc_final: 0.8289 (mm) REVERT: C 128 LEU cc_start: 0.7910 (tp) cc_final: 0.7658 (tm) REVERT: C 177 LEU cc_start: 0.7790 (tp) cc_final: 0.7388 (tm) REVERT: C 222 HIS cc_start: 0.3044 (OUTLIER) cc_final: 0.2557 (t-170) REVERT: C 237 ASP cc_start: 0.7376 (t0) cc_final: 0.6973 (t0) REVERT: C 387 LYS cc_start: 0.8316 (tttt) cc_final: 0.8052 (tttm) REVERT: C 397 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7439 (pmm-80) REVERT: C 464 TYR cc_start: 0.7644 (t80) cc_final: 0.7162 (t80) REVERT: C 511 ASP cc_start: 0.7589 (p0) cc_final: 0.7380 (p0) REVERT: C 522 VAL cc_start: 0.8750 (t) cc_final: 0.8423 (p) REVERT: C 538 LYS cc_start: 0.8190 (tptp) cc_final: 0.7620 (tptp) REVERT: C 575 LYS cc_start: 0.7490 (mmtm) cc_final: 0.7209 (mmtm) REVERT: G 68 LEU cc_start: 0.7853 (tp) cc_final: 0.7545 (tm) REVERT: G 77 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7553 (mm-30) REVERT: G 83 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8141 (m) REVERT: G 138 LEU cc_start: 0.8766 (tp) cc_final: 0.8531 (tp) REVERT: G 190 MET cc_start: 0.7485 (mmm) cc_final: 0.6761 (mmm) REVERT: G 191 ARG cc_start: 0.8137 (mmt-90) cc_final: 0.7893 (mmt-90) REVERT: G 204 ILE cc_start: 0.8661 (pt) cc_final: 0.8331 (pp) REVERT: G 276 THR cc_start: 0.8249 (p) cc_final: 0.7978 (p) REVERT: G 318 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7912 (mt0) REVERT: G 408 ARG cc_start: 0.8151 (mmt-90) cc_final: 0.7573 (mmt90) REVERT: G 439 LYS cc_start: 0.7779 (mmtm) cc_final: 0.7350 (mmtm) REVERT: G 469 ILE cc_start: 0.8623 (mt) cc_final: 0.8402 (mm) REVERT: G 475 ASP cc_start: 0.7729 (t0) cc_final: 0.7516 (t0) REVERT: G 527 PHE cc_start: 0.7974 (p90) cc_final: 0.7717 (p90) REVERT: G 530 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8220 (ttmt) REVERT: G 550 GLN cc_start: 0.8173 (mm110) cc_final: 0.7824 (mm110) REVERT: G 577 GLN cc_start: 0.8354 (mt0) cc_final: 0.8032 (mt0) REVERT: F 81 ARG cc_start: 0.7554 (ttp-170) cc_final: 0.7266 (pmt170) REVERT: F 109 TRP cc_start: 0.8343 (m100) cc_final: 0.8097 (m100) REVERT: F 177 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7786 (tp) REVERT: F 186 THR cc_start: 0.8470 (p) cc_final: 0.8131 (p) REVERT: F 214 TRP cc_start: 0.8647 (p90) cc_final: 0.8032 (p90) REVERT: F 216 ARG cc_start: 0.7651 (ttt90) cc_final: 0.7046 (ttt-90) REVERT: F 254 LEU cc_start: 0.8311 (mt) cc_final: 0.8082 (mt) REVERT: F 326 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8208 (t) REVERT: F 475 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.6813 (t0) REVERT: F 479 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7700 (tppp) REVERT: F 491 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7454 (mm-40) REVERT: F 528 TRP cc_start: 0.8251 (m100) cc_final: 0.7770 (m100) outliers start: 119 outliers final: 58 residues processed: 1219 average time/residue: 1.3385 time to fit residues: 1958.3867 Evaluate side-chains 1223 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1157 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 565 ASN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 413 ASP Chi-restraints excluded: chain I residue 415 ILE Chi-restraints excluded: chain I residue 448 PHE Chi-restraints excluded: chain I residue 490 CYS Chi-restraints excluded: chain I residue 572 VAL Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 442 ILE Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 466 ASN Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 475 ASP Chi-restraints excluded: chain F residue 479 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 335 optimal weight: 5.9990 chunk 228 optimal weight: 0.7980 chunk 5 optimal weight: 20.0000 chunk 300 optimal weight: 9.9990 chunk 166 optimal weight: 20.0000 chunk 343 optimal weight: 9.9990 chunk 278 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 361 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN D 104 GLN D 127 GLN D 231 ASN D 383 GLN B 137 HIS B 242 GLN B 560 ASN ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 ASN E 48 GLN E 64 ASN E 280 GLN E 350 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 GLN F 147 ASN F 309 GLN F 497 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 33944 Z= 0.380 Angle : 0.583 8.571 46423 Z= 0.297 Chirality : 0.045 0.161 5053 Planarity : 0.005 0.055 6105 Dihedral : 5.152 54.691 4509 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.02 % Allowed : 21.44 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % 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: -0.77 (0.13), residues: 3937 helix: 0.25 (0.46), residues: 101 sheet: -0.57 (0.16), residues: 980 loop : -0.51 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 109 HIS 0.005 0.001 HIS A 70 PHE 0.035 0.002 PHE C 53 TYR 0.024 0.002 TYR F 342 ARG 0.008 0.001 ARG I 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1336 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1195 time to evaluate : 3.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.7996 (t0) REVERT: A 75 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7173 (mm-30) REVERT: A 133 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7654 (mmt) REVERT: A 457 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8310 (mp) REVERT: A 510 TYR cc_start: 0.8645 (t80) cc_final: 0.7937 (t80) REVERT: A 576 SER cc_start: 0.8646 (t) cc_final: 0.8218 (m) REVERT: D 77 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6725 (mm-30) REVERT: D 79 TYR cc_start: 0.8813 (m-80) cc_final: 0.8552 (m-80) REVERT: D 177 LEU cc_start: 0.8551 (tp) cc_final: 0.8341 (tp) REVERT: D 209 ARG cc_start: 0.8221 (pmt170) cc_final: 0.5892 (ptm160) REVERT: D 214 TRP cc_start: 0.8061 (p90) cc_final: 0.7788 (p90) REVERT: D 237 ASP cc_start: 0.7597 (t0) cc_final: 0.7373 (t0) REVERT: D 241 VAL cc_start: 0.8034 (t) cc_final: 0.7809 (t) REVERT: D 269 ASP cc_start: 0.7014 (p0) cc_final: 0.6648 (p0) REVERT: D 398 PHE cc_start: 0.8590 (p90) cc_final: 0.8334 (p90) REVERT: D 544 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7637 (t) REVERT: D 558 GLN cc_start: 0.8350 (pt0) cc_final: 0.8095 (pt0) REVERT: D 573 TYR cc_start: 0.7812 (p90) cc_final: 0.7020 (p90) REVERT: D 574 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6864 (mm-30) REVERT: B 60 GLU cc_start: 0.7450 (tp30) cc_final: 0.7102 (tp30) REVERT: B 89 LYS cc_start: 0.8474 (tptt) cc_final: 0.8235 (tptm) REVERT: B 96 MET cc_start: 0.8043 (ptp) cc_final: 0.7687 (ptp) REVERT: B 133 MET cc_start: 0.7338 (mmt) cc_final: 0.6962 (mmt) REVERT: B 151 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8381 (mttm) REVERT: B 167 ASN cc_start: 0.8056 (m-40) cc_final: 0.7585 (m-40) REVERT: B 236 THR cc_start: 0.8005 (m) cc_final: 0.7684 (p) REVERT: B 269 ASP cc_start: 0.7075 (p0) cc_final: 0.6793 (p0) REVERT: B 346 GLU cc_start: 0.7039 (tt0) cc_final: 0.6795 (tt0) REVERT: B 378 TYR cc_start: 0.8263 (m-80) cc_final: 0.7511 (m-80) REVERT: B 394 THR cc_start: 0.8716 (t) cc_final: 0.8505 (p) REVERT: B 396 GLU cc_start: 0.7783 (tt0) cc_final: 0.7265 (tt0) REVERT: B 408 ARG cc_start: 0.7843 (mmt-90) cc_final: 0.7191 (mpt180) REVERT: B 435 PRO cc_start: 0.8642 (Cg_endo) cc_final: 0.8348 (Cg_exo) REVERT: B 473 GLU cc_start: 0.7533 (mm-30) cc_final: 0.6893 (mm-30) REVERT: B 476 THR cc_start: 0.8142 (p) cc_final: 0.7859 (p) REVERT: B 509 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7195 (mm-30) REVERT: B 511 ASP cc_start: 0.7347 (p0) cc_final: 0.7043 (p0) REVERT: B 528 TRP cc_start: 0.8523 (m100) cc_final: 0.7031 (m100) REVERT: B 535 PHE cc_start: 0.8219 (m-80) cc_final: 0.7681 (m-80) REVERT: B 560 ASN cc_start: 0.8610 (t0) cc_final: 0.8005 (t0) REVERT: B 575 LYS cc_start: 0.7975 (mmtm) cc_final: 0.7700 (mmtm) REVERT: I 71 LEU cc_start: 0.8445 (tp) cc_final: 0.8194 (tm) REVERT: I 73 MET cc_start: 0.7140 (ptt) cc_final: 0.6720 (ptt) REVERT: I 87 MET cc_start: 0.8390 (tpt) cc_final: 0.8069 (tpt) REVERT: I 107 THR cc_start: 0.8589 (m) cc_final: 0.8328 (t) REVERT: I 127 GLN cc_start: 0.8522 (tt0) cc_final: 0.8309 (tt0) REVERT: I 151 LYS cc_start: 0.7652 (mmmt) cc_final: 0.7200 (mmmt) REVERT: I 242 GLN cc_start: 0.7276 (mm110) cc_final: 0.7048 (mm110) REVERT: I 283 ARG cc_start: 0.8456 (mmm-85) cc_final: 0.8098 (mmm160) REVERT: I 319 MET cc_start: 0.7741 (mtp) cc_final: 0.7345 (mtp) REVERT: I 572 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8228 (m) REVERT: I 574 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6969 (mm-30) REVERT: E 125 ASP cc_start: 0.7921 (m-30) cc_final: 0.7704 (m-30) REVERT: E 168 ASP cc_start: 0.7264 (t0) cc_final: 0.6638 (t0) REVERT: E 190 MET cc_start: 0.8328 (tpp) cc_final: 0.7884 (ttp) REVERT: E 213 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7872 (tm-30) REVERT: E 240 ASP cc_start: 0.7409 (m-30) cc_final: 0.7025 (m-30) REVERT: E 257 THR cc_start: 0.8430 (p) cc_final: 0.8201 (t) REVERT: E 309 GLN cc_start: 0.7432 (mt0) cc_final: 0.7090 (mt0) REVERT: E 404 GLN cc_start: 0.8005 (pt0) cc_final: 0.7704 (tt0) REVERT: E 411 GLU cc_start: 0.7489 (mp0) cc_final: 0.6926 (mp0) REVERT: E 416 GLN cc_start: 0.8356 (pt0) cc_final: 0.7985 (pt0) REVERT: E 444 TYR cc_start: 0.7824 (p90) cc_final: 0.7619 (p90) REVERT: E 447 ILE cc_start: 0.7992 (pt) cc_final: 0.7654 (mm) REVERT: C 54 LEU cc_start: 0.8567 (mt) cc_final: 0.8322 (mm) REVERT: C 71 LEU cc_start: 0.8503 (tp) cc_final: 0.8267 (tp) REVERT: C 128 LEU cc_start: 0.7913 (tp) cc_final: 0.7669 (tm) REVERT: C 177 LEU cc_start: 0.7835 (tp) cc_final: 0.7439 (tm) REVERT: C 222 HIS cc_start: 0.3149 (OUTLIER) cc_final: 0.2631 (t-170) REVERT: C 247 GLU cc_start: 0.7609 (mp0) cc_final: 0.7265 (mp0) REVERT: C 387 LYS cc_start: 0.8299 (tttt) cc_final: 0.8027 (tttm) REVERT: C 397 ARG cc_start: 0.7737 (mtt180) cc_final: 0.7437 (pmm-80) REVERT: C 464 TYR cc_start: 0.7771 (t80) cc_final: 0.7179 (t80) REVERT: C 511 ASP cc_start: 0.7559 (p0) cc_final: 0.7336 (p0) REVERT: C 522 VAL cc_start: 0.8766 (t) cc_final: 0.8405 (m) REVERT: C 538 LYS cc_start: 0.8218 (tptp) cc_final: 0.7603 (tptp) REVERT: C 559 PHE cc_start: 0.8267 (m-80) cc_final: 0.8024 (m-80) REVERT: G 68 LEU cc_start: 0.8052 (tp) cc_final: 0.7718 (tm) REVERT: G 77 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7052 (tm-30) REVERT: G 83 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8170 (m) REVERT: G 96 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7672 (ptp) REVERT: G 190 MET cc_start: 0.7480 (mmm) cc_final: 0.6776 (mmm) REVERT: G 204 ILE cc_start: 0.8680 (pt) cc_final: 0.8360 (pp) REVERT: G 276 THR cc_start: 0.8259 (p) cc_final: 0.7988 (p) REVERT: G 398 PHE cc_start: 0.8347 (p90) cc_final: 0.7868 (p90) REVERT: G 408 ARG cc_start: 0.8268 (mmt-90) cc_final: 0.7735 (mmt90) REVERT: G 434 ASP cc_start: 0.7454 (m-30) cc_final: 0.7238 (m-30) REVERT: G 439 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7422 (mmtm) REVERT: G 440 THR cc_start: 0.8228 (p) cc_final: 0.7967 (t) REVERT: G 469 ILE cc_start: 0.8634 (mt) cc_final: 0.8434 (mm) REVERT: G 475 ASP cc_start: 0.7748 (t0) cc_final: 0.7520 (t0) REVERT: G 530 LYS cc_start: 0.8465 (ttmt) cc_final: 0.8189 (ttmt) REVERT: G 538 LYS cc_start: 0.8302 (tptp) cc_final: 0.8076 (tptp) REVERT: G 582 LYS cc_start: 0.7884 (mtmt) cc_final: 0.7626 (mtmt) REVERT: F 80 ARG cc_start: 0.5481 (tpt170) cc_final: 0.5228 (tpt170) REVERT: F 81 ARG cc_start: 0.7507 (ttp-170) cc_final: 0.7294 (ttp-170) REVERT: F 126 TRP cc_start: 0.8426 (t-100) cc_final: 0.8103 (t-100) REVERT: F 148 VAL cc_start: 0.8677 (t) cc_final: 0.8311 (m) REVERT: F 177 LEU cc_start: 0.8028 (tt) cc_final: 0.7770 (tp) REVERT: F 214 TRP cc_start: 0.8671 (p90) cc_final: 0.8047 (p90) REVERT: F 216 ARG cc_start: 0.7707 (ttt90) cc_final: 0.7183 (ttt-90) REVERT: F 254 LEU cc_start: 0.8299 (mt) cc_final: 0.8066 (mt) REVERT: F 326 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8277 (t) REVERT: F 346 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7032 (mt-10) REVERT: F 448 PHE cc_start: 0.8467 (t80) cc_final: 0.8242 (t80) REVERT: F 473 GLU cc_start: 0.6740 (tm-30) cc_final: 0.6009 (tm-30) REVERT: F 475 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.6737 (t0) REVERT: F 491 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7510 (mm-40) REVERT: F 497 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: F 528 TRP cc_start: 0.8292 (m100) cc_final: 0.7839 (m100) REVERT: F 530 LYS cc_start: 0.8404 (ttpp) cc_final: 0.8144 (ttpp) outliers start: 141 outliers final: 89 residues processed: 1241 average time/residue: 1.3284 time to fit residues: 1978.5124 Evaluate side-chains 1275 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1174 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 444 TYR Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 415 ILE Chi-restraints excluded: chain I residue 448 PHE Chi-restraints excluded: chain I residue 476 THR Chi-restraints excluded: chain I residue 481 ARG Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 490 CYS Chi-restraints excluded: chain I residue 572 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 442 ILE Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 280 GLN Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 439 LYS Chi-restraints excluded: chain G residue 466 ASN Chi-restraints excluded: chain G residue 518 MET Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 475 ASP Chi-restraints excluded: chain F residue 497 GLN Chi-restraints excluded: chain F residue 536 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 135 optimal weight: 1.9990 chunk 362 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 236 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 chunk 403 optimal weight: 0.5980 chunk 334 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 211 optimal weight: 30.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN D 104 GLN D 231 ASN B 137 HIS ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 ASN I 213 GLN E 280 GLN E 302 ASN E 350 GLN C 549 GLN C 558 GLN G 85 ASN G 95 ASN G 213 GLN G 416 GLN F 47 ASN F 147 ASN F 309 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33944 Z= 0.240 Angle : 0.545 8.942 46423 Z= 0.277 Chirality : 0.043 0.170 5053 Planarity : 0.005 0.079 6105 Dihedral : 4.910 53.970 4509 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.82 % Allowed : 22.58 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % 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: -0.68 (0.13), residues: 3937 helix: 0.55 (0.48), residues: 95 sheet: -0.53 (0.16), residues: 979 loop : -0.44 (0.11), residues: 2863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP I 214 HIS 0.005 0.001 HIS A 70 PHE 0.036 0.001 PHE C 53 TYR 0.024 0.001 TYR B 524 ARG 0.010 0.001 ARG F 382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1302 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1168 time to evaluate : 3.617 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: A 47 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.7987 (t0) REVERT: A 75 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7145 (mm-30) REVERT: A 326 THR cc_start: 0.8462 (p) cc_final: 0.8249 (t) REVERT: A 457 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8194 (mp) REVERT: A 540 ARG cc_start: 0.8465 (ptt90) cc_final: 0.8223 (ptt180) REVERT: A 569 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8140 (tpp) REVERT: A 576 SER cc_start: 0.8624 (t) cc_final: 0.8204 (m) REVERT: D 60 GLU cc_start: 0.7342 (tm-30) cc_final: 0.7091 (tm-30) REVERT: D 77 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6703 (mm-30) REVERT: D 78 ASN cc_start: 0.7917 (m-40) cc_final: 0.7666 (m-40) REVERT: D 79 TYR cc_start: 0.8797 (m-80) cc_final: 0.8528 (m-80) REVERT: D 209 ARG cc_start: 0.8200 (pmt170) cc_final: 0.5837 (ptm160) REVERT: D 214 TRP cc_start: 0.8058 (p90) cc_final: 0.7762 (p90) REVERT: D 237 ASP cc_start: 0.7619 (t0) cc_final: 0.7393 (t0) REVERT: D 241 VAL cc_start: 0.8027 (t) cc_final: 0.7805 (t) REVERT: D 269 ASP cc_start: 0.6940 (p0) cc_final: 0.6600 (p0) REVERT: D 544 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7623 (t) REVERT: D 573 TYR cc_start: 0.7787 (p90) cc_final: 0.6969 (p90) REVERT: D 574 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6874 (mm-30) REVERT: B 60 GLU cc_start: 0.7465 (tp30) cc_final: 0.7062 (tp30) REVERT: B 89 LYS cc_start: 0.8470 (tptt) cc_final: 0.8213 (tptm) REVERT: B 96 MET cc_start: 0.8050 (ptp) cc_final: 0.7702 (ptp) REVERT: B 133 MET cc_start: 0.7318 (mmt) cc_final: 0.6939 (mmt) REVERT: B 236 THR cc_start: 0.7976 (m) cc_final: 0.7666 (p) REVERT: B 269 ASP cc_start: 0.7091 (p0) cc_final: 0.6822 (p0) REVERT: B 378 TYR cc_start: 0.8253 (m-80) cc_final: 0.7503 (m-80) REVERT: B 394 THR cc_start: 0.8666 (t) cc_final: 0.8463 (p) REVERT: B 396 GLU cc_start: 0.7736 (tt0) cc_final: 0.7215 (tt0) REVERT: B 408 ARG cc_start: 0.7822 (mmt-90) cc_final: 0.7183 (mpt180) REVERT: B 435 PRO cc_start: 0.8597 (Cg_endo) cc_final: 0.8288 (Cg_exo) REVERT: B 473 GLU cc_start: 0.7573 (mm-30) cc_final: 0.6933 (mm-30) REVERT: B 476 THR cc_start: 0.8157 (p) cc_final: 0.7891 (p) REVERT: B 509 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7118 (mm-30) REVERT: B 511 ASP cc_start: 0.7316 (p0) cc_final: 0.7019 (p0) REVERT: B 535 PHE cc_start: 0.8136 (m-80) cc_final: 0.7673 (m-10) REVERT: B 551 MET cc_start: 0.6937 (ttt) cc_final: 0.6725 (ttt) REVERT: B 560 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8003 (t0) REVERT: I 71 LEU cc_start: 0.8458 (tp) cc_final: 0.8213 (tm) REVERT: I 73 MET cc_start: 0.7146 (ptt) cc_final: 0.6706 (ptt) REVERT: I 87 MET cc_start: 0.8325 (tpt) cc_final: 0.8053 (tpt) REVERT: I 107 THR cc_start: 0.8556 (m) cc_final: 0.8307 (t) REVERT: I 151 LYS cc_start: 0.7601 (mmmt) cc_final: 0.7155 (mmmt) REVERT: I 198 TYR cc_start: 0.8527 (m-80) cc_final: 0.8319 (m-80) REVERT: I 213 GLN cc_start: 0.7847 (tp-100) cc_final: 0.7589 (tp-100) REVERT: I 242 GLN cc_start: 0.7358 (mm110) cc_final: 0.7095 (mm110) REVERT: I 283 ARG cc_start: 0.8418 (mmm-85) cc_final: 0.8068 (mmm160) REVERT: I 314 ARG cc_start: 0.8128 (ttm-80) cc_final: 0.7771 (ttm110) REVERT: I 319 MET cc_start: 0.7653 (mtp) cc_final: 0.7280 (mtp) REVERT: I 324 TYR cc_start: 0.8278 (m-80) cc_final: 0.7971 (m-10) REVERT: I 420 PHE cc_start: 0.7992 (t80) cc_final: 0.7568 (t80) REVERT: I 572 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8216 (m) REVERT: I 574 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6972 (mm-30) REVERT: E 125 ASP cc_start: 0.7843 (m-30) cc_final: 0.7599 (m-30) REVERT: E 164 VAL cc_start: 0.8754 (m) cc_final: 0.8440 (p) REVERT: E 168 ASP cc_start: 0.7278 (t0) cc_final: 0.6694 (t0) REVERT: E 190 MET cc_start: 0.8295 (tpp) cc_final: 0.7810 (ttp) REVERT: E 240 ASP cc_start: 0.7349 (m-30) cc_final: 0.6986 (m-30) REVERT: E 257 THR cc_start: 0.8426 (p) cc_final: 0.8205 (t) REVERT: E 302 ASN cc_start: 0.7457 (t160) cc_final: 0.7208 (t0) REVERT: E 309 GLN cc_start: 0.7399 (mt0) cc_final: 0.7060 (mt0) REVERT: E 346 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7183 (mt-10) REVERT: E 411 GLU cc_start: 0.7483 (mp0) cc_final: 0.6932 (mp0) REVERT: E 416 GLN cc_start: 0.8224 (pt0) cc_final: 0.7863 (pt0) REVERT: E 419 ASN cc_start: 0.8601 (m-40) cc_final: 0.8140 (p0) REVERT: E 434 ASP cc_start: 0.7622 (m-30) cc_final: 0.7327 (m-30) REVERT: E 447 ILE cc_start: 0.8007 (pt) cc_final: 0.7672 (mm) REVERT: E 448 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7751 (t80) REVERT: E 479 LYS cc_start: 0.8566 (mttp) cc_final: 0.8284 (mttp) REVERT: C 54 LEU cc_start: 0.8520 (mt) cc_final: 0.8272 (mm) REVERT: C 71 LEU cc_start: 0.8476 (tp) cc_final: 0.8247 (tp) REVERT: C 128 LEU cc_start: 0.7916 (tp) cc_final: 0.7657 (tm) REVERT: C 177 LEU cc_start: 0.7841 (tp) cc_final: 0.7465 (tm) REVERT: C 222 HIS cc_start: 0.3054 (OUTLIER) cc_final: 0.2647 (t-170) REVERT: C 247 GLU cc_start: 0.7619 (mp0) cc_final: 0.7224 (mp0) REVERT: C 387 LYS cc_start: 0.8311 (tttt) cc_final: 0.8026 (tttm) REVERT: C 397 ARG cc_start: 0.7733 (mtt180) cc_final: 0.7429 (pmm-80) REVERT: C 464 TYR cc_start: 0.7699 (t80) cc_final: 0.7062 (t80) REVERT: C 511 ASP cc_start: 0.7520 (p0) cc_final: 0.7280 (p0) REVERT: C 522 VAL cc_start: 0.8756 (t) cc_final: 0.8383 (m) REVERT: C 526 ASP cc_start: 0.7640 (m-30) cc_final: 0.7388 (m-30) REVERT: C 538 LYS cc_start: 0.8225 (tptp) cc_final: 0.7602 (tptp) REVERT: G 68 LEU cc_start: 0.8004 (tp) cc_final: 0.7678 (tm) REVERT: G 77 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7064 (tm-30) REVERT: G 83 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8146 (m) REVERT: G 190 MET cc_start: 0.7458 (mmm) cc_final: 0.6754 (mmm) REVERT: G 204 ILE cc_start: 0.8681 (pt) cc_final: 0.8343 (pp) REVERT: G 213 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: G 276 THR cc_start: 0.8243 (p) cc_final: 0.7962 (p) REVERT: G 285 LEU cc_start: 0.8410 (mm) cc_final: 0.8193 (mm) REVERT: G 318 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7921 (mt0) REVERT: G 408 ARG cc_start: 0.8240 (mmt-90) cc_final: 0.7703 (mmt90) REVERT: G 434 ASP cc_start: 0.7439 (m-30) cc_final: 0.7208 (m-30) REVERT: G 439 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7586 (mmtm) REVERT: G 469 ILE cc_start: 0.8629 (mt) cc_final: 0.8413 (mm) REVERT: G 475 ASP cc_start: 0.7721 (t0) cc_final: 0.7505 (t0) REVERT: G 530 LYS cc_start: 0.8503 (ttmt) cc_final: 0.8243 (ttmt) REVERT: F 81 ARG cc_start: 0.7513 (ttp-170) cc_final: 0.7142 (pmm150) REVERT: F 109 TRP cc_start: 0.8395 (m100) cc_final: 0.8142 (m100) REVERT: F 126 TRP cc_start: 0.8419 (t-100) cc_final: 0.8120 (t-100) REVERT: F 148 VAL cc_start: 0.8678 (t) cc_final: 0.8317 (m) REVERT: F 177 LEU cc_start: 0.7941 (tt) cc_final: 0.7723 (tp) REVERT: F 214 TRP cc_start: 0.8641 (p90) cc_final: 0.8030 (p90) REVERT: F 216 ARG cc_start: 0.7691 (ttt90) cc_final: 0.7087 (ttt-90) REVERT: F 254 LEU cc_start: 0.8302 (mt) cc_final: 0.8065 (mt) REVERT: F 326 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8247 (t) REVERT: F 346 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6992 (mt-10) REVERT: F 475 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.6697 (t0) REVERT: F 479 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7602 (tppt) REVERT: F 491 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7380 (mm-40) REVERT: F 497 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8059 (mt0) REVERT: F 528 TRP cc_start: 0.8289 (m100) cc_final: 0.7806 (m100) REVERT: F 530 LYS cc_start: 0.8413 (ttpp) cc_final: 0.8099 (ttpp) outliers start: 134 outliers final: 86 residues processed: 1215 average time/residue: 1.3676 time to fit residues: 2011.4003 Evaluate side-chains 1266 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1164 time to evaluate : 3.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 401 ILE Chi-restraints excluded: chain I residue 413 ASP Chi-restraints excluded: chain I residue 415 ILE Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 444 TYR Chi-restraints excluded: chain I residue 448 PHE Chi-restraints excluded: chain I residue 458 ASN Chi-restraints excluded: chain I residue 476 THR Chi-restraints excluded: chain I residue 481 ARG Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 490 CYS Chi-restraints excluded: chain I residue 564 SER Chi-restraints excluded: chain I residue 572 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 448 PHE Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 213 GLN Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 439 LYS Chi-restraints excluded: chain G residue 458 ASN Chi-restraints excluded: chain G residue 466 ASN Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 475 ASP Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 497 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 388 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 chunk 294 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 339 optimal weight: 10.0000 chunk 225 optimal weight: 4.9990 chunk 401 optimal weight: 0.9990 chunk 251 optimal weight: 7.9990 chunk 245 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN D 104 GLN D 127 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 ASN D 577 GLN B 137 HIS B 242 GLN ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 HIS ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN E 350 GLN E 404 GLN C 549 GLN G 85 ASN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN G 416 GLN F 47 ASN F 147 ASN F 309 GLN F 458 ASN F 497 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 33944 Z= 0.444 Angle : 0.612 8.814 46423 Z= 0.313 Chirality : 0.046 0.169 5053 Planarity : 0.005 0.096 6105 Dihedral : 5.157 53.542 4509 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.19 % Allowed : 22.98 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % 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: -0.83 (0.13), residues: 3937 helix: 0.55 (0.50), residues: 95 sheet: -0.67 (0.16), residues: 1004 loop : -0.52 (0.11), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 214 HIS 0.005 0.001 HIS F 277 PHE 0.037 0.002 PHE C 53 TYR 0.032 0.002 TYR I 233 ARG 0.011 0.001 ARG F 382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1336 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1189 time to evaluate : 4.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.8004 (t0) REVERT: A 75 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7155 (mm-30) REVERT: A 133 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7646 (mmt) REVERT: A 149 VAL cc_start: 0.8662 (t) cc_final: 0.8289 (p) REVERT: A 326 THR cc_start: 0.8488 (p) cc_final: 0.8261 (t) REVERT: A 457 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8260 (mp) REVERT: A 510 TYR cc_start: 0.8667 (t80) cc_final: 0.7935 (t80) REVERT: A 574 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7121 (mm-30) REVERT: D 60 GLU cc_start: 0.7371 (tm-30) cc_final: 0.7072 (tm-30) REVERT: D 79 TYR cc_start: 0.8830 (m-80) cc_final: 0.8523 (m-80) REVERT: D 106 VAL cc_start: 0.8255 (t) cc_final: 0.7737 (m) REVERT: D 209 ARG cc_start: 0.8271 (pmt170) cc_final: 0.5897 (ptm160) REVERT: D 212 PHE cc_start: 0.8011 (t80) cc_final: 0.7765 (t80) REVERT: D 214 TRP cc_start: 0.8164 (p90) cc_final: 0.7916 (p90) REVERT: D 237 ASP cc_start: 0.7601 (t0) cc_final: 0.7381 (t0) REVERT: D 241 VAL cc_start: 0.8060 (t) cc_final: 0.7843 (t) REVERT: D 269 ASP cc_start: 0.6988 (p0) cc_final: 0.6660 (p0) REVERT: D 398 PHE cc_start: 0.8606 (p90) cc_final: 0.7908 (p90) REVERT: D 510 TYR cc_start: 0.8611 (t80) cc_final: 0.8315 (t80) REVERT: D 544 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7665 (t) REVERT: D 573 TYR cc_start: 0.7811 (p90) cc_final: 0.7004 (p90) REVERT: D 574 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6854 (mm-30) REVERT: B 60 GLU cc_start: 0.7466 (tp30) cc_final: 0.7027 (tp30) REVERT: B 89 LYS cc_start: 0.8440 (tptt) cc_final: 0.8211 (tptm) REVERT: B 96 MET cc_start: 0.8091 (ptp) cc_final: 0.7714 (ptp) REVERT: B 133 MET cc_start: 0.7338 (mmt) cc_final: 0.6958 (mmt) REVERT: B 236 THR cc_start: 0.8007 (m) cc_final: 0.7704 (p) REVERT: B 269 ASP cc_start: 0.7113 (p0) cc_final: 0.6862 (p0) REVERT: B 378 TYR cc_start: 0.8285 (m-80) cc_final: 0.7516 (m-80) REVERT: B 387 LYS cc_start: 0.8451 (ttmm) cc_final: 0.8204 (tttm) REVERT: B 396 GLU cc_start: 0.7769 (tt0) cc_final: 0.7274 (tt0) REVERT: B 408 ARG cc_start: 0.7827 (mmt-90) cc_final: 0.7170 (mpt180) REVERT: B 435 PRO cc_start: 0.8664 (Cg_endo) cc_final: 0.8406 (Cg_exo) REVERT: B 473 GLU cc_start: 0.7590 (mm-30) cc_final: 0.6958 (mm-30) REVERT: B 476 THR cc_start: 0.8165 (p) cc_final: 0.7893 (p) REVERT: B 509 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7183 (mm-30) REVERT: B 511 ASP cc_start: 0.7262 (p0) cc_final: 0.6912 (p0) REVERT: B 518 MET cc_start: 0.8385 (ptt) cc_final: 0.8095 (ptt) REVERT: B 528 TRP cc_start: 0.8543 (m100) cc_final: 0.8209 (m100) REVERT: B 535 PHE cc_start: 0.8299 (m-80) cc_final: 0.7534 (m-10) REVERT: B 560 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.7986 (t0) REVERT: B 575 LYS cc_start: 0.7966 (mmtm) cc_final: 0.7741 (mmtm) REVERT: I 71 LEU cc_start: 0.8463 (tp) cc_final: 0.8212 (tm) REVERT: I 73 MET cc_start: 0.7126 (ptt) cc_final: 0.6710 (ptt) REVERT: I 87 MET cc_start: 0.8302 (tpt) cc_final: 0.8083 (tpt) REVERT: I 107 THR cc_start: 0.8631 (m) cc_final: 0.8396 (t) REVERT: I 127 GLN cc_start: 0.8526 (tt0) cc_final: 0.8087 (tt0) REVERT: I 198 TYR cc_start: 0.8573 (m-80) cc_final: 0.8268 (m-80) REVERT: I 242 GLN cc_start: 0.7345 (mm110) cc_final: 0.7065 (mm110) REVERT: I 283 ARG cc_start: 0.8489 (mmm-85) cc_final: 0.8147 (mmm160) REVERT: I 314 ARG cc_start: 0.8129 (ttm-80) cc_final: 0.7851 (ttm110) REVERT: I 319 MET cc_start: 0.7759 (mtp) cc_final: 0.7301 (mtp) REVERT: I 324 TYR cc_start: 0.8348 (m-80) cc_final: 0.8016 (m-10) REVERT: I 330 ILE cc_start: 0.8537 (tt) cc_final: 0.8238 (tp) REVERT: I 415 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8183 (mm) REVERT: I 420 PHE cc_start: 0.8040 (t80) cc_final: 0.7575 (t80) REVERT: I 472 LYS cc_start: 0.8238 (tptm) cc_final: 0.7947 (tppt) REVERT: I 485 ASN cc_start: 0.7582 (p0) cc_final: 0.7315 (p0) REVERT: I 548 ILE cc_start: 0.7934 (pt) cc_final: 0.7638 (pp) REVERT: I 550 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7636 (mt0) REVERT: I 572 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8233 (m) REVERT: I 574 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6966 (mm-30) REVERT: E 168 ASP cc_start: 0.7313 (t0) cc_final: 0.6692 (t0) REVERT: E 213 GLN cc_start: 0.8382 (tm-30) cc_final: 0.8007 (tm-30) REVERT: E 240 ASP cc_start: 0.7277 (m-30) cc_final: 0.6921 (m-30) REVERT: E 257 THR cc_start: 0.8436 (p) cc_final: 0.8199 (t) REVERT: E 269 ASP cc_start: 0.7208 (p0) cc_final: 0.6942 (p0) REVERT: E 309 GLN cc_start: 0.7448 (mt0) cc_final: 0.6734 (mt0) REVERT: E 312 LYS cc_start: 0.8532 (mttt) cc_final: 0.7500 (mttt) REVERT: E 346 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7167 (mt-10) REVERT: E 411 GLU cc_start: 0.7494 (mp0) cc_final: 0.6927 (mp0) REVERT: E 416 GLN cc_start: 0.8289 (pt0) cc_final: 0.7934 (pt0) REVERT: E 447 ILE cc_start: 0.7977 (pt) cc_final: 0.7663 (mm) REVERT: E 448 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7712 (t80) REVERT: E 479 LYS cc_start: 0.8588 (mttp) cc_final: 0.8315 (mttp) REVERT: C 54 LEU cc_start: 0.8557 (mt) cc_final: 0.8301 (mm) REVERT: C 71 LEU cc_start: 0.8490 (tp) cc_final: 0.8265 (tp) REVERT: C 128 LEU cc_start: 0.7950 (tp) cc_final: 0.7703 (tm) REVERT: C 144 GLU cc_start: 0.7369 (pt0) cc_final: 0.7037 (pt0) REVERT: C 177 LEU cc_start: 0.7840 (tp) cc_final: 0.7446 (tm) REVERT: C 222 HIS cc_start: 0.2996 (OUTLIER) cc_final: 0.2614 (t-170) REVERT: C 237 ASP cc_start: 0.7339 (t0) cc_final: 0.6974 (t0) REVERT: C 247 GLU cc_start: 0.7618 (mp0) cc_final: 0.7252 (mp0) REVERT: C 387 LYS cc_start: 0.8347 (tttt) cc_final: 0.8014 (tttm) REVERT: C 397 ARG cc_start: 0.7743 (mtt180) cc_final: 0.7434 (pmm-80) REVERT: C 464 TYR cc_start: 0.7808 (t80) cc_final: 0.7202 (t80) REVERT: C 509 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6618 (mm-30) REVERT: C 511 ASP cc_start: 0.7521 (p0) cc_final: 0.7257 (p0) REVERT: C 522 VAL cc_start: 0.8778 (t) cc_final: 0.8419 (m) REVERT: C 526 ASP cc_start: 0.7692 (m-30) cc_final: 0.7460 (m-30) REVERT: C 538 LYS cc_start: 0.8225 (tptp) cc_final: 0.7642 (tptp) REVERT: C 560 ASN cc_start: 0.8400 (m-40) cc_final: 0.7759 (t0) REVERT: C 572 VAL cc_start: 0.8264 (m) cc_final: 0.7732 (m) REVERT: G 68 LEU cc_start: 0.8140 (tp) cc_final: 0.7702 (tm) REVERT: G 77 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7070 (tm-30) REVERT: G 83 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8192 (m) REVERT: G 95 ASN cc_start: 0.8309 (m-40) cc_final: 0.7869 (m110) REVERT: G 121 PHE cc_start: 0.8141 (m-80) cc_final: 0.7862 (m-80) REVERT: G 138 LEU cc_start: 0.8820 (tp) cc_final: 0.8584 (tp) REVERT: G 146 PHE cc_start: 0.7765 (p90) cc_final: 0.7444 (p90) REVERT: G 190 MET cc_start: 0.7460 (mmm) cc_final: 0.6783 (mmm) REVERT: G 204 ILE cc_start: 0.8696 (pt) cc_final: 0.8363 (pp) REVERT: G 213 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: G 276 THR cc_start: 0.8260 (p) cc_final: 0.7998 (p) REVERT: G 318 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8032 (mt0) REVERT: G 408 ARG cc_start: 0.8237 (mmt-90) cc_final: 0.7811 (mmt90) REVERT: G 434 ASP cc_start: 0.7424 (m-30) cc_final: 0.7191 (m-30) REVERT: G 439 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7373 (mmtm) REVERT: G 440 THR cc_start: 0.8243 (p) cc_final: 0.7983 (t) REVERT: G 469 ILE cc_start: 0.8653 (mt) cc_final: 0.8441 (mm) REVERT: G 475 ASP cc_start: 0.7741 (t0) cc_final: 0.7498 (t0) REVERT: G 526 ASP cc_start: 0.7180 (t0) cc_final: 0.6935 (t0) REVERT: G 530 LYS cc_start: 0.8414 (ttmt) cc_final: 0.8141 (ttmt) REVERT: G 550 GLN cc_start: 0.8168 (mm110) cc_final: 0.7764 (mm110) REVERT: F 81 ARG cc_start: 0.7583 (ttp-170) cc_final: 0.7082 (pmt170) REVERT: F 109 TRP cc_start: 0.8415 (m100) cc_final: 0.8139 (m100) REVERT: F 126 TRP cc_start: 0.8428 (t-100) cc_final: 0.8117 (t-100) REVERT: F 133 MET cc_start: 0.8089 (mmt) cc_final: 0.7717 (mpp) REVERT: F 148 VAL cc_start: 0.8669 (t) cc_final: 0.8320 (m) REVERT: F 214 TRP cc_start: 0.8674 (p90) cc_final: 0.8092 (p90) REVERT: F 216 ARG cc_start: 0.7774 (ttt90) cc_final: 0.7184 (ttt-90) REVERT: F 254 LEU cc_start: 0.8296 (mt) cc_final: 0.8061 (mt) REVERT: F 326 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8336 (t) REVERT: F 382 ARG cc_start: 0.7395 (mtt90) cc_final: 0.7187 (mtt-85) REVERT: F 448 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8228 (t80) REVERT: F 475 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6711 (t0) REVERT: F 479 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7694 (tptm) REVERT: F 491 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7872 (tp-100) REVERT: F 497 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8031 (mt0) REVERT: F 522 VAL cc_start: 0.8252 (p) cc_final: 0.8029 (m) REVERT: F 528 TRP cc_start: 0.8331 (m100) cc_final: 0.7869 (m100) outliers start: 147 outliers final: 94 residues processed: 1234 average time/residue: 1.3203 time to fit residues: 1958.6068 Evaluate side-chains 1301 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1188 time to evaluate : 3.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 444 TYR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 209 ARG Chi-restraints excluded: chain I residue 415 ILE Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 444 TYR Chi-restraints excluded: chain I residue 448 PHE Chi-restraints excluded: chain I residue 458 ASN Chi-restraints excluded: chain I residue 476 THR Chi-restraints excluded: chain I residue 481 ARG Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 490 CYS Chi-restraints excluded: chain I residue 550 GLN Chi-restraints excluded: chain I residue 556 ASP Chi-restraints excluded: chain I residue 564 SER Chi-restraints excluded: chain I residue 572 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 442 ILE Chi-restraints excluded: chain E residue 448 PHE Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 582 LYS Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 213 GLN Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 280 GLN Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 439 LYS Chi-restraints excluded: chain G residue 458 ASN Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 475 ASP Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 497 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 248 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 chunk 240 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 78 optimal weight: 30.0000 chunk 77 optimal weight: 9.9990 chunk 255 optimal weight: 2.9990 chunk 273 optimal weight: 10.0000 chunk 198 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 315 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN D 104 GLN D 127 GLN D 383 GLN D 558 GLN D 577 GLN B 137 HIS ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN I 213 GLN E 222 HIS E 280 GLN E 302 ASN E 350 GLN E 404 GLN C 127 GLN C 549 GLN G 85 ASN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN G 253 HIS G 416 GLN F 47 ASN F 147 ASN F 242 GLN F 309 GLN ** F 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 33944 Z= 0.287 Angle : 0.574 10.643 46423 Z= 0.291 Chirality : 0.044 0.197 5053 Planarity : 0.005 0.081 6105 Dihedral : 4.965 54.281 4509 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.91 % Allowed : 23.72 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % 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: -0.76 (0.13), residues: 3937 helix: 0.52 (0.49), residues: 95 sheet: -0.61 (0.16), residues: 993 loop : -0.48 (0.11), residues: 2849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 214 HIS 0.008 0.001 HIS E 222 PHE 0.034 0.002 PHE C 53 TYR 0.028 0.002 TYR B 524 ARG 0.010 0.001 ARG F 382 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1318 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1181 time to evaluate : 3.700 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: A 47 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.7993 (t0) REVERT: A 75 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7131 (mm-30) REVERT: A 101 ILE cc_start: 0.8661 (mm) cc_final: 0.8340 (tp) REVERT: A 344 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8566 (p) REVERT: A 457 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8236 (mp) REVERT: A 510 TYR cc_start: 0.8640 (t80) cc_final: 0.7932 (t80) REVERT: A 576 SER cc_start: 0.8647 (t) cc_final: 0.8210 (m) REVERT: D 60 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7017 (tm-30) REVERT: D 78 ASN cc_start: 0.7848 (m-40) cc_final: 0.7618 (m-40) REVERT: D 79 TYR cc_start: 0.8824 (m-80) cc_final: 0.8505 (m-80) REVERT: D 209 ARG cc_start: 0.8227 (pmt170) cc_final: 0.5814 (ptm160) REVERT: D 212 PHE cc_start: 0.7975 (t80) cc_final: 0.7734 (t80) REVERT: D 214 TRP cc_start: 0.8158 (p90) cc_final: 0.7898 (p90) REVERT: D 237 ASP cc_start: 0.7584 (t0) cc_final: 0.7352 (t0) REVERT: D 241 VAL cc_start: 0.8050 (t) cc_final: 0.7825 (t) REVERT: D 269 ASP cc_start: 0.6927 (p0) cc_final: 0.6598 (p0) REVERT: D 383 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7750 (mt0) REVERT: D 398 PHE cc_start: 0.8601 (p90) cc_final: 0.7934 (p90) REVERT: D 544 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7646 (t) REVERT: D 573 TYR cc_start: 0.7804 (p90) cc_final: 0.6994 (p90) REVERT: D 574 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6848 (mm-30) REVERT: B 42 THR cc_start: 0.8063 (t) cc_final: 0.7860 (t) REVERT: B 60 GLU cc_start: 0.7481 (tp30) cc_final: 0.6989 (tp30) REVERT: B 89 LYS cc_start: 0.8440 (tptt) cc_final: 0.8218 (tptm) REVERT: B 96 MET cc_start: 0.8091 (ptp) cc_final: 0.7701 (ptp) REVERT: B 133 MET cc_start: 0.7317 (mmt) cc_final: 0.6942 (mmt) REVERT: B 236 THR cc_start: 0.7987 (m) cc_final: 0.7668 (p) REVERT: B 269 ASP cc_start: 0.7109 (p0) cc_final: 0.6840 (p0) REVERT: B 378 TYR cc_start: 0.8265 (m-80) cc_final: 0.7494 (m-80) REVERT: B 387 LYS cc_start: 0.8409 (tttm) cc_final: 0.8174 (tttm) REVERT: B 396 GLU cc_start: 0.7791 (tt0) cc_final: 0.7272 (tt0) REVERT: B 408 ARG cc_start: 0.7864 (mmt-90) cc_final: 0.7253 (mpt180) REVERT: B 435 PRO cc_start: 0.8666 (Cg_endo) cc_final: 0.8403 (Cg_exo) REVERT: B 476 THR cc_start: 0.8181 (p) cc_final: 0.7912 (p) REVERT: B 509 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7133 (mm-30) REVERT: B 511 ASP cc_start: 0.7262 (p0) cc_final: 0.6909 (p0) REVERT: B 528 TRP cc_start: 0.8520 (m100) cc_final: 0.8233 (m100) REVERT: B 535 PHE cc_start: 0.8203 (m-80) cc_final: 0.7545 (m-10) REVERT: B 560 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8002 (t0) REVERT: B 575 LYS cc_start: 0.7962 (mmtm) cc_final: 0.7754 (mmtm) REVERT: I 71 LEU cc_start: 0.8458 (tp) cc_final: 0.8194 (tm) REVERT: I 73 MET cc_start: 0.7096 (ptt) cc_final: 0.6701 (ptt) REVERT: I 96 MET cc_start: 0.5228 (ttp) cc_final: 0.4335 (tmm) REVERT: I 107 THR cc_start: 0.8622 (m) cc_final: 0.8385 (t) REVERT: I 242 GLN cc_start: 0.7365 (mm110) cc_final: 0.7088 (mm110) REVERT: I 283 ARG cc_start: 0.8506 (mmm-85) cc_final: 0.8152 (mmm160) REVERT: I 314 ARG cc_start: 0.8118 (ttm-80) cc_final: 0.7783 (ttm110) REVERT: I 319 MET cc_start: 0.7673 (mtp) cc_final: 0.7258 (mtp) REVERT: I 323 ASN cc_start: 0.7893 (m-40) cc_final: 0.7301 (m-40) REVERT: I 330 ILE cc_start: 0.8542 (tt) cc_final: 0.8240 (tp) REVERT: I 415 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8256 (mm) REVERT: I 420 PHE cc_start: 0.8008 (t80) cc_final: 0.7524 (t80) REVERT: I 471 ASP cc_start: 0.6913 (t0) cc_final: 0.6689 (t0) REVERT: I 485 ASN cc_start: 0.7592 (p0) cc_final: 0.7354 (p0) REVERT: I 536 LYS cc_start: 0.8127 (ttpp) cc_final: 0.7827 (mtpp) REVERT: I 548 ILE cc_start: 0.7914 (pt) cc_final: 0.7600 (pp) REVERT: I 572 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8234 (m) REVERT: I 574 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6970 (mm-30) REVERT: E 164 VAL cc_start: 0.8742 (m) cc_final: 0.8420 (p) REVERT: E 168 ASP cc_start: 0.7294 (t0) cc_final: 0.6682 (t0) REVERT: E 190 MET cc_start: 0.8314 (tpp) cc_final: 0.7824 (ttp) REVERT: E 240 ASP cc_start: 0.7320 (m-30) cc_final: 0.6987 (m-30) REVERT: E 257 THR cc_start: 0.8429 (p) cc_final: 0.8188 (t) REVERT: E 269 ASP cc_start: 0.7162 (p0) cc_final: 0.6893 (p0) REVERT: E 302 ASN cc_start: 0.7454 (t160) cc_final: 0.7223 (t0) REVERT: E 309 GLN cc_start: 0.7416 (mt0) cc_final: 0.6682 (mt0) REVERT: E 312 LYS cc_start: 0.8526 (mttt) cc_final: 0.7472 (mttt) REVERT: E 346 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7145 (mt-10) REVERT: E 350 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7165 (mp-120) REVERT: E 411 GLU cc_start: 0.7487 (mp0) cc_final: 0.6908 (mp0) REVERT: E 416 GLN cc_start: 0.8193 (pt0) cc_final: 0.7828 (pt0) REVERT: E 434 ASP cc_start: 0.7626 (m-30) cc_final: 0.7332 (m-30) REVERT: E 447 ILE cc_start: 0.7987 (pt) cc_final: 0.7656 (mm) REVERT: E 448 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7676 (t80) REVERT: C 54 LEU cc_start: 0.8524 (mt) cc_final: 0.8267 (mm) REVERT: C 71 LEU cc_start: 0.8476 (tp) cc_final: 0.8258 (tp) REVERT: C 128 LEU cc_start: 0.7924 (tp) cc_final: 0.7711 (tm) REVERT: C 144 GLU cc_start: 0.7326 (pt0) cc_final: 0.6998 (pt0) REVERT: C 222 HIS cc_start: 0.2839 (OUTLIER) cc_final: 0.2603 (t-170) REVERT: C 247 GLU cc_start: 0.7627 (mp0) cc_final: 0.7260 (mp0) REVERT: C 387 LYS cc_start: 0.8338 (tttt) cc_final: 0.7998 (tttm) REVERT: C 397 ARG cc_start: 0.7737 (mtt180) cc_final: 0.7437 (pmm-80) REVERT: C 464 TYR cc_start: 0.7739 (t80) cc_final: 0.7171 (t80) REVERT: C 509 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6588 (mm-30) REVERT: C 511 ASP cc_start: 0.7481 (p0) cc_final: 0.7217 (p0) REVERT: C 522 VAL cc_start: 0.8762 (t) cc_final: 0.8392 (m) REVERT: C 526 ASP cc_start: 0.7645 (m-30) cc_final: 0.7395 (m-30) REVERT: C 538 LYS cc_start: 0.8216 (tptp) cc_final: 0.7622 (tptp) REVERT: C 560 ASN cc_start: 0.8434 (m-40) cc_final: 0.7787 (t0) REVERT: C 572 VAL cc_start: 0.8276 (m) cc_final: 0.7680 (m) REVERT: G 68 LEU cc_start: 0.8138 (tp) cc_final: 0.7665 (tm) REVERT: G 77 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7074 (tm-30) REVERT: G 95 ASN cc_start: 0.8278 (m-40) cc_final: 0.7901 (m110) REVERT: G 121 PHE cc_start: 0.8150 (m-80) cc_final: 0.7861 (m-80) REVERT: G 138 LEU cc_start: 0.8784 (tp) cc_final: 0.8535 (tp) REVERT: G 190 MET cc_start: 0.7432 (mmm) cc_final: 0.6772 (mmm) REVERT: G 194 THR cc_start: 0.8370 (p) cc_final: 0.8051 (t) REVERT: G 204 ILE cc_start: 0.8694 (pt) cc_final: 0.8351 (pp) REVERT: G 213 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: G 276 THR cc_start: 0.8238 (p) cc_final: 0.7970 (p) REVERT: G 310 GLN cc_start: 0.7967 (mt0) cc_final: 0.7621 (mt0) REVERT: G 313 ARG cc_start: 0.8329 (mtt180) cc_final: 0.7967 (mtt180) REVERT: G 318 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8039 (mt0) REVERT: G 408 ARG cc_start: 0.8184 (mmt-90) cc_final: 0.7853 (mmt90) REVERT: G 434 ASP cc_start: 0.7428 (m-30) cc_final: 0.7200 (m-30) REVERT: G 439 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7380 (mmtm) REVERT: G 440 THR cc_start: 0.8210 (p) cc_final: 0.7938 (t) REVERT: G 469 ILE cc_start: 0.8632 (mt) cc_final: 0.8418 (mm) REVERT: G 475 ASP cc_start: 0.7753 (t0) cc_final: 0.7519 (t0) REVERT: G 526 ASP cc_start: 0.7256 (t0) cc_final: 0.6968 (t0) REVERT: G 530 LYS cc_start: 0.8519 (ttmt) cc_final: 0.8305 (ttmt) REVERT: G 578 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8246 (mm) REVERT: F 73 MET cc_start: 0.7948 (ptm) cc_final: 0.7135 (ptm) REVERT: F 81 ARG cc_start: 0.7531 (ttp-170) cc_final: 0.7263 (pmm150) REVERT: F 109 TRP cc_start: 0.8372 (m100) cc_final: 0.8110 (m100) REVERT: F 126 TRP cc_start: 0.8411 (t-100) cc_final: 0.8096 (t-100) REVERT: F 133 MET cc_start: 0.8040 (mmt) cc_final: 0.7676 (mpp) REVERT: F 148 VAL cc_start: 0.8684 (t) cc_final: 0.8331 (m) REVERT: F 214 TRP cc_start: 0.8676 (p90) cc_final: 0.8080 (p90) REVERT: F 216 ARG cc_start: 0.7730 (ttt90) cc_final: 0.7112 (ttt-90) REVERT: F 254 LEU cc_start: 0.8294 (mt) cc_final: 0.8069 (mt) REVERT: F 326 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8261 (t) REVERT: F 382 ARG cc_start: 0.7396 (mtt90) cc_final: 0.7153 (mtt-85) REVERT: F 448 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8188 (t80) REVERT: F 457 LEU cc_start: 0.8371 (mt) cc_final: 0.8143 (mt) REVERT: F 473 GLU cc_start: 0.6781 (tm-30) cc_final: 0.6133 (tm-30) REVERT: F 475 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.6684 (t0) REVERT: F 522 VAL cc_start: 0.8249 (p) cc_final: 0.8047 (m) outliers start: 137 outliers final: 90 residues processed: 1229 average time/residue: 1.3295 time to fit residues: 1966.7022 Evaluate side-chains 1286 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1178 time to evaluate : 3.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 383 GLN Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 413 ASP Chi-restraints excluded: chain I residue 415 ILE Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 444 TYR Chi-restraints excluded: chain I residue 448 PHE Chi-restraints excluded: chain I residue 476 THR Chi-restraints excluded: chain I residue 481 ARG Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 490 CYS Chi-restraints excluded: chain I residue 564 SER Chi-restraints excluded: chain I residue 572 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 448 PHE Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 213 GLN Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 439 LYS Chi-restraints excluded: chain G residue 444 TYR Chi-restraints excluded: chain G residue 458 ASN Chi-restraints excluded: chain G residue 578 LEU Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 475 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 365 optimal weight: 6.9990 chunk 385 optimal weight: 8.9990 chunk 351 optimal weight: 6.9990 chunk 374 optimal weight: 3.9990 chunk 384 optimal weight: 7.9990 chunk 225 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 294 optimal weight: 0.0170 chunk 114 optimal weight: 9.9990 chunk 338 optimal weight: 8.9990 chunk 354 optimal weight: 1.9990 overall best weight: 2.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN D 104 GLN D 127 GLN D 231 ASN B 137 HIS ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 GLN E 48 GLN E 104 GLN E 222 HIS E 280 GLN E 350 GLN ** C 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN G 416 GLN F 47 ASN F 147 ASN F 242 GLN F 309 GLN F 497 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 33944 Z= 0.304 Angle : 0.586 12.199 46423 Z= 0.297 Chirality : 0.044 0.188 5053 Planarity : 0.005 0.074 6105 Dihedral : 4.928 53.789 4509 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.91 % Allowed : 24.12 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % 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: -0.79 (0.13), residues: 3937 helix: 0.45 (0.49), residues: 95 sheet: -0.63 (0.16), residues: 992 loop : -0.50 (0.11), residues: 2850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP I 214 HIS 0.006 0.001 HIS D 384 PHE 0.035 0.002 PHE C 53 TYR 0.027 0.002 TYR B 524 ARG 0.010 0.001 ARG F 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1318 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1181 time to evaluate : 3.605 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: A 47 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.7996 (t0) REVERT: A 60 GLU cc_start: 0.7813 (tt0) cc_final: 0.7522 (tp30) REVERT: A 75 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7126 (mm-30) REVERT: A 149 VAL cc_start: 0.8653 (t) cc_final: 0.8296 (p) REVERT: A 457 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8241 (mp) REVERT: A 551 MET cc_start: 0.7556 (ttt) cc_final: 0.7306 (ttp) REVERT: A 576 SER cc_start: 0.8641 (t) cc_final: 0.8202 (m) REVERT: D 60 GLU cc_start: 0.7351 (tm-30) cc_final: 0.7006 (tm-30) REVERT: D 78 ASN cc_start: 0.7840 (m-40) cc_final: 0.7609 (m-40) REVERT: D 79 TYR cc_start: 0.8830 (m-80) cc_final: 0.8581 (m-80) REVERT: D 209 ARG cc_start: 0.8236 (pmt170) cc_final: 0.5806 (ptm160) REVERT: D 212 PHE cc_start: 0.7973 (t80) cc_final: 0.7721 (t80) REVERT: D 214 TRP cc_start: 0.8141 (p90) cc_final: 0.7875 (p90) REVERT: D 237 ASP cc_start: 0.7557 (t0) cc_final: 0.7320 (t0) REVERT: D 241 VAL cc_start: 0.8057 (t) cc_final: 0.7841 (t) REVERT: D 269 ASP cc_start: 0.6906 (p0) cc_final: 0.6576 (p0) REVERT: D 398 PHE cc_start: 0.8597 (p90) cc_final: 0.7943 (p90) REVERT: D 510 TYR cc_start: 0.8603 (t80) cc_final: 0.8321 (t80) REVERT: D 544 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7655 (t) REVERT: D 573 TYR cc_start: 0.7791 (p90) cc_final: 0.6982 (p90) REVERT: D 574 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6878 (mm-30) REVERT: B 60 GLU cc_start: 0.7490 (tp30) cc_final: 0.6979 (tp30) REVERT: B 89 LYS cc_start: 0.8437 (tptt) cc_final: 0.8218 (tptm) REVERT: B 96 MET cc_start: 0.8088 (ptp) cc_final: 0.7708 (ptp) REVERT: B 133 MET cc_start: 0.7310 (mmt) cc_final: 0.6933 (mmt) REVERT: B 137 HIS cc_start: 0.7783 (OUTLIER) cc_final: 0.7558 (m90) REVERT: B 236 THR cc_start: 0.8004 (m) cc_final: 0.7668 (p) REVERT: B 269 ASP cc_start: 0.7124 (p0) cc_final: 0.6837 (p0) REVERT: B 378 TYR cc_start: 0.8268 (m-80) cc_final: 0.7494 (m-80) REVERT: B 387 LYS cc_start: 0.8437 (tttm) cc_final: 0.8199 (tttm) REVERT: B 396 GLU cc_start: 0.7763 (tt0) cc_final: 0.7275 (tt0) REVERT: B 397 ARG cc_start: 0.8151 (mtt-85) cc_final: 0.7784 (mtt-85) REVERT: B 408 ARG cc_start: 0.7831 (mmt-90) cc_final: 0.7205 (mpt180) REVERT: B 435 PRO cc_start: 0.8679 (Cg_endo) cc_final: 0.8417 (Cg_exo) REVERT: B 476 THR cc_start: 0.8165 (p) cc_final: 0.7941 (p) REVERT: B 509 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7109 (mm-30) REVERT: B 511 ASP cc_start: 0.7261 (p0) cc_final: 0.6902 (p0) REVERT: B 528 TRP cc_start: 0.8521 (m100) cc_final: 0.8228 (m100) REVERT: B 535 PHE cc_start: 0.8234 (m-80) cc_final: 0.7319 (m-80) REVERT: B 551 MET cc_start: 0.6854 (ttt) cc_final: 0.6624 (ttt) REVERT: B 560 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8034 (t0) REVERT: B 575 LYS cc_start: 0.7967 (mmtm) cc_final: 0.7764 (mmtm) REVERT: I 71 LEU cc_start: 0.8453 (tp) cc_final: 0.8173 (tm) REVERT: I 73 MET cc_start: 0.7104 (ptt) cc_final: 0.6734 (ptt) REVERT: I 96 MET cc_start: 0.5236 (ttp) cc_final: 0.4368 (tmm) REVERT: I 107 THR cc_start: 0.8598 (m) cc_final: 0.8375 (t) REVERT: I 242 GLN cc_start: 0.7306 (mm110) cc_final: 0.7018 (mm110) REVERT: I 283 ARG cc_start: 0.8512 (mmm-85) cc_final: 0.8162 (mmm160) REVERT: I 319 MET cc_start: 0.7711 (mtp) cc_final: 0.7241 (mtp) REVERT: I 323 ASN cc_start: 0.7856 (m-40) cc_final: 0.7279 (m-40) REVERT: I 330 ILE cc_start: 0.8547 (tt) cc_final: 0.8243 (tp) REVERT: I 415 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8301 (mm) REVERT: I 420 PHE cc_start: 0.7955 (t80) cc_final: 0.7536 (t80) REVERT: I 471 ASP cc_start: 0.6917 (t0) cc_final: 0.6704 (t0) REVERT: I 472 LYS cc_start: 0.8220 (tptm) cc_final: 0.7808 (tppt) REVERT: I 485 ASN cc_start: 0.7568 (p0) cc_final: 0.7314 (p0) REVERT: I 536 LYS cc_start: 0.8134 (ttpp) cc_final: 0.7840 (mtpp) REVERT: I 548 ILE cc_start: 0.7924 (pt) cc_final: 0.7627 (pp) REVERT: I 572 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8242 (m) REVERT: I 574 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6971 (mm-30) REVERT: E 168 ASP cc_start: 0.7301 (t0) cc_final: 0.6686 (t0) REVERT: E 190 MET cc_start: 0.8320 (tpp) cc_final: 0.7823 (ttp) REVERT: E 240 ASP cc_start: 0.7348 (m-30) cc_final: 0.6987 (m-30) REVERT: E 257 THR cc_start: 0.8451 (p) cc_final: 0.8210 (t) REVERT: E 269 ASP cc_start: 0.7154 (p0) cc_final: 0.6876 (p0) REVERT: E 302 ASN cc_start: 0.7436 (t160) cc_final: 0.7198 (t0) REVERT: E 309 GLN cc_start: 0.7412 (mt0) cc_final: 0.6693 (mt0) REVERT: E 312 LYS cc_start: 0.8527 (mttt) cc_final: 0.7467 (mttt) REVERT: E 346 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7138 (mt-10) REVERT: E 350 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8162 (mp10) REVERT: E 357 ILE cc_start: 0.8392 (mm) cc_final: 0.8191 (mm) REVERT: E 411 GLU cc_start: 0.7481 (mp0) cc_final: 0.6896 (mp0) REVERT: E 416 GLN cc_start: 0.8172 (pt0) cc_final: 0.7798 (pt0) REVERT: E 421 ASN cc_start: 0.7831 (m-40) cc_final: 0.7062 (p0) REVERT: E 434 ASP cc_start: 0.7626 (m-30) cc_final: 0.7334 (m-30) REVERT: E 447 ILE cc_start: 0.7972 (pt) cc_final: 0.7623 (mm) REVERT: E 448 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7672 (t80) REVERT: C 54 LEU cc_start: 0.8517 (mt) cc_final: 0.8266 (mm) REVERT: C 71 LEU cc_start: 0.8483 (tp) cc_final: 0.8271 (tp) REVERT: C 128 LEU cc_start: 0.7913 (tp) cc_final: 0.7712 (tm) REVERT: C 144 GLU cc_start: 0.7293 (pt0) cc_final: 0.6944 (pt0) REVERT: C 168 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7154 (m-30) REVERT: C 247 GLU cc_start: 0.7640 (mp0) cc_final: 0.7270 (mp0) REVERT: C 387 LYS cc_start: 0.8345 (tttt) cc_final: 0.7906 (tttm) REVERT: C 389 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8256 (p) REVERT: C 397 ARG cc_start: 0.7740 (mtt180) cc_final: 0.7447 (pmm-80) REVERT: C 464 TYR cc_start: 0.7747 (t80) cc_final: 0.7171 (t80) REVERT: C 509 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6567 (mm-30) REVERT: C 511 ASP cc_start: 0.7459 (p0) cc_final: 0.7192 (p0) REVERT: C 522 VAL cc_start: 0.8748 (t) cc_final: 0.8381 (m) REVERT: C 526 ASP cc_start: 0.7653 (m-30) cc_final: 0.7387 (m-30) REVERT: C 538 LYS cc_start: 0.8214 (tptp) cc_final: 0.7616 (tptp) REVERT: C 560 ASN cc_start: 0.8435 (m-40) cc_final: 0.7802 (t0) REVERT: C 572 VAL cc_start: 0.8286 (m) cc_final: 0.7700 (m) REVERT: G 68 LEU cc_start: 0.8149 (tp) cc_final: 0.7651 (tm) REVERT: G 77 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7079 (tm-30) REVERT: G 95 ASN cc_start: 0.8269 (m-40) cc_final: 0.7900 (m110) REVERT: G 121 PHE cc_start: 0.8147 (m-80) cc_final: 0.7866 (m-80) REVERT: G 190 MET cc_start: 0.7445 (mmm) cc_final: 0.6776 (mmm) REVERT: G 194 THR cc_start: 0.8363 (p) cc_final: 0.8052 (t) REVERT: G 204 ILE cc_start: 0.8706 (pt) cc_final: 0.8354 (pp) REVERT: G 213 GLN cc_start: 0.8108 (tp-100) cc_final: 0.7766 (tm-30) REVERT: G 276 THR cc_start: 0.8236 (p) cc_final: 0.7967 (p) REVERT: G 318 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8032 (mt0) REVERT: G 408 ARG cc_start: 0.8202 (mmt-90) cc_final: 0.7803 (mmt90) REVERT: G 434 ASP cc_start: 0.7384 (m-30) cc_final: 0.7144 (m-30) REVERT: G 439 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7397 (mmtm) REVERT: G 440 THR cc_start: 0.8205 (p) cc_final: 0.7940 (t) REVERT: G 469 ILE cc_start: 0.8632 (mt) cc_final: 0.8429 (mm) REVERT: G 475 ASP cc_start: 0.7758 (t0) cc_final: 0.7546 (t0) REVERT: G 526 ASP cc_start: 0.7278 (t0) cc_final: 0.6953 (t0) REVERT: G 530 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8307 (ttmt) REVERT: G 578 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8220 (mm) REVERT: F 80 ARG cc_start: 0.5449 (tpt170) cc_final: 0.5241 (tpt170) REVERT: F 81 ARG cc_start: 0.7533 (ttp-170) cc_final: 0.7142 (pmm150) REVERT: F 109 TRP cc_start: 0.8389 (m100) cc_final: 0.8099 (m100) REVERT: F 126 TRP cc_start: 0.8409 (t-100) cc_final: 0.8093 (t-100) REVERT: F 133 MET cc_start: 0.8038 (mmt) cc_final: 0.7653 (mpp) REVERT: F 148 VAL cc_start: 0.8687 (t) cc_final: 0.8330 (m) REVERT: F 214 TRP cc_start: 0.8677 (p90) cc_final: 0.8084 (p90) REVERT: F 216 ARG cc_start: 0.7752 (ttt90) cc_final: 0.7106 (ttt-90) REVERT: F 254 LEU cc_start: 0.8296 (mt) cc_final: 0.8069 (mt) REVERT: F 326 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8338 (t) REVERT: F 382 ARG cc_start: 0.7436 (mtt90) cc_final: 0.7191 (mtt-85) REVERT: F 448 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8188 (t80) REVERT: F 457 LEU cc_start: 0.8380 (mt) cc_final: 0.8149 (mt) REVERT: F 473 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6215 (tm-30) REVERT: F 475 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.6677 (t0) REVERT: F 522 VAL cc_start: 0.8203 (p) cc_final: 0.7936 (m) REVERT: F 528 TRP cc_start: 0.8279 (m100) cc_final: 0.7917 (m100) REVERT: F 530 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8108 (ttpp) outliers start: 137 outliers final: 95 residues processed: 1227 average time/residue: 1.3374 time to fit residues: 1974.6518 Evaluate side-chains 1288 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1175 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 444 TYR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 180 ASN Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 265 THR Chi-restraints excluded: chain I residue 413 ASP Chi-restraints excluded: chain I residue 415 ILE Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 444 TYR Chi-restraints excluded: chain I residue 448 PHE Chi-restraints excluded: chain I residue 476 THR Chi-restraints excluded: chain I residue 481 ARG Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 490 CYS Chi-restraints excluded: chain I residue 564 SER Chi-restraints excluded: chain I residue 572 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 442 ILE Chi-restraints excluded: chain E residue 448 PHE Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 439 LYS Chi-restraints excluded: chain G residue 444 TYR Chi-restraints excluded: chain G residue 458 ASN Chi-restraints excluded: chain G residue 578 LEU Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 475 ASP Chi-restraints excluded: chain F residue 530 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 373 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 396 optimal weight: 0.6980 chunk 241 optimal weight: 0.8980 chunk 187 optimal weight: 30.0000 chunk 275 optimal weight: 6.9990 chunk 415 optimal weight: 0.0170 chunk 382 optimal weight: 0.4980 chunk 330 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 255 optimal weight: 2.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN D 104 GLN D 127 GLN D 577 GLN B 137 HIS B 302 ASN ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 HIS E 280 GLN E 350 GLN E 404 GLN ** E 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 HIS C 549 GLN G 85 ASN ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 GLN F 47 ASN F 147 ASN F 242 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 33944 Z= 0.144 Angle : 0.545 11.939 46423 Z= 0.274 Chirality : 0.042 0.210 5053 Planarity : 0.004 0.060 6105 Dihedral : 4.522 51.923 4509 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.02 % Allowed : 25.29 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % 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: -0.59 (0.13), residues: 3937 helix: 0.45 (0.48), residues: 95 sheet: -0.38 (0.17), residues: 942 loop : -0.40 (0.11), residues: 2900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP I 214 HIS 0.016 0.001 HIS C 222 PHE 0.036 0.001 PHE C 53 TYR 0.027 0.001 TYR E 233 ARG 0.009 0.001 ARG F 382 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7874 Ramachandran restraints generated. 3937 Oldfield, 0 Emsley, 3937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1165 time to evaluate : 3.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.8014 (t0) REVERT: A 60 GLU cc_start: 0.7853 (tt0) cc_final: 0.7628 (tp30) REVERT: A 75 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7103 (mm-30) REVERT: A 149 VAL cc_start: 0.8596 (t) cc_final: 0.8228 (p) REVERT: A 380 PHE cc_start: 0.8727 (p90) cc_final: 0.8452 (p90) REVERT: A 457 LEU cc_start: 0.8285 (mp) cc_final: 0.7984 (mp) REVERT: A 576 SER cc_start: 0.8529 (t) cc_final: 0.8197 (m) REVERT: D 60 GLU cc_start: 0.7381 (tm-30) cc_final: 0.7046 (tm-30) REVERT: D 78 ASN cc_start: 0.7837 (m-40) cc_final: 0.7597 (m-40) REVERT: D 79 TYR cc_start: 0.8805 (m-80) cc_final: 0.8559 (m-80) REVERT: D 120 TRP cc_start: 0.8584 (m100) cc_final: 0.8185 (m100) REVERT: D 209 ARG cc_start: 0.8133 (pmt170) cc_final: 0.5813 (ptm160) REVERT: D 214 TRP cc_start: 0.8139 (p90) cc_final: 0.7859 (p90) REVERT: D 237 ASP cc_start: 0.7531 (t0) cc_final: 0.7299 (t0) REVERT: D 269 ASP cc_start: 0.6750 (p0) cc_final: 0.6421 (p0) REVERT: D 544 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7613 (t) REVERT: D 573 TYR cc_start: 0.7822 (p90) cc_final: 0.7100 (p90) REVERT: B 60 GLU cc_start: 0.7506 (tp30) cc_final: 0.6948 (tp30) REVERT: B 89 LYS cc_start: 0.8421 (tptt) cc_final: 0.7947 (tptm) REVERT: B 95 ASN cc_start: 0.7857 (m110) cc_final: 0.7301 (p0) REVERT: B 96 MET cc_start: 0.8056 (ptp) cc_final: 0.7652 (ptp) REVERT: B 133 MET cc_start: 0.7226 (mmt) cc_final: 0.6852 (mmt) REVERT: B 217 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7813 (p) REVERT: B 269 ASP cc_start: 0.7150 (p0) cc_final: 0.6799 (p0) REVERT: B 378 TYR cc_start: 0.8220 (m-80) cc_final: 0.7462 (m-80) REVERT: B 387 LYS cc_start: 0.8445 (tttm) cc_final: 0.8235 (ttmm) REVERT: B 396 GLU cc_start: 0.7734 (tt0) cc_final: 0.7288 (tt0) REVERT: B 408 ARG cc_start: 0.7828 (mmt-90) cc_final: 0.7201 (mpt180) REVERT: B 435 PRO cc_start: 0.8686 (Cg_endo) cc_final: 0.8409 (Cg_exo) REVERT: B 476 THR cc_start: 0.8103 (p) cc_final: 0.7890 (p) REVERT: B 509 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7057 (mm-30) REVERT: B 511 ASP cc_start: 0.7248 (p0) cc_final: 0.6885 (p0) REVERT: B 528 TRP cc_start: 0.8534 (m100) cc_final: 0.8253 (m100) REVERT: B 535 PHE cc_start: 0.7955 (m-80) cc_final: 0.7443 (m-10) REVERT: B 551 MET cc_start: 0.6863 (ttt) cc_final: 0.6619 (ttt) REVERT: B 560 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8029 (t0) REVERT: I 73 MET cc_start: 0.7151 (ptt) cc_final: 0.6761 (ptt) REVERT: I 96 MET cc_start: 0.4701 (ttp) cc_final: 0.4190 (tmm) REVERT: I 107 THR cc_start: 0.8565 (m) cc_final: 0.8313 (t) REVERT: I 151 LYS cc_start: 0.7585 (mmmt) cc_final: 0.7113 (mmmt) REVERT: I 242 GLN cc_start: 0.7335 (mm110) cc_final: 0.7060 (mm110) REVERT: I 283 ARG cc_start: 0.8542 (mmm-85) cc_final: 0.8131 (mmm160) REVERT: I 314 ARG cc_start: 0.8058 (ttm-80) cc_final: 0.7720 (ttm110) REVERT: I 319 MET cc_start: 0.7596 (mtp) cc_final: 0.7170 (mtp) REVERT: I 382 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7920 (mtt90) REVERT: I 420 PHE cc_start: 0.7885 (t80) cc_final: 0.7403 (t80) REVERT: I 471 ASP cc_start: 0.6911 (t0) cc_final: 0.6634 (t0) REVERT: I 485 ASN cc_start: 0.7583 (p0) cc_final: 0.7289 (p0) REVERT: I 536 LYS cc_start: 0.8049 (ttpp) cc_final: 0.7802 (mtpp) REVERT: I 548 ILE cc_start: 0.7879 (pt) cc_final: 0.7570 (pp) REVERT: I 572 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8203 (m) REVERT: I 574 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6889 (mm-30) REVERT: I 582 LYS cc_start: 0.7802 (tmmt) cc_final: 0.7483 (ttmt) REVERT: E 99 ASP cc_start: 0.8356 (t0) cc_final: 0.7565 (t0) REVERT: E 164 VAL cc_start: 0.8746 (m) cc_final: 0.8428 (p) REVERT: E 168 ASP cc_start: 0.7264 (t0) cc_final: 0.6662 (t0) REVERT: E 190 MET cc_start: 0.8287 (tpp) cc_final: 0.7815 (ttp) REVERT: E 240 ASP cc_start: 0.7318 (m-30) cc_final: 0.6967 (m-30) REVERT: E 257 THR cc_start: 0.8428 (p) cc_final: 0.8173 (t) REVERT: E 309 GLN cc_start: 0.7302 (mt0) cc_final: 0.6998 (mt0) REVERT: E 346 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7147 (mt-10) REVERT: E 350 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8028 (mp10) REVERT: E 411 GLU cc_start: 0.7457 (mp0) cc_final: 0.6866 (mp0) REVERT: E 416 GLN cc_start: 0.8029 (pt0) cc_final: 0.7688 (pt0) REVERT: E 434 ASP cc_start: 0.7628 (m-30) cc_final: 0.7331 (m-30) REVERT: E 442 ILE cc_start: 0.8284 (mm) cc_final: 0.8071 (mp) REVERT: E 448 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7669 (t80) REVERT: C 128 LEU cc_start: 0.7885 (tp) cc_final: 0.7655 (tm) REVERT: C 144 GLU cc_start: 0.7370 (pt0) cc_final: 0.7026 (pt0) REVERT: C 168 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7218 (m-30) REVERT: C 174 MET cc_start: 0.7891 (mtp) cc_final: 0.7670 (mtp) REVERT: C 190 MET cc_start: 0.7592 (mmm) cc_final: 0.7005 (mmm) REVERT: C 247 GLU cc_start: 0.7648 (mp0) cc_final: 0.7245 (mp0) REVERT: C 387 LYS cc_start: 0.8232 (tttt) cc_final: 0.7748 (tttt) REVERT: C 389 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.7994 (p) REVERT: C 397 ARG cc_start: 0.7724 (mtt180) cc_final: 0.7433 (pmm-80) REVERT: C 509 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6548 (mm-30) REVERT: C 511 ASP cc_start: 0.7389 (p0) cc_final: 0.7181 (p0) REVERT: C 522 VAL cc_start: 0.8712 (t) cc_final: 0.8362 (p) REVERT: C 526 ASP cc_start: 0.7601 (m-30) cc_final: 0.7318 (m-30) REVERT: C 538 LYS cc_start: 0.8182 (tptp) cc_final: 0.7612 (tptp) REVERT: G 68 LEU cc_start: 0.8082 (tp) cc_final: 0.7615 (tm) REVERT: G 77 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7034 (tm-30) REVERT: G 87 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7568 (ttp) REVERT: G 106 VAL cc_start: 0.8077 (t) cc_final: 0.7644 (m) REVERT: G 177 LEU cc_start: 0.7818 (tp) cc_final: 0.7599 (tm) REVERT: G 190 MET cc_start: 0.7403 (mmm) cc_final: 0.6700 (mmm) REVERT: G 194 THR cc_start: 0.8322 (p) cc_final: 0.8019 (t) REVERT: G 204 ILE cc_start: 0.8685 (pt) cc_final: 0.8333 (pp) REVERT: G 213 GLN cc_start: 0.8147 (tp-100) cc_final: 0.7685 (tm-30) REVERT: G 239 ASP cc_start: 0.7370 (p0) cc_final: 0.7114 (p0) REVERT: G 247 GLU cc_start: 0.7954 (mp0) cc_final: 0.7413 (mp0) REVERT: G 276 THR cc_start: 0.8178 (p) cc_final: 0.7891 (p) REVERT: G 318 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8001 (mt0) REVERT: G 408 ARG cc_start: 0.8175 (mmt-90) cc_final: 0.7877 (mmt90) REVERT: G 434 ASP cc_start: 0.7392 (m-30) cc_final: 0.7177 (m-30) REVERT: G 469 ILE cc_start: 0.8607 (mt) cc_final: 0.8387 (mm) REVERT: G 476 THR cc_start: 0.8104 (p) cc_final: 0.7887 (p) REVERT: G 526 ASP cc_start: 0.7303 (t0) cc_final: 0.7021 (t0) REVERT: G 530 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8312 (ttmt) REVERT: G 538 LYS cc_start: 0.8329 (tptp) cc_final: 0.7991 (ttmm) REVERT: G 578 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8161 (mm) REVERT: F 50 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7168 (mp0) REVERT: F 80 ARG cc_start: 0.5506 (tpt170) cc_final: 0.5247 (tpt170) REVERT: F 81 ARG cc_start: 0.7520 (ttp-170) cc_final: 0.7277 (ttp-170) REVERT: F 96 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7628 (ptp) REVERT: F 133 MET cc_start: 0.7943 (mmt) cc_final: 0.7567 (mpp) REVERT: F 148 VAL cc_start: 0.8713 (t) cc_final: 0.8354 (m) REVERT: F 214 TRP cc_start: 0.8627 (p90) cc_final: 0.7991 (p90) REVERT: F 216 ARG cc_start: 0.7639 (ttt90) cc_final: 0.6906 (ttt-90) REVERT: F 254 LEU cc_start: 0.8302 (mt) cc_final: 0.8074 (mt) REVERT: F 382 ARG cc_start: 0.7261 (mtt90) cc_final: 0.7052 (mtt90) REVERT: F 457 LEU cc_start: 0.8335 (mt) cc_final: 0.8082 (mt) REVERT: F 473 GLU cc_start: 0.6949 (tm-30) cc_final: 0.6170 (tm-30) REVERT: F 475 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.6834 (t0) REVERT: F 528 TRP cc_start: 0.8284 (m100) cc_final: 0.7882 (m100) REVERT: F 530 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8179 (ttpp) outliers start: 106 outliers final: 68 residues processed: 1203 average time/residue: 1.3212 time to fit residues: 1910.9458 Evaluate side-chains 1229 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1146 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 265 THR Chi-restraints excluded: chain I residue 296 GLN Chi-restraints excluded: chain I residue 413 ASP Chi-restraints excluded: chain I residue 415 ILE Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 444 TYR Chi-restraints excluded: chain I residue 448 PHE Chi-restraints excluded: chain I residue 476 THR Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 490 CYS Chi-restraints excluded: chain I residue 572 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 448 PHE Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 458 ASN Chi-restraints excluded: chain G residue 466 ASN Chi-restraints excluded: chain G residue 578 LEU Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 475 ASP Chi-restraints excluded: chain F residue 530 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 202 optimal weight: 10.0000 chunk 262 optimal weight: 2.9990 chunk 352 optimal weight: 10.0000 chunk 101 optimal weight: 0.3980 chunk 305 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 91 optimal weight: 30.0000 chunk 331 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 340 optimal weight: 0.0270 chunk 41 optimal weight: 6.9990 overall best weight: 2.0844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 GLN D 127 GLN D 383 GLN D 558 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 242 GLN B 302 ASN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 222 HIS E 280 GLN ** E 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 GLN C 549 GLN G 85 ASN G 416 GLN F 47 ASN F 147 ASN F 242 GLN F 466 ASN F 497 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.157834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128593 restraints weight = 48352.058| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.29 r_work: 0.3430 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.293 33944 Z= 0.313 Angle : 0.721 59.133 46423 Z= 0.410 Chirality : 0.046 1.036 5053 Planarity : 0.005 0.189 6105 Dihedral : 4.577 51.852 4509 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.88 % Favored : 98.09 % Rotamer: Outliers : 2.48 % Allowed : 26.45 % Favored : 71.07 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 3937 helix: 0.44 (0.48), residues: 95 sheet: -0.36 (0.17), residues: 942 loop : -0.41 (0.11), residues: 2900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I 214 HIS 0.007 0.001 HIS C 222 PHE 0.033 0.001 PHE C 53 TYR 0.025 0.001 TYR E 233 ARG 0.023 0.001 ARG B 520 =============================================================================== Job complete usr+sys time: 24242.31 seconds wall clock time: 418 minutes 8.42 seconds (25088.42 seconds total)