Starting phenix.real_space_refine on Fri Jul 26 08:08:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utv_26790/07_2024/7utv_26790.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utv_26790/07_2024/7utv_26790.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/7utv_26790/07_2024/7utv_26790.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utv_26790/07_2024/7utv_26790.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utv_26790/07_2024/7utv_26790.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utv_26790/07_2024/7utv_26790.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= 0.011 sd= 0.077 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 122 5.16 5 C 20703 2.51 5 N 5570 2.21 5 O 6151 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 413": "OD1" <-> "OD2" Residue "F TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 32546 Number of models: 1 Model: "" Number of chains: 10 Chain: "L" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 456 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'CIS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 91 Planarities with less than four sites: {'UNK:plan-1': 90} Unresolved non-hydrogen planarities: 90 Chain: "H" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 501 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'CIS': 1, 'TRANS': 98} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 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: "B" Number of atoms: 3780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3780 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 437} Chain breaks: 3 Chain: "C" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3216 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 372} Chain breaks: 5 Chain: "D" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3449 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 398} Chain breaks: 4 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: "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 Chain: "G" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4238 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492} Chain breaks: 2 Chain: "I" Number of atoms: 4192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4192 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 487} Chain breaks: 3 Time building chain proxies: 16.94, per 1000 atoms: 0.52 Number of scatterers: 32546 At special positions: 0 Unit cell: (182.6, 202.4, 128.7, 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 122 16.00 O 6151 8.00 N 5570 7.00 C 20703 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 B 490 " - pdb=" SG CYS B 494 " distance=2.03 Simple disulfide: pdb=" SG CYS C 490 " - pdb=" SG CYS C 494 " distance=2.04 Simple disulfide: pdb=" SG CYS D 490 " - pdb=" SG CYS D 494 " distance=2.04 Simple disulfide: pdb=" SG CYS E 490 " - pdb=" SG CYS E 494 " distance=2.04 Simple disulfide: pdb=" SG CYS F 490 " - pdb=" SG CYS F 494 " distance=2.04 Simple disulfide: pdb=" SG CYS G 490 " - pdb=" SG CYS G 494 " distance=2.04 Simple disulfide: pdb=" SG CYS I 490 " - pdb=" SG CYS I 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: 11.64 Conformation dependent library (CDL) restraints added in 5.1 seconds 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7766 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 72 sheets defined 13.2% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'H' and resid 34 through 38 Processing helix chain 'A' and resid 86 through 92 removed outlier: 4.138A pdb=" N VAL A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 122 through 132 removed outlier: 3.833A pdb=" N THR A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.668A pdb=" N MET A 190 " --> pdb=" O PRO A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.590A pdb=" N VAL A 241 " --> pdb=" O PRO A 238 " (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 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 448 removed outlier: 3.791A pdb=" N PHE A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 561 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 116 through 121 removed outlier: 4.098A 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 187 through 191 removed outlier: 3.504A pdb=" N MET B 190 " --> pdb=" O PRO B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.814A pdb=" N VAL B 241 " --> pdb=" O PRO B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.502A pdb=" N SER B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 443 through 448 removed outlier: 4.269A pdb=" N ILE B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 95 through 99 removed outlier: 3.817A pdb=" N ASP C 99 " --> pdb=" O MET C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 237 through 241 removed outlier: 3.737A pdb=" N VAL C 241 " --> pdb=" O PRO C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 557 through 562 removed outlier: 3.519A pdb=" N TYR C 561 " --> pdb=" O GLN C 558 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL C 562 " --> pdb=" O PHE C 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 92 removed outlier: 3.964A pdb=" N VAL D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 99 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 237 through 241 removed outlier: 3.516A pdb=" N VAL D 241 " --> pdb=" O PRO D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 250 Processing helix chain 'D' and resid 557 through 561 Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 187 through 192 removed outlier: 3.588A pdb=" N MET E 190 " --> pdb=" O PRO E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 241 removed outlier: 3.515A pdb=" N VAL E 241 " --> pdb=" O PRO E 238 " (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: 3.779A pdb=" N ARG E 313 " --> pdb=" O GLN E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 413 Processing helix chain 'E' and resid 443 through 447 Processing helix chain 'E' and resid 557 through 561 Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 116 through 120 Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'F' and resid 237 through 241 removed outlier: 3.561A pdb=" N VAL F 241 " --> pdb=" O PRO F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 250 Processing helix chain 'F' and resid 281 through 285 Processing helix chain 'F' and resid 309 through 313 removed outlier: 3.858A pdb=" N ARG F 313 " --> pdb=" O GLN F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 413 Processing helix chain 'F' and resid 425 through 427 No H-bonds generated for 'chain 'F' and resid 425 through 427' Processing helix chain 'F' and resid 443 through 448 removed outlier: 3.992A pdb=" N ILE F 447 " --> pdb=" O ASN F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 561 removed outlier: 3.601A pdb=" N TYR F 561 " --> pdb=" O GLN F 558 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 91 Processing helix chain 'G' and resid 95 through 99 Processing helix chain 'G' and resid 116 through 120 Processing helix chain 'G' and resid 122 through 132 Processing helix chain 'G' and resid 187 through 192 removed outlier: 3.916A pdb=" N MET G 190 " --> pdb=" O PRO G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 241 removed outlier: 3.583A pdb=" N VAL G 241 " --> pdb=" O PRO G 238 " (cutoff:3.500A) 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: 4.091A pdb=" N ARG G 313 " --> pdb=" O GLN G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 385 removed outlier: 4.087A pdb=" N GLY G 385 " --> pdb=" O ARG G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 413 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 443 through 448 Processing helix chain 'G' and resid 557 through 561 Processing helix chain 'I' and resid 86 through 91 Processing helix chain 'I' and resid 95 through 99 Processing helix chain 'I' and resid 116 through 120 Processing helix chain 'I' and resid 122 through 132 Processing helix chain 'I' and resid 187 through 192 removed outlier: 3.510A pdb=" N MET I 190 " --> pdb=" O PRO I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 241 Processing helix chain 'I' and resid 245 through 249 Processing helix chain 'I' and resid 281 through 285 Processing helix chain 'I' and resid 309 through 313 removed outlier: 4.088A pdb=" N ARG I 313 " --> pdb=" O GLN I 310 " (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 447 Processing helix chain 'I' and resid 557 through 561 removed outlier: 3.530A pdb=" N TYR I 561 " --> pdb=" O GLN I 558 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 39 through 40 Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 4 Processing sheet with id=AA3, first strand: chain 'H' and resid 49 through 50 removed outlier: 6.429A pdb=" N UNK H 41 " --> pdb=" O UNK H 32 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N UNK H 32 " --> pdb=" O UNK H 41 " (cutoff:3.500A) Processing sheet with id=AA4, 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=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 58 through 72 current: chain 'A' and resid 164 through 167 Processing sheet with id=AA6, first strand: chain 'A' and resid 80 through 84 Processing sheet with id=AA7, first strand: chain 'A' and resid 216 through 218 Processing sheet with id=AA8, first strand: chain 'A' and resid 276 through 278 removed outlier: 6.018A pdb=" N HIS A 277 " --> pdb=" O ARG A 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 315 through 319 removed outlier: 4.190A pdb=" N MET A 319 " --> pdb=" O ASN G 375 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASN G 375 " --> pdb=" O MET A 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 335 through 336 removed outlier: 6.866A pdb=" N GLU A 335 " --> pdb=" O ALA A 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 351 through 354 removed outlier: 3.738A pdb=" N SER A 348 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 396 through 399 removed outlier: 7.036A pdb=" N ASN A 375 " --> pdb=" O MET F 319 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET F 319 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 429 through 430 removed outlier: 3.628A pdb=" N SER G 348 " --> pdb=" O GLY G 351 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 463 through 464 removed outlier: 4.186A pdb=" N TYR A 464 " --> pdb=" O GLU A 574 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 574 " --> pdb=" O TYR A 464 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 470 through 472 removed outlier: 7.021A pdb=" N ASP A 471 " --> pdb=" O CYS A 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, 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=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 58 through 72 current: chain 'B' and resid 164 through 167 Processing sheet with id=AB9, first strand: chain 'B' and resid 216 through 218 Processing sheet with id=AC1, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.034A pdb=" N HIS B 277 " --> pdb=" O ARG B 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 346 through 348 removed outlier: 3.557A pdb=" N SER B 348 " --> pdb=" O GLY B 351 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 396 through 399 removed outlier: 7.044A pdb=" N ASN B 375 " --> pdb=" O MET I 319 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N MET I 319 " --> pdb=" O ASN B 375 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 415 through 416 Processing sheet with id=AC5, first strand: chain 'B' and resid 463 through 464 removed outlier: 4.127A pdb=" N TYR B 464 " --> pdb=" O GLU B 574 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 574 " --> pdb=" O TYR B 464 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 470 through 472 removed outlier: 6.698A pdb=" N ASP B 471 " --> pdb=" O CYS B 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 44 through 45 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 44 through 45 current: chain 'D' and resid 102 through 112 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, 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 261 through 262 Processing sheet with id=AC9, first strand: chain 'C' and resid 216 through 218 Processing sheet with id=AD1, first strand: chain 'C' and resid 345 through 347 Processing sheet with id=AD2, first strand: chain 'C' and resid 377 through 380 Processing sheet with id=AD3, first strand: chain 'C' and resid 470 through 472 removed outlier: 6.607A pdb=" N ASP C 471 " --> pdb=" O CYS C 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 49 through 54 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=AD5, first strand: chain 'D' and resid 216 through 218 Processing sheet with id=AD6, first strand: chain 'D' and resid 276 through 278 removed outlier: 5.998A pdb=" N HIS D 277 " --> pdb=" O ARG D 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 345 through 348 removed outlier: 3.988A pdb=" N SER D 348 " --> pdb=" O GLY D 351 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 377 through 380 Processing sheet with id=AD9, first strand: chain 'D' and resid 463 through 464 removed outlier: 4.213A pdb=" N TYR D 464 " --> pdb=" O GLU D 574 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 470 through 472 removed outlier: 6.805A pdb=" N ASP D 471 " --> pdb=" O CYS D 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, 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=AE3, first strand: chain 'E' and resid 80 through 84 Processing sheet with id=AE4, first strand: chain 'E' and resid 215 through 218 removed outlier: 4.024A pdb=" N GLY E 235 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR E 217 " --> pdb=" O TYR E 233 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TYR E 233 " --> pdb=" O THR E 217 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 276 through 278 Processing sheet with id=AE6, first strand: chain 'E' and resid 335 through 336 removed outlier: 6.648A pdb=" N GLU E 335 " --> pdb=" O ALA E 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 345 through 348 removed outlier: 3.972A pdb=" N SER E 348 " --> pdb=" O GLY E 351 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 377 through 380 Processing sheet with id=AE9, first strand: chain 'E' and resid 415 through 416 Processing sheet with id=AF1, first strand: chain 'E' and resid 463 through 464 removed outlier: 4.270A pdb=" N TYR E 464 " --> pdb=" O GLU E 574 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU E 574 " --> pdb=" O TYR E 464 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 470 through 472 removed outlier: 6.935A pdb=" N ASP E 471 " --> pdb=" O CYS E 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, 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=AF4, first strand: chain 'F' and resid 80 through 84 Processing sheet with id=AF5, first strand: chain 'F' and resid 215 through 218 removed outlier: 3.871A pdb=" N GLY F 235 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N THR F 217 " --> pdb=" O TYR F 233 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N TYR F 233 " --> pdb=" O THR F 217 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 276 through 278 removed outlier: 5.788A pdb=" N HIS F 277 " --> pdb=" O ARG F 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'F' and resid 335 through 336 removed outlier: 6.657A pdb=" N GLU F 335 " --> pdb=" O ALA F 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'F' and resid 351 through 354 removed outlier: 3.710A pdb=" N GLY F 351 " --> pdb=" O SER F 348 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 396 through 399 removed outlier: 7.226A pdb=" N ASN F 375 " --> pdb=" O MET G 319 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET G 319 " --> pdb=" O ASN F 375 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 463 through 464 removed outlier: 3.861A pdb=" N TYR F 464 " --> pdb=" O GLU F 574 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 470 through 472 removed outlier: 6.931A pdb=" N ASP F 471 " --> pdb=" O CYS F 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, 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=AG4, first strand: chain 'G' and resid 80 through 84 Processing sheet with id=AG5, first strand: chain 'G' and resid 215 through 218 removed outlier: 6.253A pdb=" N ASP G 215 " --> pdb=" O HIS G 234 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 276 through 278 removed outlier: 6.267A pdb=" N HIS G 277 " --> pdb=" O ARG G 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'G' and resid 335 through 336 removed outlier: 6.671A pdb=" N GLU G 335 " --> pdb=" O ALA G 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'G' and resid 470 through 472 removed outlier: 6.674A pdb=" N ASP G 471 " --> pdb=" O CYS G 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, 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=AH1, first strand: chain 'I' and resid 80 through 84 Processing sheet with id=AH2, first strand: chain 'I' and resid 215 through 218 removed outlier: 6.507A pdb=" N ASP I 215 " --> pdb=" O HIS I 234 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 276 through 278 removed outlier: 6.127A pdb=" N HIS I 277 " --> pdb=" O ARG I 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'I' and resid 335 through 336 removed outlier: 6.828A pdb=" N GLU I 335 " --> pdb=" O ALA I 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'I' and resid 345 through 347 Processing sheet with id=AH6, first strand: chain 'I' and resid 377 through 380 Processing sheet with id=AH7, first strand: chain 'I' and resid 415 through 416 Processing sheet with id=AH8, first strand: chain 'I' and resid 463 through 464 removed outlier: 4.044A pdb=" N TYR I 464 " --> pdb=" O GLU I 574 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 470 through 472 removed outlier: 6.816A pdb=" N ASP I 471 " --> pdb=" O CYS I 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 386 hydrogen bonds defined for protein. 702 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: 9.42 Time building geometry restraints manager: 12.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10686 1.35 - 1.47: 9169 1.47 - 1.60: 13411 1.60 - 1.73: 0 1.73 - 1.85: 212 Bond restraints: 33478 Sorted by residual: bond pdb=" N GLY F 37 " pdb=" CA GLY F 37 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.18e+00 bond pdb=" N GLY G 37 " pdb=" CA GLY G 37 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.10e+00 bond pdb=" N GLY A 37 " pdb=" CA GLY A 37 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.79e+00 bond pdb=" N GLY D 37 " pdb=" CA GLY D 37 " ideal model delta sigma weight residual 1.451 1.489 -0.038 1.60e-02 3.91e+03 5.63e+00 bond pdb=" N GLY B 37 " pdb=" CA GLY B 37 " ideal model delta sigma weight residual 1.451 1.489 -0.038 1.60e-02 3.91e+03 5.58e+00 ... (remaining 33473 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.15: 1130 106.15 - 113.15: 17395 113.15 - 120.14: 11945 120.14 - 127.13: 14704 127.13 - 134.12: 614 Bond angle restraints: 45788 Sorted by residual: angle pdb=" CA UNK L 57 " pdb=" C UNK L 57 " pdb=" N UNK L 58 " ideal model delta sigma weight residual 116.20 127.29 -11.09 2.00e+00 2.50e-01 3.07e+01 angle pdb=" CA VAL I 562 " pdb=" C VAL I 562 " pdb=" N PRO I 563 " ideal model delta sigma weight residual 116.57 121.31 -4.74 9.80e-01 1.04e+00 2.34e+01 angle pdb=" N UNK L 57 " pdb=" CA UNK L 57 " pdb=" C UNK L 57 " ideal model delta sigma weight residual 110.74 124.99 -14.25 3.00e+00 1.11e-01 2.26e+01 angle pdb=" C UNK L 57 " pdb=" N UNK L 58 " pdb=" CA UNK L 58 " ideal model delta sigma weight residual 121.70 129.70 -8.00 1.80e+00 3.09e-01 1.97e+01 angle pdb=" N LEU A 255 " pdb=" CA LEU A 255 " pdb=" C LEU A 255 " ideal model delta sigma weight residual 111.28 116.10 -4.82 1.09e+00 8.42e-01 1.96e+01 ... (remaining 45783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18341 17.98 - 35.96: 955 35.96 - 53.94: 198 53.94 - 71.92: 60 71.92 - 89.90: 51 Dihedral angle restraints: 19605 sinusoidal: 7563 harmonic: 12042 Sorted by residual: dihedral pdb=" CA ASN G 421 " pdb=" C ASN G 421 " pdb=" N LEU G 422 " pdb=" CA LEU G 422 " ideal model delta harmonic sigma weight residual -180.00 -149.25 -30.75 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA GLU D 55 " pdb=" C GLU D 55 " pdb=" N ASN D 56 " pdb=" CA ASN D 56 " ideal model delta harmonic sigma weight residual -180.00 -153.25 -26.75 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA PRO E 272 " pdb=" C PRO E 272 " pdb=" N CYS E 273 " pdb=" CA CYS E 273 " ideal model delta harmonic sigma weight residual 180.00 155.01 24.99 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 19602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3300 0.048 - 0.096: 1270 0.096 - 0.144: 381 0.144 - 0.192: 27 0.192 - 0.240: 2 Chirality restraints: 4980 Sorted by residual: chirality pdb=" CA UNK L 57 " pdb=" N UNK L 57 " pdb=" C UNK L 57 " pdb=" CB UNK L 57 " both_signs ideal model delta sigma weight residual False 2.52 2.28 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA LEU G 422 " pdb=" N LEU G 422 " pdb=" C LEU G 422 " pdb=" CB LEU G 422 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" CA VAL I 562 " pdb=" N VAL I 562 " pdb=" C VAL I 562 " pdb=" CB VAL I 562 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.57e-01 ... (remaining 4977 not shown) Planarity restraints: 6021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 45 " 0.015 2.00e-02 2.50e+03 1.75e-02 5.33e+00 pdb=" CG PHE D 45 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE D 45 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE D 45 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE D 45 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE D 45 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 45 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 198 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B 199 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 199 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 199 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 198 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO C 199 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 199 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 199 " -0.030 5.00e-02 4.00e+02 ... (remaining 6018 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5784 2.77 - 3.30: 30454 3.30 - 3.83: 53768 3.83 - 4.37: 66200 4.37 - 4.90: 113532 Nonbonded interactions: 269738 Sorted by model distance: nonbonded pdb=" OG SER F 339 " pdb=" OG1 THR F 450 " model vdw 2.234 2.440 nonbonded pdb=" OG1 THR D 278 " pdb=" OD1 ASN D 458 " model vdw 2.270 2.440 nonbonded pdb=" O SER B 192 " pdb=" OG SER B 192 " model vdw 2.305 2.440 nonbonded pdb=" OG1 THR G 152 " pdb=" OD2 ASP G 168 " model vdw 2.313 2.440 nonbonded pdb=" OH TYR F 343 " pdb=" OD1 ASN G 321 " model vdw 2.321 2.440 ... (remaining 269733 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 284 or resid 345 through 509 or resid 516 throu \ gh 584)) selection = (chain 'B' and (resid 37 through 509 or resid 516 through 584)) selection = (chain 'E' and (resid 37 through 284 or resid 345 through 509 or resid 516 throu \ gh 584)) selection = (chain 'F' and (resid 37 through 284 or resid 345 through 509 or resid 516 throu \ gh 584)) selection = (chain 'G' and (resid 37 through 284 or resid 345 through 509 or resid 516 throu \ gh 584)) selection = (chain 'I' and (resid 37 through 284 or resid 345 through 584)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 37 through 277 or resid 341 through 361 or resid 373 throu \ gh 404 or resid 458 through 540 or resid 550 through 579)) } ncs_group { reference = (chain 'H' and resid 10 through 100) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.400 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: 1.040 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 77.570 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.009 0.091 33478 Z= 0.608 Angle : 0.923 14.246 45788 Z= 0.492 Chirality : 0.053 0.240 4980 Planarity : 0.006 0.065 6021 Dihedral : 13.274 89.900 11815 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.44 % Favored : 97.54 % Rotamer: Outliers : 1.24 % Allowed : 3.43 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.60 (0.12), residues: 3895 helix: -1.05 (0.40), residues: 110 sheet: 0.07 (0.16), residues: 916 loop : -0.53 (0.11), residues: 2869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP G 545 HIS 0.009 0.002 HIS G 137 PHE 0.040 0.003 PHE D 45 TYR 0.034 0.003 TYR G 342 ARG 0.011 0.001 ARG C 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1273 time to evaluate : 3.448 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: 0.8567 (OUTLIER) cc_final: 0.8069 (t0) REVERT: A 48 GLN cc_start: 0.8257 (mt0) cc_final: 0.8020 (mt0) REVERT: A 60 GLU cc_start: 0.7810 (tt0) cc_final: 0.7509 (tt0) REVERT: A 87 MET cc_start: 0.7142 (ttm) cc_final: 0.6847 (ttm) REVERT: A 89 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7976 (ttmt) REVERT: A 100 ASP cc_start: 0.7745 (m-30) cc_final: 0.7446 (m-30) REVERT: A 128 LEU cc_start: 0.8654 (tp) cc_final: 0.8415 (tp) REVERT: A 131 ASN cc_start: 0.8448 (m-40) cc_final: 0.8215 (m-40) REVERT: A 144 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7459 (mt-10) REVERT: A 153 VAL cc_start: 0.8873 (t) cc_final: 0.8478 (m) REVERT: A 167 ASN cc_start: 0.8000 (m-40) cc_final: 0.7776 (m-40) REVERT: A 230 THR cc_start: 0.8518 (p) cc_final: 0.8303 (p) REVERT: A 239 ASP cc_start: 0.8053 (t0) cc_final: 0.7820 (t0) REVERT: A 249 SER cc_start: 0.8160 (p) cc_final: 0.7907 (p) REVERT: A 269 ASP cc_start: 0.7064 (p0) cc_final: 0.6643 (p0) REVERT: A 276 THR cc_start: 0.8823 (p) cc_final: 0.8609 (p) REVERT: A 296 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7695 (mm-40) REVERT: A 401 ILE cc_start: 0.8421 (mm) cc_final: 0.8182 (pp) REVERT: A 439 LYS cc_start: 0.8544 (mmtp) cc_final: 0.7951 (mmtt) REVERT: A 471 ASP cc_start: 0.7651 (t0) cc_final: 0.7439 (t0) REVERT: A 519 SER cc_start: 0.8481 (t) cc_final: 0.8257 (t) REVERT: A 536 LYS cc_start: 0.8325 (ttpp) cc_final: 0.8081 (ttpp) REVERT: A 556 ASP cc_start: 0.8015 (m-30) cc_final: 0.7790 (m-30) REVERT: A 575 LYS cc_start: 0.8625 (mttt) cc_final: 0.8349 (mttt) REVERT: B 47 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8379 (t160) REVERT: B 51 PHE cc_start: 0.8280 (m-80) cc_final: 0.8060 (m-80) REVERT: B 77 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 87 MET cc_start: 0.7536 (ptm) cc_final: 0.7329 (ptm) REVERT: B 109 TRP cc_start: 0.8693 (m100) cc_final: 0.8050 (m100) REVERT: B 113 ASP cc_start: 0.7803 (t0) cc_final: 0.7570 (t0) REVERT: B 145 ILE cc_start: 0.8739 (mt) cc_final: 0.8455 (mp) REVERT: B 180 ASN cc_start: 0.8169 (m-40) cc_final: 0.7940 (m-40) REVERT: B 219 ILE cc_start: 0.8733 (mt) cc_final: 0.8525 (OUTLIER) REVERT: B 221 SER cc_start: 0.8733 (p) cc_final: 0.8435 (p) REVERT: B 234 HIS cc_start: 0.8512 (m170) cc_final: 0.7927 (m-70) REVERT: B 248 ASN cc_start: 0.8436 (m-40) cc_final: 0.8201 (m-40) REVERT: B 271 LYS cc_start: 0.8225 (ptmt) cc_final: 0.7917 (ptmt) REVERT: B 384 HIS cc_start: 0.8683 (m90) cc_final: 0.8355 (m170) REVERT: B 408 ARG cc_start: 0.4888 (mtm110) cc_final: 0.4383 (mtm180) REVERT: B 409 TYR cc_start: 0.8110 (t80) cc_final: 0.7593 (t80) REVERT: B 411 GLU cc_start: 0.7945 (tt0) cc_final: 0.7195 (tt0) REVERT: B 468 GLN cc_start: 0.8578 (mt0) cc_final: 0.7901 (mt0) REVERT: B 475 ASP cc_start: 0.7491 (t0) cc_final: 0.6891 (t0) REVERT: B 479 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8138 (mmtm) REVERT: B 549 GLN cc_start: 0.8069 (tt0) cc_final: 0.7813 (tt0) REVERT: B 569 MET cc_start: 0.8333 (mmm) cc_final: 0.7991 (mmm) REVERT: B 573 TYR cc_start: 0.8164 (p90) cc_final: 0.7525 (p90) REVERT: C 42 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7279 (t) REVERT: C 47 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7895 (t160) REVERT: C 52 LYS cc_start: 0.8295 (ttpt) cc_final: 0.7865 (ttpt) REVERT: C 71 LEU cc_start: 0.8311 (tp) cc_final: 0.8039 (tm) REVERT: C 73 MET cc_start: 0.8129 (mtm) cc_final: 0.7913 (mtm) REVERT: C 77 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7302 (tm-30) REVERT: C 89 LYS cc_start: 0.8453 (ttmt) cc_final: 0.8100 (ttmt) REVERT: C 96 MET cc_start: 0.6499 (ptm) cc_final: 0.5597 (ptm) REVERT: C 125 ASP cc_start: 0.7886 (m-30) cc_final: 0.7590 (m-30) REVERT: C 130 VAL cc_start: 0.8339 (m) cc_final: 0.8101 (t) REVERT: C 133 MET cc_start: 0.8214 (mmt) cc_final: 0.7994 (mmm) REVERT: C 151 LYS cc_start: 0.8335 (mttp) cc_final: 0.8039 (mtpp) REVERT: C 155 GLU cc_start: 0.6999 (pp20) cc_final: 0.6744 (pp20) REVERT: C 183 MET cc_start: 0.8394 (mmm) cc_final: 0.8115 (mmp) REVERT: C 193 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7230 (mt-10) REVERT: C 204 ILE cc_start: 0.8853 (pt) cc_final: 0.8637 (pp) REVERT: C 260 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6199 (mt-10) REVERT: C 271 LYS cc_start: 0.8116 (ptmt) cc_final: 0.7775 (ptmt) REVERT: C 344 SER cc_start: 0.8274 (t) cc_final: 0.7984 (t) REVERT: C 377 ARG cc_start: 0.8686 (ttt90) cc_final: 0.8463 (ttt180) REVERT: C 470 TRP cc_start: 0.8722 (p90) cc_final: 0.8224 (p90) REVERT: C 473 GLU cc_start: 0.7885 (tp30) cc_final: 0.7679 (tp30) REVERT: C 501 LYS cc_start: 0.8569 (tttt) cc_final: 0.8293 (tttt) REVERT: C 511 ASP cc_start: 0.7745 (t0) cc_final: 0.7438 (t0) REVERT: C 530 LYS cc_start: 0.8855 (ttmt) cc_final: 0.8652 (ttpp) REVERT: C 535 PHE cc_start: 0.8629 (m-80) cc_final: 0.8304 (m-80) REVERT: C 561 TYR cc_start: 0.8813 (m-80) cc_final: 0.8611 (m-80) REVERT: C 572 VAL cc_start: 0.8907 (m) cc_final: 0.8380 (p) REVERT: C 574 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7015 (mm-30) REVERT: D 60 GLU cc_start: 0.7852 (tt0) cc_final: 0.7600 (tt0) REVERT: D 77 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7133 (mm-30) REVERT: D 113 ASP cc_start: 0.7523 (t0) cc_final: 0.7304 (t0) REVERT: D 135 GLU cc_start: 0.7967 (pt0) cc_final: 0.7740 (pt0) REVERT: D 209 ARG cc_start: 0.8561 (pmt170) cc_final: 0.6214 (pmt-80) REVERT: D 246 ILE cc_start: 0.8454 (mm) cc_final: 0.8234 (mm) REVERT: D 260 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7128 (mt-10) REVERT: D 269 ASP cc_start: 0.7861 (p0) cc_final: 0.7306 (p0) REVERT: D 387 LYS cc_start: 0.8157 (tptm) cc_final: 0.7953 (tppp) REVERT: D 396 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7412 (mm-30) REVERT: D 400 TYR cc_start: 0.8548 (t80) cc_final: 0.8254 (t80) REVERT: D 472 LYS cc_start: 0.8229 (mmmm) cc_final: 0.8001 (mmmm) REVERT: D 511 ASP cc_start: 0.7956 (t0) cc_final: 0.7606 (t0) REVERT: D 513 ASP cc_start: 0.7796 (t0) cc_final: 0.7381 (t0) REVERT: D 538 LYS cc_start: 0.7993 (ttmm) cc_final: 0.7689 (ttmm) REVERT: D 573 TYR cc_start: 0.7958 (p90) cc_final: 0.7157 (p90) REVERT: E 48 GLN cc_start: 0.8154 (mt0) cc_final: 0.7796 (mt0) REVERT: E 60 GLU cc_start: 0.7429 (tt0) cc_final: 0.7180 (tt0) REVERT: E 77 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7502 (mm-30) REVERT: E 95 ASN cc_start: 0.8024 (m110) cc_final: 0.7814 (m110) REVERT: E 122 ASN cc_start: 0.8221 (p0) cc_final: 0.7907 (p0) REVERT: E 125 ASP cc_start: 0.7706 (m-30) cc_final: 0.7494 (m-30) REVERT: E 144 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7486 (mt-10) REVERT: E 166 ASN cc_start: 0.7475 (m-40) cc_final: 0.7269 (m-40) REVERT: E 167 ASN cc_start: 0.7469 (m-40) cc_final: 0.7246 (m-40) REVERT: E 179 SER cc_start: 0.8404 (p) cc_final: 0.8186 (p) REVERT: E 193 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7309 (mt-10) REVERT: E 240 ASP cc_start: 0.7299 (m-30) cc_final: 0.6992 (m-30) REVERT: E 312 LYS cc_start: 0.5706 (tptp) cc_final: 0.4966 (mtpp) REVERT: E 314 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7333 (mtp180) REVERT: E 325 ILE cc_start: 0.8797 (mt) cc_final: 0.8504 (mp) REVERT: E 353 PHE cc_start: 0.8594 (p90) cc_final: 0.8228 (p90) REVERT: E 411 GLU cc_start: 0.7745 (mp0) cc_final: 0.7225 (mp0) REVERT: E 420 PHE cc_start: 0.8884 (t80) cc_final: 0.8643 (t80) REVERT: E 426 ASN cc_start: 0.8105 (t0) cc_final: 0.7681 (t0) REVERT: E 444 TYR cc_start: 0.8507 (p90) cc_final: 0.8300 (p90) REVERT: E 473 GLU cc_start: 0.7936 (tp30) cc_final: 0.7624 (tp30) REVERT: E 479 LYS cc_start: 0.8720 (mttm) cc_final: 0.8512 (mtpp) REVERT: E 557 ASN cc_start: 0.8320 (p0) cc_final: 0.8118 (p0) REVERT: E 570 LYS cc_start: 0.8667 (ptmt) cc_final: 0.8455 (ptmm) REVERT: E 575 LYS cc_start: 0.8545 (mttp) cc_final: 0.8327 (mttp) REVERT: F 42 THR cc_start: 0.8288 (p) cc_final: 0.7715 (t) REVERT: F 72 ASN cc_start: 0.8623 (m-40) cc_final: 0.8352 (m-40) REVERT: F 77 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7555 (mm-30) REVERT: F 78 ASN cc_start: 0.8511 (m-40) cc_final: 0.8286 (m-40) REVERT: F 135 GLU cc_start: 0.8004 (pt0) cc_final: 0.7722 (pt0) REVERT: F 144 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7692 (mt-10) REVERT: F 163 LYS cc_start: 0.8233 (mttt) cc_final: 0.7953 (mttt) REVERT: F 185 PHE cc_start: 0.8530 (t80) cc_final: 0.8245 (t80) REVERT: F 213 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7907 (tm-30) REVERT: F 239 ASP cc_start: 0.7885 (m-30) cc_final: 0.7589 (m-30) REVERT: F 244 TYR cc_start: 0.8477 (m-80) cc_final: 0.8253 (m-80) REVERT: F 302 ASN cc_start: 0.7749 (m110) cc_final: 0.7426 (m-40) REVERT: F 309 GLN cc_start: 0.7231 (mt0) cc_final: 0.6984 (mt0) REVERT: F 413 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7090 (t0) REVERT: F 434 ASP cc_start: 0.7795 (m-30) cc_final: 0.7407 (m-30) REVERT: F 444 TYR cc_start: 0.8373 (p90) cc_final: 0.8154 (p90) REVERT: F 473 GLU cc_start: 0.7648 (tp30) cc_final: 0.7363 (tp30) REVERT: F 479 LYS cc_start: 0.8592 (mttm) cc_final: 0.8147 (mttm) REVERT: F 481 ARG cc_start: 0.8546 (mmm-85) cc_final: 0.8345 (mmm-85) REVERT: F 570 LYS cc_start: 0.8747 (ptpt) cc_final: 0.8371 (ptmm) REVERT: G 60 GLU cc_start: 0.7876 (tt0) cc_final: 0.7576 (tt0) REVERT: G 87 MET cc_start: 0.6876 (ptm) cc_final: 0.6483 (ptm) REVERT: G 115 ASN cc_start: 0.8476 (t0) cc_final: 0.8253 (t0) REVERT: G 151 LYS cc_start: 0.8600 (mttm) cc_final: 0.8326 (mmmm) REVERT: G 177 LEU cc_start: 0.8346 (tp) cc_final: 0.8079 (tm) REVERT: G 204 ILE cc_start: 0.8863 (pt) cc_final: 0.8625 (OUTLIER) REVERT: G 237 ASP cc_start: 0.7747 (t0) cc_final: 0.7430 (t0) REVERT: G 259 ASP cc_start: 0.7236 (m-30) cc_final: 0.6915 (m-30) REVERT: G 274 ARG cc_start: 0.8091 (ttm110) cc_final: 0.7559 (mtp-110) REVERT: G 275 LEU cc_start: 0.8398 (mt) cc_final: 0.8167 (mp) REVERT: G 319 MET cc_start: 0.8462 (mtp) cc_final: 0.8257 (mtp) REVERT: G 375 ASN cc_start: 0.7882 (m110) cc_final: 0.7616 (m110) REVERT: G 382 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.8153 (mtm-85) REVERT: G 396 GLU cc_start: 0.7837 (tp30) cc_final: 0.7607 (tp30) REVERT: G 426 ASN cc_start: 0.8304 (t0) cc_final: 0.8057 (t0) REVERT: G 473 GLU cc_start: 0.7734 (tp30) cc_final: 0.7451 (tp30) REVERT: G 484 VAL cc_start: 0.8915 (m) cc_final: 0.8603 (t) REVERT: G 526 ASP cc_start: 0.7538 (p0) cc_final: 0.7333 (p0) REVERT: G 573 TYR cc_start: 0.8198 (p90) cc_final: 0.7406 (p90) REVERT: I 40 ILE cc_start: 0.8619 (mt) cc_final: 0.8304 (mp) REVERT: I 49 THR cc_start: 0.8310 (p) cc_final: 0.7946 (t) REVERT: I 88 ASP cc_start: 0.7692 (t0) cc_final: 0.7479 (t0) REVERT: I 125 ASP cc_start: 0.7518 (m-30) cc_final: 0.7318 (m-30) REVERT: I 133 MET cc_start: 0.8453 (mmt) cc_final: 0.8232 (mpm) REVERT: I 183 MET cc_start: 0.8330 (mmm) cc_final: 0.8109 (mmm) REVERT: I 193 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7316 (mt-10) REVERT: I 278 THR cc_start: 0.8855 (p) cc_final: 0.8648 (p) REVERT: I 303 PHE cc_start: 0.8310 (m-80) cc_final: 0.7951 (m-10) REVERT: I 311 ASP cc_start: 0.7682 (p0) cc_final: 0.7459 (p0) REVERT: I 312 LYS cc_start: 0.8623 (mttt) cc_final: 0.8291 (mttt) REVERT: I 342 TYR cc_start: 0.7978 (p90) cc_final: 0.7528 (p90) REVERT: I 350 GLN cc_start: 0.8783 (mt0) cc_final: 0.8534 (mt0) REVERT: I 387 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8154 (mmmm) REVERT: I 408 ARG cc_start: 0.8065 (mmt-90) cc_final: 0.7237 (mpt180) REVERT: I 414 TRP cc_start: 0.8717 (p90) cc_final: 0.8491 (p90) REVERT: I 439 LYS cc_start: 0.3149 (mmmt) cc_final: 0.2425 (mmmt) REVERT: I 457 LEU cc_start: 0.8293 (mt) cc_final: 0.8081 (OUTLIER) REVERT: I 501 LYS cc_start: 0.8408 (tttt) cc_final: 0.8111 (tttm) REVERT: I 518 MET cc_start: 0.6797 (ptp) cc_final: 0.6380 (ptp) outliers start: 43 outliers final: 16 residues processed: 1296 average time/residue: 1.1832 time to fit residues: 1860.6088 Evaluate side-chains 1155 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1136 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 387 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 348 optimal weight: 0.7980 chunk 313 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 323 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 chunk 240 optimal weight: 0.0570 chunk 375 optimal weight: 2.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 280 GLN A 403 HIS A 468 GLN B 48 GLN B 85 ASN B 95 ASN B 122 ASN B 181 ASN B 248 ASN B 280 GLN B 383 GLN B 404 GLN B 419 ASN C 383 GLN C 508 ASN D 383 GLN ** D 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 ASN E 102 HIS ** E 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 ASN E 497 GLN F 166 ASN F 180 ASN F 280 GLN F 350 GLN F 493 ASN F 549 GLN G 47 ASN G 234 HIS ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 419 ASN G 549 GLN I 47 ASN I 48 GLN I 147 ASN I 310 GLN I 404 GLN I 459 ASN ** I 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 549 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 33478 Z= 0.148 Angle : 0.547 15.303 45788 Z= 0.276 Chirality : 0.042 0.191 4980 Planarity : 0.004 0.044 6021 Dihedral : 6.155 80.655 4468 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.45 % Allowed : 12.51 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.27 (0.13), residues: 3895 helix: -0.66 (0.39), residues: 116 sheet: 0.02 (0.16), residues: 1025 loop : -0.18 (0.11), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 414 HIS 0.007 0.001 HIS A 234 PHE 0.017 0.001 PHE E 448 TYR 0.028 0.001 TYR G 233 ARG 0.008 0.000 ARG G 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1245 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1160 time to evaluate : 3.340 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 42 THR cc_start: 0.8033 (p) cc_final: 0.7649 (t) REVERT: A 47 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8362 (t0) REVERT: A 48 GLN cc_start: 0.7960 (mt0) cc_final: 0.7705 (mt0) REVERT: A 60 GLU cc_start: 0.7681 (tt0) cc_final: 0.7407 (tt0) REVERT: A 77 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7474 (mm-30) REVERT: A 125 ASP cc_start: 0.7763 (m-30) cc_final: 0.7560 (m-30) REVERT: A 144 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7369 (mt-10) REVERT: A 239 ASP cc_start: 0.7991 (t0) cc_final: 0.7751 (t0) REVERT: A 296 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7713 (mm-40) REVERT: A 302 ASN cc_start: 0.7316 (m110) cc_final: 0.6826 (m110) REVERT: A 313 ARG cc_start: 0.8648 (mtt180) cc_final: 0.8446 (mtt-85) REVERT: A 339 SER cc_start: 0.8633 (m) cc_final: 0.8194 (p) REVERT: A 380 PHE cc_start: 0.8451 (p90) cc_final: 0.8241 (p90) REVERT: A 439 LYS cc_start: 0.8574 (mmtp) cc_final: 0.7733 (mmtt) REVERT: A 460 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8461 (p) REVERT: A 471 ASP cc_start: 0.7665 (t0) cc_final: 0.7345 (t0) REVERT: A 511 ASP cc_start: 0.7388 (t0) cc_final: 0.7179 (t0) REVERT: A 519 SER cc_start: 0.8533 (t) cc_final: 0.8315 (t) REVERT: B 47 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8334 (t160) REVERT: B 51 PHE cc_start: 0.8278 (m-80) cc_final: 0.7991 (m-80) REVERT: B 53 PHE cc_start: 0.8521 (m-80) cc_final: 0.8197 (m-80) REVERT: B 77 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7351 (tm-30) REVERT: B 82 VAL cc_start: 0.8954 (t) cc_final: 0.8682 (p) REVERT: B 85 ASN cc_start: 0.7805 (t0) cc_final: 0.7495 (t0) REVERT: B 87 MET cc_start: 0.7618 (ptm) cc_final: 0.7381 (ptm) REVERT: B 101 ILE cc_start: 0.8590 (mt) cc_final: 0.8149 (mt) REVERT: B 109 TRP cc_start: 0.8704 (m100) cc_final: 0.8002 (m100) REVERT: B 113 ASP cc_start: 0.7801 (t0) cc_final: 0.7577 (t0) REVERT: B 135 GLU cc_start: 0.7946 (pt0) cc_final: 0.7644 (pt0) REVERT: B 180 ASN cc_start: 0.8139 (m-40) cc_final: 0.7897 (m-40) REVERT: B 216 ARG cc_start: 0.7988 (ttt90) cc_final: 0.7703 (ttt90) REVERT: B 217 THR cc_start: 0.8035 (OUTLIER) cc_final: 0.7713 (p) REVERT: B 219 ILE cc_start: 0.8712 (mt) cc_final: 0.8487 (OUTLIER) REVERT: B 221 SER cc_start: 0.8828 (p) cc_final: 0.8544 (p) REVERT: B 232 ILE cc_start: 0.8505 (pt) cc_final: 0.8294 (pp) REVERT: B 271 LYS cc_start: 0.8220 (ptmt) cc_final: 0.7927 (ptmt) REVERT: B 357 ILE cc_start: 0.8163 (mm) cc_final: 0.7921 (mp) REVERT: B 384 HIS cc_start: 0.8705 (m90) cc_final: 0.8410 (m170) REVERT: B 408 ARG cc_start: 0.4815 (mtm110) cc_final: 0.4392 (mtm180) REVERT: B 411 GLU cc_start: 0.7896 (tt0) cc_final: 0.7192 (tt0) REVERT: B 436 ILE cc_start: 0.8225 (tt) cc_final: 0.7939 (OUTLIER) REVERT: B 479 LYS cc_start: 0.8624 (mmtm) cc_final: 0.8064 (mmtm) REVERT: B 549 GLN cc_start: 0.8072 (tt0) cc_final: 0.7819 (tt0) REVERT: B 556 ASP cc_start: 0.7811 (m-30) cc_final: 0.7588 (m-30) REVERT: B 559 PHE cc_start: 0.8665 (m-80) cc_final: 0.8418 (m-80) REVERT: B 573 TYR cc_start: 0.8101 (p90) cc_final: 0.7654 (p90) REVERT: B 576 SER cc_start: 0.8564 (t) cc_final: 0.8095 (p) REVERT: C 42 THR cc_start: 0.8125 (p) cc_final: 0.7324 (m) REVERT: C 47 ASN cc_start: 0.8164 (t0) cc_final: 0.7875 (t160) REVERT: C 52 LYS cc_start: 0.8288 (ttpt) cc_final: 0.7835 (ttpt) REVERT: C 71 LEU cc_start: 0.8364 (tp) cc_final: 0.8016 (tm) REVERT: C 73 MET cc_start: 0.8084 (mtm) cc_final: 0.7874 (mtm) REVERT: C 77 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7376 (tm-30) REVERT: C 89 LYS cc_start: 0.8523 (ttmt) cc_final: 0.8200 (ttmt) REVERT: C 96 MET cc_start: 0.5951 (ptm) cc_final: 0.5564 (ptm) REVERT: C 133 MET cc_start: 0.8168 (mmt) cc_final: 0.7912 (mmm) REVERT: C 155 GLU cc_start: 0.7075 (pp20) cc_final: 0.6773 (pp20) REVERT: C 193 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7206 (mt-10) REVERT: C 204 ILE cc_start: 0.8933 (pt) cc_final: 0.8679 (pp) REVERT: C 232 ILE cc_start: 0.8409 (pt) cc_final: 0.8189 (pp) REVERT: C 260 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6174 (mt-10) REVERT: C 271 LYS cc_start: 0.8044 (ptmt) cc_final: 0.7822 (ptmt) REVERT: C 344 SER cc_start: 0.8226 (t) cc_final: 0.7952 (t) REVERT: C 377 ARG cc_start: 0.8686 (ttt90) cc_final: 0.8482 (ttt180) REVERT: C 470 TRP cc_start: 0.8732 (p90) cc_final: 0.8257 (p90) REVERT: C 473 GLU cc_start: 0.7819 (tp30) cc_final: 0.7583 (tp30) REVERT: C 479 LYS cc_start: 0.8471 (mttm) cc_final: 0.8229 (mttm) REVERT: C 511 ASP cc_start: 0.7705 (t0) cc_final: 0.7354 (t0) REVERT: C 530 LYS cc_start: 0.8839 (ttmt) cc_final: 0.8635 (ttpp) REVERT: C 535 PHE cc_start: 0.8466 (m-80) cc_final: 0.8191 (m-80) REVERT: C 550 GLN cc_start: 0.6128 (mm-40) cc_final: 0.5732 (mp-120) REVERT: C 574 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6938 (mm-30) REVERT: C 575 LYS cc_start: 0.8262 (mmtp) cc_final: 0.8022 (mmtp) REVERT: D 40 ILE cc_start: 0.8148 (mt) cc_final: 0.7947 (pp) REVERT: D 60 GLU cc_start: 0.7846 (tt0) cc_final: 0.7628 (tt0) REVERT: D 80 ARG cc_start: 0.8560 (mtp-110) cc_final: 0.8260 (mtp85) REVERT: D 101 ILE cc_start: 0.8680 (mt) cc_final: 0.8382 (mp) REVERT: D 113 ASP cc_start: 0.7600 (t0) cc_final: 0.7387 (t0) REVERT: D 135 GLU cc_start: 0.7909 (pt0) cc_final: 0.7671 (pt0) REVERT: D 260 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7142 (mt-10) REVERT: D 387 LYS cc_start: 0.8132 (tptm) cc_final: 0.7857 (tppp) REVERT: D 396 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7251 (mm-30) REVERT: D 400 TYR cc_start: 0.8552 (t80) cc_final: 0.8287 (t80) REVERT: D 511 ASP cc_start: 0.7929 (t0) cc_final: 0.7579 (t0) REVERT: D 513 ASP cc_start: 0.7829 (t0) cc_final: 0.7510 (t0) REVERT: D 538 LYS cc_start: 0.7970 (ttmm) cc_final: 0.7738 (ttmm) REVERT: E 42 THR cc_start: 0.8213 (m) cc_final: 0.7875 (p) REVERT: E 47 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8062 (t160) REVERT: E 48 GLN cc_start: 0.8115 (mt0) cc_final: 0.7876 (mt0) REVERT: E 60 GLU cc_start: 0.7334 (tt0) cc_final: 0.7077 (tt0) REVERT: E 77 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7452 (mm-30) REVERT: E 95 ASN cc_start: 0.7918 (m110) cc_final: 0.7716 (m110) REVERT: E 101 ILE cc_start: 0.8330 (mt) cc_final: 0.7648 (mt) REVERT: E 122 ASN cc_start: 0.8150 (p0) cc_final: 0.7939 (p0) REVERT: E 163 LYS cc_start: 0.8094 (mttp) cc_final: 0.7878 (mttp) REVERT: E 166 ASN cc_start: 0.7399 (m-40) cc_final: 0.7181 (m-40) REVERT: E 167 ASN cc_start: 0.7398 (m-40) cc_final: 0.7125 (m-40) REVERT: E 193 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7292 (mt-10) REVERT: E 240 ASP cc_start: 0.7249 (m-30) cc_final: 0.6929 (m-30) REVERT: E 312 LYS cc_start: 0.5282 (tptp) cc_final: 0.4896 (tptp) REVERT: E 314 ARG cc_start: 0.8181 (mtt90) cc_final: 0.7255 (mtp180) REVERT: E 325 ILE cc_start: 0.8782 (mt) cc_final: 0.8496 (mp) REVERT: E 411 GLU cc_start: 0.7860 (mp0) cc_final: 0.7360 (mp0) REVERT: E 426 ASN cc_start: 0.8083 (t0) cc_final: 0.7605 (t0) REVERT: E 460 VAL cc_start: 0.8532 (p) cc_final: 0.8291 (m) REVERT: E 473 GLU cc_start: 0.7986 (tp30) cc_final: 0.7608 (tp30) REVERT: E 570 LYS cc_start: 0.8720 (ptmt) cc_final: 0.8490 (ptmm) REVERT: F 40 ILE cc_start: 0.8500 (mt) cc_final: 0.8160 (tp) REVERT: F 42 THR cc_start: 0.8237 (p) cc_final: 0.7660 (t) REVERT: F 60 GLU cc_start: 0.7750 (tt0) cc_final: 0.7518 (tt0) REVERT: F 72 ASN cc_start: 0.8582 (m-40) cc_final: 0.8314 (m-40) REVERT: F 77 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7504 (mm-30) REVERT: F 135 GLU cc_start: 0.7966 (pt0) cc_final: 0.7731 (pt0) REVERT: F 144 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7626 (mt-10) REVERT: F 163 LYS cc_start: 0.8210 (mttt) cc_final: 0.7914 (mttt) REVERT: F 185 PHE cc_start: 0.8570 (t80) cc_final: 0.8300 (t80) REVERT: F 192 SER cc_start: 0.8362 (t) cc_final: 0.7926 (p) REVERT: F 239 ASP cc_start: 0.7815 (m-30) cc_final: 0.7521 (m-30) REVERT: F 244 TYR cc_start: 0.8443 (m-80) cc_final: 0.8214 (m-80) REVERT: F 413 ASP cc_start: 0.7583 (t70) cc_final: 0.7110 (t0) REVERT: F 417 ASN cc_start: 0.8373 (t0) cc_final: 0.8143 (t0) REVERT: F 434 ASP cc_start: 0.7753 (m-30) cc_final: 0.7297 (m-30) REVERT: F 473 GLU cc_start: 0.7645 (tp30) cc_final: 0.7347 (tp30) REVERT: F 479 LYS cc_start: 0.8542 (mttm) cc_final: 0.8150 (mttm) REVERT: F 570 LYS cc_start: 0.8778 (ptpt) cc_final: 0.8405 (ptmm) REVERT: G 49 THR cc_start: 0.8384 (m) cc_final: 0.7980 (p) REVERT: G 60 GLU cc_start: 0.7814 (tt0) cc_final: 0.7492 (tt0) REVERT: G 87 MET cc_start: 0.6932 (ptm) cc_final: 0.6652 (ptm) REVERT: G 89 LYS cc_start: 0.8518 (tttt) cc_final: 0.8268 (ttmm) REVERT: G 99 ASP cc_start: 0.7631 (t0) cc_final: 0.7037 (t0) REVERT: G 101 ILE cc_start: 0.8294 (mt) cc_final: 0.7660 (mt) REVERT: G 133 MET cc_start: 0.8252 (mmt) cc_final: 0.8046 (mmt) REVERT: G 151 LYS cc_start: 0.8577 (mttm) cc_final: 0.8344 (mmmm) REVERT: G 177 LEU cc_start: 0.8334 (tp) cc_final: 0.8045 (tm) REVERT: G 201 LYS cc_start: 0.8340 (mtpt) cc_final: 0.8110 (mtpt) REVERT: G 204 ILE cc_start: 0.8811 (pt) cc_final: 0.8597 (OUTLIER) REVERT: G 216 ARG cc_start: 0.7633 (tmt-80) cc_final: 0.7390 (tmt90) REVERT: G 237 ASP cc_start: 0.7544 (t0) cc_final: 0.7122 (t0) REVERT: G 275 LEU cc_start: 0.8368 (mt) cc_final: 0.8167 (mp) REVERT: G 303 PHE cc_start: 0.8676 (m-80) cc_final: 0.8469 (m-80) REVERT: G 335 GLU cc_start: 0.7686 (tt0) cc_final: 0.7254 (tt0) REVERT: G 344 SER cc_start: 0.8944 (t) cc_final: 0.8653 (p) REVERT: G 350 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8192 (mt0) REVERT: G 375 ASN cc_start: 0.7829 (m110) cc_final: 0.7544 (m110) REVERT: G 387 LYS cc_start: 0.8284 (tttt) cc_final: 0.7906 (ttmm) REVERT: G 396 GLU cc_start: 0.7775 (tp30) cc_final: 0.7515 (tp30) REVERT: G 400 TYR cc_start: 0.8219 (t80) cc_final: 0.7646 (t80) REVERT: G 426 ASN cc_start: 0.8479 (t0) cc_final: 0.8208 (t0) REVERT: G 473 GLU cc_start: 0.7735 (tp30) cc_final: 0.7495 (tp30) REVERT: G 549 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7675 (tp40) REVERT: G 559 PHE cc_start: 0.8754 (m-10) cc_final: 0.8479 (m-10) REVERT: G 573 TYR cc_start: 0.7993 (p90) cc_final: 0.7774 (p90) REVERT: I 40 ILE cc_start: 0.8556 (mt) cc_final: 0.8313 (mp) REVERT: I 88 ASP cc_start: 0.7755 (t0) cc_final: 0.7509 (t0) REVERT: I 107 THR cc_start: 0.8807 (m) cc_final: 0.8320 (p) REVERT: I 151 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7997 (mttp) REVERT: I 183 MET cc_start: 0.8255 (mmm) cc_final: 0.8039 (mmm) REVERT: I 193 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7317 (mt-10) REVERT: I 303 PHE cc_start: 0.8248 (m-80) cc_final: 0.7846 (m-10) REVERT: I 308 VAL cc_start: 0.8738 (m) cc_final: 0.8504 (p) REVERT: I 312 LYS cc_start: 0.8595 (mttt) cc_final: 0.8234 (mttt) REVERT: I 387 LYS cc_start: 0.8439 (mmmm) cc_final: 0.8079 (mmmm) REVERT: I 501 LYS cc_start: 0.8396 (tttt) cc_final: 0.8059 (tttm) REVERT: I 518 MET cc_start: 0.6807 (ptp) cc_final: 0.6386 (ptp) REVERT: I 561 TYR cc_start: 0.8686 (m-80) cc_final: 0.8479 (m-80) outliers start: 85 outliers final: 49 residues processed: 1187 average time/residue: 1.2347 time to fit residues: 1767.9599 Evaluate side-chains 1134 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1081 time to evaluate : 3.742 ------------------------------------------------------------------------------- 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 129 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 383 GLN Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 556 ASP Chi-restraints excluded: chain E residue 583 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 350 GLN Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 549 GLN Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 555 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 208 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 312 optimal weight: 9.9990 chunk 255 optimal weight: 9.9990 chunk 103 optimal weight: 0.0000 chunk 375 optimal weight: 10.0000 chunk 405 optimal weight: 7.9990 chunk 334 optimal weight: 9.9990 chunk 372 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 301 optimal weight: 9.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 HIS A 404 GLN A 446 ASN A 468 GLN B 48 GLN B 70 HIS B 383 GLN B 419 ASN C 70 HIS ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN D 383 GLN D 508 ASN E 47 ASN E 102 HIS E 137 HIS E 180 ASN E 181 ASN E 419 ASN E 483 HIS E 497 GLN F 180 ASN ** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 493 ASN G 47 ASN G 115 ASN G 310 GLN G 404 GLN G 550 GLN I 47 ASN I 72 ASN I 137 HIS I 147 ASN ** I 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 318 GLN I 416 GLN I 458 ASN ** I 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 549 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.132 33478 Z= 0.702 Angle : 0.705 16.154 45788 Z= 0.359 Chirality : 0.052 0.188 4980 Planarity : 0.006 0.062 6021 Dihedral : 6.186 80.832 4448 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.38 % Allowed : 15.13 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.12), residues: 3895 helix: -0.53 (0.42), residues: 116 sheet: -0.24 (0.15), residues: 1054 loop : -0.45 (0.11), residues: 2725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP G 545 HIS 0.008 0.002 HIS I 102 PHE 0.034 0.003 PHE F 45 TYR 0.034 0.003 TYR E 584 ARG 0.010 0.001 ARG I 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1119 time to evaluate : 3.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8215 (t0) REVERT: A 48 GLN cc_start: 0.8145 (mt0) cc_final: 0.7874 (mt0) REVERT: A 52 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7941 (ttmt) REVERT: A 60 GLU cc_start: 0.7695 (tt0) cc_final: 0.7492 (tt0) REVERT: A 77 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7460 (mm-30) REVERT: A 87 MET cc_start: 0.7396 (ttm) cc_final: 0.7054 (ttm) REVERT: A 89 LYS cc_start: 0.8355 (ttmt) cc_final: 0.8117 (ttmt) REVERT: A 144 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7492 (mt-10) REVERT: A 221 SER cc_start: 0.8726 (m) cc_final: 0.8487 (t) REVERT: A 239 ASP cc_start: 0.7992 (t0) cc_final: 0.7699 (t0) REVERT: A 296 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7705 (mm-40) REVERT: A 302 ASN cc_start: 0.7433 (m110) cc_final: 0.6891 (m-40) REVERT: A 313 ARG cc_start: 0.8824 (mtt180) cc_final: 0.8519 (mtt-85) REVERT: A 380 PHE cc_start: 0.8535 (p90) cc_final: 0.8301 (p90) REVERT: A 382 ARG cc_start: 0.8367 (mtm-85) cc_final: 0.8141 (mtm180) REVERT: A 400 TYR cc_start: 0.8550 (t80) cc_final: 0.7759 (t80) REVERT: A 439 LYS cc_start: 0.8509 (mmtp) cc_final: 0.8155 (mmtt) REVERT: A 460 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8473 (p) REVERT: A 511 ASP cc_start: 0.7541 (t0) cc_final: 0.7252 (t0) REVERT: A 519 SER cc_start: 0.8625 (t) cc_final: 0.8419 (t) REVERT: B 51 PHE cc_start: 0.8442 (m-80) cc_final: 0.8167 (m-80) REVERT: B 77 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7238 (tm-30) REVERT: B 87 MET cc_start: 0.7719 (ptm) cc_final: 0.7404 (ptm) REVERT: B 96 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8231 (ptp) REVERT: B 101 ILE cc_start: 0.8642 (mt) cc_final: 0.8165 (mt) REVERT: B 113 ASP cc_start: 0.7840 (t0) cc_final: 0.7595 (t0) REVERT: B 135 GLU cc_start: 0.8143 (pt0) cc_final: 0.7826 (pt0) REVERT: B 180 ASN cc_start: 0.8082 (m-40) cc_final: 0.7828 (m-40) REVERT: B 216 ARG cc_start: 0.8169 (ttt90) cc_final: 0.7657 (ttt90) REVERT: B 217 THR cc_start: 0.8291 (p) cc_final: 0.7968 (p) REVERT: B 221 SER cc_start: 0.8870 (p) cc_final: 0.8426 (p) REVERT: B 232 ILE cc_start: 0.8548 (pt) cc_final: 0.8339 (pp) REVERT: B 271 LYS cc_start: 0.8318 (ptmt) cc_final: 0.7982 (ptmt) REVERT: B 384 HIS cc_start: 0.8695 (m90) cc_final: 0.8451 (m170) REVERT: B 408 ARG cc_start: 0.4723 (mtm110) cc_final: 0.4294 (mtm180) REVERT: B 411 GLU cc_start: 0.7919 (tt0) cc_final: 0.7336 (tt0) REVERT: B 479 LYS cc_start: 0.8528 (mmtm) cc_final: 0.7930 (mmtm) REVERT: B 549 GLN cc_start: 0.8055 (tt0) cc_final: 0.7841 (tt0) REVERT: B 553 ILE cc_start: 0.6357 (mp) cc_final: 0.5832 (tt) REVERT: B 556 ASP cc_start: 0.7879 (m-30) cc_final: 0.7555 (m-30) REVERT: B 573 TYR cc_start: 0.8048 (p90) cc_final: 0.7549 (p90) REVERT: B 575 LYS cc_start: 0.8268 (mttp) cc_final: 0.7959 (mmmm) REVERT: B 582 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8002 (mtmm) REVERT: C 42 THR cc_start: 0.8217 (p) cc_final: 0.7811 (t) REVERT: C 52 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7779 (ttpt) REVERT: C 71 LEU cc_start: 0.8356 (tp) cc_final: 0.8031 (tm) REVERT: C 73 MET cc_start: 0.8071 (mtm) cc_final: 0.7870 (mtm) REVERT: C 77 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7312 (tm-30) REVERT: C 100 ASP cc_start: 0.7242 (m-30) cc_final: 0.6912 (m-30) REVERT: C 155 GLU cc_start: 0.6977 (pp20) cc_final: 0.6728 (pp20) REVERT: C 186 THR cc_start: 0.8256 (m) cc_final: 0.7958 (p) REVERT: C 192 SER cc_start: 0.8626 (m) cc_final: 0.8351 (p) REVERT: C 193 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7260 (mt-10) REVERT: C 204 ILE cc_start: 0.9017 (pt) cc_final: 0.8730 (pp) REVERT: C 237 ASP cc_start: 0.7526 (t0) cc_final: 0.7296 (t0) REVERT: C 271 LYS cc_start: 0.8167 (ptmt) cc_final: 0.7822 (ptmt) REVERT: C 349 THR cc_start: 0.8327 (p) cc_final: 0.8040 (t) REVERT: C 470 TRP cc_start: 0.8796 (p90) cc_final: 0.8266 (p90) REVERT: C 479 LYS cc_start: 0.8530 (mttm) cc_final: 0.8244 (mttm) REVERT: C 501 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8629 (tttt) REVERT: C 509 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6895 (mm-30) REVERT: C 511 ASP cc_start: 0.7683 (t0) cc_final: 0.7338 (t0) REVERT: C 550 GLN cc_start: 0.5355 (mm-40) cc_final: 0.5104 (mp-120) REVERT: C 574 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6927 (mm-30) REVERT: C 575 LYS cc_start: 0.8368 (mmtp) cc_final: 0.7998 (mmtp) REVERT: D 51 PHE cc_start: 0.8321 (m-80) cc_final: 0.7765 (m-80) REVERT: D 77 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7161 (mm-30) REVERT: D 101 ILE cc_start: 0.8735 (mt) cc_final: 0.8434 (mp) REVERT: D 125 ASP cc_start: 0.7849 (m-30) cc_final: 0.7560 (m-30) REVERT: D 135 GLU cc_start: 0.7898 (pt0) cc_final: 0.7698 (pt0) REVERT: D 178 ASP cc_start: 0.7828 (t0) cc_final: 0.7339 (t0) REVERT: D 183 MET cc_start: 0.8372 (tpp) cc_final: 0.8136 (mmm) REVERT: D 260 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7107 (mt-10) REVERT: D 387 LYS cc_start: 0.8262 (tptm) cc_final: 0.8026 (tppp) REVERT: D 396 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7281 (mm-30) REVERT: D 400 TYR cc_start: 0.8577 (t80) cc_final: 0.8220 (t80) REVERT: D 492 ASN cc_start: 0.8254 (p0) cc_final: 0.8040 (p0) REVERT: D 511 ASP cc_start: 0.7997 (t0) cc_final: 0.7688 (t0) REVERT: D 513 ASP cc_start: 0.7913 (t0) cc_final: 0.7655 (t0) REVERT: D 574 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7445 (mm-30) REVERT: E 53 PHE cc_start: 0.8236 (m-80) cc_final: 0.8024 (m-80) REVERT: E 60 GLU cc_start: 0.7319 (tt0) cc_final: 0.7074 (tt0) REVERT: E 77 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7443 (mm-30) REVERT: E 101 ILE cc_start: 0.8514 (mt) cc_final: 0.8160 (mt) REVERT: E 122 ASN cc_start: 0.8169 (p0) cc_final: 0.7749 (p0) REVERT: E 125 ASP cc_start: 0.7739 (m-30) cc_final: 0.7393 (m-30) REVERT: E 135 GLU cc_start: 0.7843 (pt0) cc_final: 0.7520 (pt0) REVERT: E 149 VAL cc_start: 0.8833 (t) cc_final: 0.8281 (p) REVERT: E 151 LYS cc_start: 0.8600 (mtpp) cc_final: 0.8370 (mtpp) REVERT: E 163 LYS cc_start: 0.8136 (mttp) cc_final: 0.7879 (mttp) REVERT: E 167 ASN cc_start: 0.7617 (m-40) cc_final: 0.7306 (m-40) REVERT: E 193 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7345 (mt-10) REVERT: E 221 SER cc_start: 0.8686 (p) cc_final: 0.8470 (p) REVERT: E 296 GLN cc_start: 0.8310 (mm-40) cc_final: 0.8067 (mm-40) REVERT: E 312 LYS cc_start: 0.5727 (tptp) cc_final: 0.4926 (mtpp) REVERT: E 314 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7203 (mtp180) REVERT: E 325 ILE cc_start: 0.8831 (mt) cc_final: 0.8493 (mp) REVERT: E 411 GLU cc_start: 0.7831 (mp0) cc_final: 0.7307 (mp0) REVERT: E 460 VAL cc_start: 0.8546 (p) cc_final: 0.8346 (m) REVERT: E 473 GLU cc_start: 0.8009 (tp30) cc_final: 0.7666 (tp30) REVERT: E 549 GLN cc_start: 0.8238 (tp40) cc_final: 0.8000 (tt0) REVERT: E 570 LYS cc_start: 0.8721 (ptmt) cc_final: 0.8440 (ptmm) REVERT: F 40 ILE cc_start: 0.8508 (mt) cc_final: 0.8123 (tp) REVERT: F 77 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7510 (mm-30) REVERT: F 89 LYS cc_start: 0.8361 (tppt) cc_final: 0.7925 (tppt) REVERT: F 163 LYS cc_start: 0.8223 (mttt) cc_final: 0.7965 (mttt) REVERT: F 173 LEU cc_start: 0.8817 (tp) cc_final: 0.8512 (tt) REVERT: F 185 PHE cc_start: 0.8579 (t80) cc_final: 0.8324 (t80) REVERT: F 192 SER cc_start: 0.8506 (t) cc_final: 0.8174 (t) REVERT: F 215 ASP cc_start: 0.7724 (m-30) cc_final: 0.7522 (m-30) REVERT: F 239 ASP cc_start: 0.8018 (m-30) cc_final: 0.7682 (m-30) REVERT: F 244 TYR cc_start: 0.8509 (m-80) cc_final: 0.8274 (m-80) REVERT: F 265 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8363 (p) REVERT: F 293 SER cc_start: 0.8454 (t) cc_final: 0.8072 (p) REVERT: F 331 MET cc_start: 0.8085 (ttp) cc_final: 0.7867 (ttp) REVERT: F 413 ASP cc_start: 0.7538 (t70) cc_final: 0.7162 (t0) REVERT: F 425 THR cc_start: 0.8545 (m) cc_final: 0.8208 (t) REVERT: F 434 ASP cc_start: 0.7759 (m-30) cc_final: 0.7478 (m-30) REVERT: F 448 PHE cc_start: 0.8646 (t80) cc_final: 0.8445 (t80) REVERT: F 473 GLU cc_start: 0.7680 (tp30) cc_final: 0.7476 (tp30) REVERT: F 544 THR cc_start: 0.8421 (p) cc_final: 0.8202 (p) REVERT: F 566 ILE cc_start: 0.9139 (pt) cc_final: 0.8814 (pp) REVERT: F 570 LYS cc_start: 0.8777 (ptpt) cc_final: 0.8387 (ptmm) REVERT: G 49 THR cc_start: 0.8370 (m) cc_final: 0.7947 (p) REVERT: G 60 GLU cc_start: 0.7736 (tt0) cc_final: 0.7465 (tt0) REVERT: G 87 MET cc_start: 0.7007 (ptm) cc_final: 0.6709 (ptm) REVERT: G 89 LYS cc_start: 0.8588 (tttt) cc_final: 0.8261 (ttmm) REVERT: G 101 ILE cc_start: 0.8398 (mt) cc_final: 0.8151 (mt) REVERT: G 133 MET cc_start: 0.8321 (mmt) cc_final: 0.8012 (mmt) REVERT: G 151 LYS cc_start: 0.8558 (mttm) cc_final: 0.8353 (mttm) REVERT: G 177 LEU cc_start: 0.8363 (tp) cc_final: 0.8103 (tm) REVERT: G 201 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7973 (mtpt) REVERT: G 204 ILE cc_start: 0.8949 (pt) cc_final: 0.8708 (pp) REVERT: G 237 ASP cc_start: 0.7705 (t0) cc_final: 0.7348 (t0) REVERT: G 335 GLU cc_start: 0.7767 (tt0) cc_final: 0.7320 (tt0) REVERT: G 375 ASN cc_start: 0.7833 (m110) cc_final: 0.7495 (m110) REVERT: G 396 GLU cc_start: 0.7783 (tp30) cc_final: 0.7499 (tp30) REVERT: G 426 ASN cc_start: 0.8638 (t0) cc_final: 0.8389 (t0) REVERT: G 473 GLU cc_start: 0.7773 (tp30) cc_final: 0.7469 (tp30) REVERT: G 532 LYS cc_start: 0.8873 (ttmt) cc_final: 0.8426 (ttpp) REVERT: G 536 LYS cc_start: 0.8183 (ttpp) cc_final: 0.7917 (ttpp) REVERT: G 549 GLN cc_start: 0.8022 (tp40) cc_final: 0.7680 (tt0) REVERT: I 40 ILE cc_start: 0.8595 (mt) cc_final: 0.8348 (mp) REVERT: I 88 ASP cc_start: 0.7775 (t0) cc_final: 0.7562 (t0) REVERT: I 89 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8233 (ttmt) REVERT: I 193 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7311 (mt-10) REVERT: I 249 SER cc_start: 0.8561 (t) cc_final: 0.8087 (p) REVERT: I 303 PHE cc_start: 0.8344 (m-80) cc_final: 0.8018 (m-10) REVERT: I 305 ASP cc_start: 0.8186 (m-30) cc_final: 0.7977 (m-30) REVERT: I 312 LYS cc_start: 0.8586 (mttt) cc_final: 0.8330 (mttt) REVERT: I 375 ASN cc_start: 0.7780 (m110) cc_final: 0.7459 (m110) REVERT: I 380 PHE cc_start: 0.8604 (p90) cc_final: 0.8395 (p90) REVERT: I 387 LYS cc_start: 0.8677 (mmmm) cc_final: 0.8204 (mmmm) REVERT: I 439 LYS cc_start: 0.4071 (mmtt) cc_final: 0.1979 (mmmt) REVERT: I 475 ASP cc_start: 0.7985 (m-30) cc_final: 0.7779 (t0) REVERT: I 501 LYS cc_start: 0.8650 (tttt) cc_final: 0.8284 (tttm) REVERT: I 518 MET cc_start: 0.6915 (ptp) cc_final: 0.6508 (ptp) REVERT: I 546 ASN cc_start: 0.8472 (p0) cc_final: 0.8224 (p0) REVERT: I 565 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7984 (t0) outliers start: 152 outliers final: 97 residues processed: 1181 average time/residue: 1.2512 time to fit residues: 1777.2440 Evaluate side-chains 1173 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1069 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 582 LYS Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain F residue 44 THR 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 106 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 302 ASN Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 342 TYR Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 180 ASN Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 413 ASP Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain I residue 526 ASP Chi-restraints excluded: chain I residue 565 ASN Chi-restraints excluded: chain I residue 569 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 371 optimal weight: 4.9990 chunk 282 optimal weight: 0.8980 chunk 194 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 252 optimal weight: 0.8980 chunk 377 optimal weight: 2.9990 chunk 399 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 357 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 GLN A 468 GLN B 48 GLN B 147 ASN B 181 ASN B 383 GLN B 404 GLN B 554 ASN C 248 ASN C 383 GLN D 72 ASN D 383 GLN E 47 ASN E 95 ASN E 102 HIS E 137 HIS E 180 ASN E 181 ASN E 375 ASN E 483 HIS ** E 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN F 180 ASN G 47 ASN G 166 ASN G 310 GLN G 419 ASN G 550 GLN I 72 ASN I 147 ASN I 234 HIS I 302 ASN I 310 GLN I 459 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33478 Z= 0.258 Angle : 0.553 15.607 45788 Z= 0.276 Chirality : 0.043 0.186 4980 Planarity : 0.004 0.051 6021 Dihedral : 5.639 87.239 4446 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.57 % Allowed : 18.07 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.48 (0.13), residues: 3895 helix: -0.38 (0.42), residues: 116 sheet: -0.19 (0.16), residues: 1045 loop : -0.33 (0.11), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 414 HIS 0.009 0.001 HIS B 70 PHE 0.019 0.002 PHE C 535 TYR 0.022 0.002 TYR G 233 ARG 0.010 0.001 ARG C 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1097 time to evaluate : 3.334 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: 0.8674 (OUTLIER) cc_final: 0.8234 (t0) REVERT: A 48 GLN cc_start: 0.8067 (mt0) cc_final: 0.7782 (mt0) REVERT: A 52 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7844 (ttmt) REVERT: A 77 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7411 (mm-30) REVERT: A 87 MET cc_start: 0.7353 (ttm) cc_final: 0.7077 (ttm) REVERT: A 89 LYS cc_start: 0.8367 (ttmt) cc_final: 0.8141 (ttmt) REVERT: A 131 ASN cc_start: 0.8464 (m-40) cc_final: 0.7992 (m-40) REVERT: A 144 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7349 (mt-10) REVERT: A 221 SER cc_start: 0.8748 (m) cc_final: 0.8475 (t) REVERT: A 239 ASP cc_start: 0.7975 (t0) cc_final: 0.7632 (t0) REVERT: A 296 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7677 (mm-40) REVERT: A 302 ASN cc_start: 0.7428 (m110) cc_final: 0.6904 (m110) REVERT: A 313 ARG cc_start: 0.8737 (mtt180) cc_final: 0.8421 (mtt-85) REVERT: A 339 SER cc_start: 0.8693 (m) cc_final: 0.8029 (p) REVERT: A 401 ILE cc_start: 0.8418 (mm) cc_final: 0.8122 (pp) REVERT: A 439 LYS cc_start: 0.8585 (mmtp) cc_final: 0.8273 (mmtt) REVERT: A 460 VAL cc_start: 0.8828 (m) cc_final: 0.8526 (p) REVERT: A 511 ASP cc_start: 0.7485 (t0) cc_final: 0.7179 (t0) REVERT: A 519 SER cc_start: 0.8591 (t) cc_final: 0.8378 (t) REVERT: A 530 LYS cc_start: 0.8669 (ttmt) cc_final: 0.8443 (ttmt) REVERT: A 536 LYS cc_start: 0.8466 (ttpp) cc_final: 0.8260 (ttpp) REVERT: A 549 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7840 (tp40) REVERT: B 51 PHE cc_start: 0.8382 (m-80) cc_final: 0.8082 (m-80) REVERT: B 77 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7143 (tm-30) REVERT: B 87 MET cc_start: 0.7706 (ptm) cc_final: 0.7391 (ptm) REVERT: B 101 ILE cc_start: 0.8627 (mt) cc_final: 0.8285 (mt) REVERT: B 113 ASP cc_start: 0.7790 (t0) cc_final: 0.7523 (t0) REVERT: B 180 ASN cc_start: 0.8061 (m-40) cc_final: 0.7838 (m-40) REVERT: B 219 ILE cc_start: 0.8712 (mt) cc_final: 0.8451 (mm) REVERT: B 221 SER cc_start: 0.8781 (p) cc_final: 0.8459 (p) REVERT: B 234 HIS cc_start: 0.8509 (m170) cc_final: 0.8139 (m90) REVERT: B 271 LYS cc_start: 0.8262 (ptmt) cc_final: 0.7949 (ptmt) REVERT: B 382 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.8159 (mtm-85) REVERT: B 405 ASP cc_start: 0.6643 (m-30) cc_final: 0.6435 (m-30) REVERT: B 408 ARG cc_start: 0.4839 (mtm180) cc_final: 0.4000 (mtt-85) REVERT: B 411 GLU cc_start: 0.7916 (tt0) cc_final: 0.7294 (tt0) REVERT: B 479 LYS cc_start: 0.8583 (mmtm) cc_final: 0.7996 (mmtm) REVERT: B 549 GLN cc_start: 0.8040 (tt0) cc_final: 0.7825 (tt0) REVERT: B 553 ILE cc_start: 0.6403 (mp) cc_final: 0.5862 (tt) REVERT: B 573 TYR cc_start: 0.8019 (p90) cc_final: 0.7674 (p90) REVERT: B 575 LYS cc_start: 0.8196 (mttp) cc_final: 0.7931 (mmmm) REVERT: B 576 SER cc_start: 0.8534 (t) cc_final: 0.8046 (p) REVERT: C 52 LYS cc_start: 0.8239 (ttpt) cc_final: 0.7760 (ttpt) REVERT: C 71 LEU cc_start: 0.8355 (tp) cc_final: 0.8036 (tm) REVERT: C 77 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7238 (tm-30) REVERT: C 133 MET cc_start: 0.8057 (mmt) cc_final: 0.7508 (mmm) REVERT: C 155 GLU cc_start: 0.7023 (pp20) cc_final: 0.6737 (pp20) REVERT: C 186 THR cc_start: 0.8213 (m) cc_final: 0.7943 (p) REVERT: C 193 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7203 (mt-10) REVERT: C 204 ILE cc_start: 0.8990 (pt) cc_final: 0.8708 (pp) REVERT: C 221 SER cc_start: 0.8777 (p) cc_final: 0.8523 (t) REVERT: C 237 ASP cc_start: 0.7460 (t0) cc_final: 0.7219 (t0) REVERT: C 271 LYS cc_start: 0.8131 (ptmt) cc_final: 0.7796 (ptmt) REVERT: C 349 THR cc_start: 0.8316 (p) cc_final: 0.8034 (t) REVERT: C 382 ARG cc_start: 0.8511 (mtt90) cc_final: 0.8182 (mtt90) REVERT: C 404 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7187 (pp30) REVERT: C 470 TRP cc_start: 0.8725 (p90) cc_final: 0.8275 (p90) REVERT: C 473 GLU cc_start: 0.7920 (tp30) cc_final: 0.7608 (tp30) REVERT: C 479 LYS cc_start: 0.8556 (mttm) cc_final: 0.8269 (mttm) REVERT: C 501 LYS cc_start: 0.8652 (tttp) cc_final: 0.8344 (tttt) REVERT: C 509 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6856 (mm-30) REVERT: C 511 ASP cc_start: 0.7668 (t0) cc_final: 0.7311 (t0) REVERT: C 550 GLN cc_start: 0.5432 (mm-40) cc_final: 0.4909 (tp40) REVERT: C 574 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6847 (mm-30) REVERT: C 575 LYS cc_start: 0.8322 (mmtp) cc_final: 0.7962 (mmtp) REVERT: D 51 PHE cc_start: 0.8310 (m-80) cc_final: 0.7797 (m-80) REVERT: D 77 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7133 (mm-30) REVERT: D 82 VAL cc_start: 0.8401 (t) cc_final: 0.8057 (m) REVERT: D 101 ILE cc_start: 0.8576 (mt) cc_final: 0.8254 (mp) REVERT: D 122 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.7842 (p0) REVERT: D 125 ASP cc_start: 0.7818 (m-30) cc_final: 0.7520 (m-30) REVERT: D 182 THR cc_start: 0.8141 (m) cc_final: 0.7907 (p) REVERT: D 345 PHE cc_start: 0.8406 (m-80) cc_final: 0.7997 (m-80) REVERT: D 387 LYS cc_start: 0.8177 (tptm) cc_final: 0.7951 (tppp) REVERT: D 396 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7280 (tm-30) REVERT: D 400 TYR cc_start: 0.8580 (t80) cc_final: 0.8282 (t80) REVERT: D 511 ASP cc_start: 0.7893 (t0) cc_final: 0.7606 (t0) REVERT: D 574 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7343 (mm-30) REVERT: E 50 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7151 (mt-10) REVERT: E 60 GLU cc_start: 0.7283 (tt0) cc_final: 0.7063 (tt0) REVERT: E 77 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7320 (mm-30) REVERT: E 96 MET cc_start: 0.8012 (pmm) cc_final: 0.6387 (ptt) REVERT: E 101 ILE cc_start: 0.8522 (mt) cc_final: 0.8130 (mt) REVERT: E 135 GLU cc_start: 0.7793 (pt0) cc_final: 0.7474 (pt0) REVERT: E 146 PHE cc_start: 0.8521 (p90) cc_final: 0.8245 (p90) REVERT: E 149 VAL cc_start: 0.8910 (t) cc_final: 0.8386 (p) REVERT: E 151 LYS cc_start: 0.8574 (mtpp) cc_final: 0.8361 (mtpp) REVERT: E 163 LYS cc_start: 0.8082 (mttp) cc_final: 0.7840 (mttp) REVERT: E 167 ASN cc_start: 0.7452 (m-40) cc_final: 0.7117 (m-40) REVERT: E 179 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8263 (t) REVERT: E 193 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7362 (mt-10) REVERT: E 255 LEU cc_start: 0.8341 (mp) cc_final: 0.8056 (mm) REVERT: E 296 GLN cc_start: 0.8278 (mm-40) cc_final: 0.8047 (mm-40) REVERT: E 312 LYS cc_start: 0.5426 (tptp) cc_final: 0.4876 (mtpt) REVERT: E 314 ARG cc_start: 0.8144 (mtt90) cc_final: 0.7184 (mtt-85) REVERT: E 325 ILE cc_start: 0.8795 (mt) cc_final: 0.8457 (mp) REVERT: E 342 TYR cc_start: 0.7937 (p90) cc_final: 0.7675 (p90) REVERT: E 411 GLU cc_start: 0.7791 (mp0) cc_final: 0.7249 (mp0) REVERT: E 460 VAL cc_start: 0.8533 (p) cc_final: 0.8324 (m) REVERT: E 473 GLU cc_start: 0.8008 (tp30) cc_final: 0.7655 (tp30) REVERT: E 526 ASP cc_start: 0.7706 (p0) cc_final: 0.7166 (p0) REVERT: E 549 GLN cc_start: 0.8156 (tp40) cc_final: 0.7889 (tt0) REVERT: E 555 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8659 (m) REVERT: E 570 LYS cc_start: 0.8683 (ptmt) cc_final: 0.8454 (ptmm) REVERT: F 40 ILE cc_start: 0.8472 (mt) cc_final: 0.8100 (tp) REVERT: F 77 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7438 (mm-30) REVERT: F 163 LYS cc_start: 0.8221 (mttt) cc_final: 0.7955 (mttt) REVERT: F 173 LEU cc_start: 0.8748 (tp) cc_final: 0.8432 (tt) REVERT: F 185 PHE cc_start: 0.8577 (t80) cc_final: 0.8360 (t80) REVERT: F 192 SER cc_start: 0.8468 (t) cc_final: 0.8021 (p) REVERT: F 239 ASP cc_start: 0.7940 (m-30) cc_final: 0.7601 (m-30) REVERT: F 244 TYR cc_start: 0.8494 (m-80) cc_final: 0.8230 (m-80) REVERT: F 265 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8228 (p) REVERT: F 293 SER cc_start: 0.8448 (t) cc_final: 0.8080 (p) REVERT: F 297 SER cc_start: 0.8621 (t) cc_final: 0.8183 (p) REVERT: F 330 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8618 (mt) REVERT: F 331 MET cc_start: 0.8059 (ttp) cc_final: 0.7840 (ttp) REVERT: F 346 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7172 (mt-10) REVERT: F 413 ASP cc_start: 0.7533 (t70) cc_final: 0.7125 (t0) REVERT: F 434 ASP cc_start: 0.7740 (m-30) cc_final: 0.7463 (m-30) REVERT: F 566 ILE cc_start: 0.9105 (pt) cc_final: 0.8842 (OUTLIER) REVERT: F 570 LYS cc_start: 0.8763 (ptpt) cc_final: 0.8397 (ptmm) REVERT: G 49 THR cc_start: 0.8363 (m) cc_final: 0.7930 (p) REVERT: G 60 GLU cc_start: 0.7646 (tt0) cc_final: 0.7389 (tt0) REVERT: G 87 MET cc_start: 0.6904 (ptm) cc_final: 0.6602 (ptm) REVERT: G 89 LYS cc_start: 0.8576 (tttt) cc_final: 0.8260 (ttmm) REVERT: G 133 MET cc_start: 0.8296 (mmt) cc_final: 0.8007 (mmt) REVERT: G 135 GLU cc_start: 0.7928 (pt0) cc_final: 0.7564 (pt0) REVERT: G 151 LYS cc_start: 0.8593 (mttm) cc_final: 0.8382 (mttm) REVERT: G 177 LEU cc_start: 0.8335 (tp) cc_final: 0.8077 (tm) REVERT: G 201 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7971 (mtpt) REVERT: G 204 ILE cc_start: 0.8937 (pt) cc_final: 0.8697 (pp) REVERT: G 310 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8136 (mt0) REVERT: G 335 GLU cc_start: 0.7704 (tt0) cc_final: 0.7195 (tt0) REVERT: G 375 ASN cc_start: 0.7821 (m110) cc_final: 0.7473 (m110) REVERT: G 396 GLU cc_start: 0.7787 (tp30) cc_final: 0.7513 (tp30) REVERT: G 400 TYR cc_start: 0.8218 (t80) cc_final: 0.7886 (t80) REVERT: G 426 ASN cc_start: 0.8648 (t0) cc_final: 0.8378 (t0) REVERT: G 473 GLU cc_start: 0.7775 (tp30) cc_final: 0.7506 (tp30) REVERT: G 511 ASP cc_start: 0.7911 (t0) cc_final: 0.7652 (t0) REVERT: G 536 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7801 (ttpp) REVERT: G 549 GLN cc_start: 0.8092 (tp40) cc_final: 0.7655 (tp-100) REVERT: I 40 ILE cc_start: 0.8549 (mt) cc_final: 0.8318 (mp) REVERT: I 88 ASP cc_start: 0.7776 (t0) cc_final: 0.7530 (t0) REVERT: I 96 MET cc_start: 0.7973 (mpp) cc_final: 0.6469 (ppp) REVERT: I 193 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7278 (mt-10) REVERT: I 233 TYR cc_start: 0.8192 (t80) cc_final: 0.7512 (t80) REVERT: I 249 SER cc_start: 0.8531 (t) cc_final: 0.8058 (p) REVERT: I 303 PHE cc_start: 0.8313 (m-80) cc_final: 0.8008 (m-10) REVERT: I 312 LYS cc_start: 0.8582 (mttt) cc_final: 0.8263 (mttt) REVERT: I 346 GLU cc_start: 0.6046 (tt0) cc_final: 0.5560 (tt0) REVERT: I 375 ASN cc_start: 0.7767 (m110) cc_final: 0.7429 (m110) REVERT: I 380 PHE cc_start: 0.8641 (p90) cc_final: 0.8396 (p90) REVERT: I 387 LYS cc_start: 0.8661 (mmmm) cc_final: 0.8182 (mmmm) REVERT: I 439 LYS cc_start: 0.4412 (mmtt) cc_final: 0.2451 (mmmt) REVERT: I 501 LYS cc_start: 0.8537 (tttt) cc_final: 0.8152 (tttm) REVERT: I 518 MET cc_start: 0.6933 (ptp) cc_final: 0.6539 (ptp) REVERT: I 546 ASN cc_start: 0.8471 (p0) cc_final: 0.8240 (p0) outliers start: 124 outliers final: 78 residues processed: 1137 average time/residue: 1.2738 time to fit residues: 1739.5510 Evaluate side-chains 1143 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1058 time to evaluate : 3.336 ------------------------------------------------------------------------------- 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 164 VAL 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 271 LYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 493 ASN Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 556 ASP 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 206 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 271 LYS Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 310 GLN Chi-restraints excluded: chain G residue 354 LYS Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 168 ASP Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 526 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 332 optimal weight: 6.9990 chunk 226 optimal weight: 0.0570 chunk 5 optimal weight: 50.0000 chunk 297 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 340 optimal weight: 6.9990 chunk 275 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 203 optimal weight: 5.9990 chunk 358 optimal weight: 0.0870 chunk 100 optimal weight: 6.9990 overall best weight: 3.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN B 48 GLN B 115 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 468 GLN B 565 ASN C 383 GLN D 350 GLN D 383 GLN E 47 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 ASN E 102 HIS E 137 HIS E 180 ASN E 483 HIS E 497 GLN F 180 ASN ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 ASN G 310 GLN G 383 GLN I 72 ASN I 147 ASN I 234 HIS I 302 ASN I 310 GLN I 416 GLN I 459 ASN I 549 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 33478 Z= 0.360 Angle : 0.573 15.596 45788 Z= 0.285 Chirality : 0.044 0.185 4980 Planarity : 0.005 0.051 6021 Dihedral : 5.562 88.411 4446 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.44 % Allowed : 18.22 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.49 (0.13), residues: 3895 helix: -0.33 (0.43), residues: 116 sheet: -0.21 (0.16), residues: 1040 loop : -0.33 (0.11), residues: 2739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 545 HIS 0.009 0.001 HIS B 70 PHE 0.029 0.002 PHE I 266 TYR 0.022 0.002 TYR A 444 ARG 0.010 0.001 ARG C 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1228 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1074 time to evaluate : 3.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8230 (t0) REVERT: A 48 GLN cc_start: 0.8087 (mt0) cc_final: 0.7800 (mt0) REVERT: A 52 LYS cc_start: 0.8201 (ttmt) cc_final: 0.7896 (ttmt) REVERT: A 77 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7416 (mm-30) REVERT: A 87 MET cc_start: 0.7337 (ttm) cc_final: 0.7069 (ttm) REVERT: A 89 LYS cc_start: 0.8387 (ttmt) cc_final: 0.8180 (ttmt) REVERT: A 144 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7346 (mt-10) REVERT: A 221 SER cc_start: 0.8714 (m) cc_final: 0.8448 (t) REVERT: A 239 ASP cc_start: 0.7864 (t0) cc_final: 0.7513 (t0) REVERT: A 296 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7662 (mm-40) REVERT: A 302 ASN cc_start: 0.7466 (m110) cc_final: 0.6934 (m110) REVERT: A 313 ARG cc_start: 0.8749 (mtt180) cc_final: 0.8437 (mtt-85) REVERT: A 339 SER cc_start: 0.8732 (m) cc_final: 0.8092 (p) REVERT: A 401 ILE cc_start: 0.8443 (mm) cc_final: 0.8119 (pp) REVERT: A 439 LYS cc_start: 0.8602 (mmtp) cc_final: 0.8296 (mmtt) REVERT: A 460 VAL cc_start: 0.8817 (m) cc_final: 0.8537 (p) REVERT: A 511 ASP cc_start: 0.7488 (t0) cc_final: 0.7153 (t0) REVERT: A 519 SER cc_start: 0.8608 (t) cc_final: 0.8390 (t) REVERT: A 530 LYS cc_start: 0.8697 (ttmt) cc_final: 0.8465 (ttmt) REVERT: A 536 LYS cc_start: 0.8478 (ttpp) cc_final: 0.8270 (ttpp) REVERT: A 549 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7801 (tp40) REVERT: B 51 PHE cc_start: 0.8381 (m-80) cc_final: 0.8089 (m-80) REVERT: B 77 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7132 (tm-30) REVERT: B 78 ASN cc_start: 0.8459 (p0) cc_final: 0.8257 (p0) REVERT: B 87 MET cc_start: 0.7700 (ptm) cc_final: 0.7379 (ptm) REVERT: B 101 ILE cc_start: 0.8623 (mt) cc_final: 0.8267 (mt) REVERT: B 113 ASP cc_start: 0.7788 (t0) cc_final: 0.7499 (t0) REVERT: B 154 SER cc_start: 0.8680 (m) cc_final: 0.8233 (t) REVERT: B 180 ASN cc_start: 0.8067 (m-40) cc_final: 0.7826 (m-40) REVERT: B 217 THR cc_start: 0.8166 (p) cc_final: 0.7927 (p) REVERT: B 219 ILE cc_start: 0.8732 (mt) cc_final: 0.8529 (mm) REVERT: B 221 SER cc_start: 0.8658 (p) cc_final: 0.8315 (p) REVERT: B 271 LYS cc_start: 0.8279 (ptmt) cc_final: 0.7961 (ptmt) REVERT: B 408 ARG cc_start: 0.4859 (mtm180) cc_final: 0.4026 (mtt-85) REVERT: B 411 GLU cc_start: 0.7965 (tt0) cc_final: 0.7419 (tt0) REVERT: B 439 LYS cc_start: 0.8624 (mmtm) cc_final: 0.8316 (mmtt) REVERT: B 479 LYS cc_start: 0.8585 (mmtm) cc_final: 0.7988 (mmtm) REVERT: B 549 GLN cc_start: 0.8056 (tt0) cc_final: 0.7844 (tt0) REVERT: B 553 ILE cc_start: 0.6359 (mp) cc_final: 0.5820 (tt) REVERT: B 573 TYR cc_start: 0.7982 (p90) cc_final: 0.7733 (p90) REVERT: B 576 SER cc_start: 0.8532 (t) cc_final: 0.8045 (p) REVERT: B 582 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7922 (mtmm) REVERT: C 52 LYS cc_start: 0.8212 (ttpt) cc_final: 0.7704 (ttpt) REVERT: C 71 LEU cc_start: 0.8370 (tp) cc_final: 0.8081 (tm) REVERT: C 77 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7272 (tm-30) REVERT: C 155 GLU cc_start: 0.7157 (pp20) cc_final: 0.6831 (pp20) REVERT: C 186 THR cc_start: 0.8213 (m) cc_final: 0.7963 (p) REVERT: C 193 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7213 (mt-10) REVERT: C 204 ILE cc_start: 0.8983 (pt) cc_final: 0.8707 (pp) REVERT: C 221 SER cc_start: 0.8725 (p) cc_final: 0.8475 (t) REVERT: C 237 ASP cc_start: 0.7489 (t0) cc_final: 0.7241 (t0) REVERT: C 260 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7197 (mt-10) REVERT: C 349 THR cc_start: 0.8342 (p) cc_final: 0.8039 (t) REVERT: C 382 ARG cc_start: 0.8497 (mtt90) cc_final: 0.8228 (mtt90) REVERT: C 397 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7437 (mtm-85) REVERT: C 404 GLN cc_start: 0.7618 (pp30) cc_final: 0.7263 (pp30) REVERT: C 470 TRP cc_start: 0.8725 (p90) cc_final: 0.8288 (p90) REVERT: C 479 LYS cc_start: 0.8573 (mttm) cc_final: 0.8349 (mttm) REVERT: C 501 LYS cc_start: 0.8706 (tttp) cc_final: 0.8437 (tttt) REVERT: C 509 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6886 (mm-30) REVERT: C 511 ASP cc_start: 0.7693 (t0) cc_final: 0.7364 (t0) REVERT: C 550 GLN cc_start: 0.5287 (mm-40) cc_final: 0.4828 (tp40) REVERT: C 575 LYS cc_start: 0.8337 (mmtp) cc_final: 0.7973 (mmtp) REVERT: D 51 PHE cc_start: 0.8318 (m-80) cc_final: 0.7815 (m-80) REVERT: D 77 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7111 (mm-30) REVERT: D 82 VAL cc_start: 0.8381 (t) cc_final: 0.8041 (m) REVERT: D 101 ILE cc_start: 0.8609 (mt) cc_final: 0.8267 (mp) REVERT: D 122 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.7750 (p0) REVERT: D 125 ASP cc_start: 0.7833 (m-30) cc_final: 0.7523 (m-30) REVERT: D 142 GLU cc_start: 0.8004 (pt0) cc_final: 0.7800 (pt0) REVERT: D 182 THR cc_start: 0.8154 (m) cc_final: 0.7942 (p) REVERT: D 257 THR cc_start: 0.7829 (t) cc_final: 0.7431 (m) REVERT: D 387 LYS cc_start: 0.8136 (tptm) cc_final: 0.7845 (tppp) REVERT: D 396 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7306 (tm-30) REVERT: D 400 TYR cc_start: 0.8619 (t80) cc_final: 0.8355 (t80) REVERT: D 492 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7967 (p0) REVERT: D 511 ASP cc_start: 0.7872 (t0) cc_final: 0.7556 (t0) REVERT: D 530 LYS cc_start: 0.8853 (ttmt) cc_final: 0.8577 (ttpt) REVERT: D 532 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8298 (ttpp) REVERT: D 574 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7326 (mm-30) REVERT: D 583 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7641 (mt) REVERT: E 50 GLU cc_start: 0.7292 (mt-10) cc_final: 0.7090 (mt-10) REVERT: E 60 GLU cc_start: 0.7298 (tt0) cc_final: 0.7075 (tt0) REVERT: E 96 MET cc_start: 0.8103 (pmm) cc_final: 0.6555 (ptt) REVERT: E 101 ILE cc_start: 0.8484 (mt) cc_final: 0.8144 (mt) REVERT: E 133 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7803 (mpp) REVERT: E 135 GLU cc_start: 0.7803 (pt0) cc_final: 0.7499 (pt0) REVERT: E 149 VAL cc_start: 0.8932 (t) cc_final: 0.8410 (p) REVERT: E 163 LYS cc_start: 0.8080 (mttp) cc_final: 0.7849 (mttp) REVERT: E 179 SER cc_start: 0.8476 (OUTLIER) cc_final: 0.8270 (t) REVERT: E 193 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7338 (mt-10) REVERT: E 255 LEU cc_start: 0.8348 (mp) cc_final: 0.8059 (mm) REVERT: E 296 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8029 (mm-40) REVERT: E 312 LYS cc_start: 0.5479 (tptp) cc_final: 0.4952 (mtpt) REVERT: E 314 ARG cc_start: 0.8144 (mtt90) cc_final: 0.7139 (mtt-85) REVERT: E 325 ILE cc_start: 0.8799 (mt) cc_final: 0.8471 (mp) REVERT: E 411 GLU cc_start: 0.7788 (mp0) cc_final: 0.7239 (mp0) REVERT: E 526 ASP cc_start: 0.7731 (p0) cc_final: 0.7206 (p0) REVERT: E 549 GLN cc_start: 0.8109 (tp40) cc_final: 0.7832 (tt0) REVERT: E 570 LYS cc_start: 0.8716 (ptmt) cc_final: 0.8494 (ptmm) REVERT: F 40 ILE cc_start: 0.8468 (mt) cc_final: 0.8071 (tp) REVERT: F 77 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7416 (mm-30) REVERT: F 89 LYS cc_start: 0.8390 (tppt) cc_final: 0.8022 (tppt) REVERT: F 163 LYS cc_start: 0.8239 (mttt) cc_final: 0.7977 (mttt) REVERT: F 173 LEU cc_start: 0.8744 (tp) cc_final: 0.8395 (tt) REVERT: F 185 PHE cc_start: 0.8573 (t80) cc_final: 0.8369 (t80) REVERT: F 192 SER cc_start: 0.8467 (t) cc_final: 0.8014 (p) REVERT: F 239 ASP cc_start: 0.7949 (m-30) cc_final: 0.7571 (m-30) REVERT: F 244 TYR cc_start: 0.8474 (m-80) cc_final: 0.8234 (m-80) REVERT: F 265 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8269 (p) REVERT: F 293 SER cc_start: 0.8465 (t) cc_final: 0.8099 (p) REVERT: F 297 SER cc_start: 0.8643 (t) cc_final: 0.8217 (p) REVERT: F 330 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8645 (mt) REVERT: F 346 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7209 (mt-10) REVERT: F 413 ASP cc_start: 0.7535 (t70) cc_final: 0.7145 (t0) REVERT: F 434 ASP cc_start: 0.7734 (m-30) cc_final: 0.7457 (m-30) REVERT: F 566 ILE cc_start: 0.9121 (pt) cc_final: 0.8828 (pp) REVERT: G 49 THR cc_start: 0.8376 (m) cc_final: 0.7934 (p) REVERT: G 60 GLU cc_start: 0.7627 (tt0) cc_final: 0.7365 (tt0) REVERT: G 77 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7259 (mm-30) REVERT: G 87 MET cc_start: 0.6915 (ptm) cc_final: 0.6636 (ptm) REVERT: G 89 LYS cc_start: 0.8630 (tttt) cc_final: 0.8277 (ttmm) REVERT: G 133 MET cc_start: 0.8300 (mmt) cc_final: 0.7988 (mmt) REVERT: G 135 GLU cc_start: 0.7935 (pt0) cc_final: 0.7515 (pt0) REVERT: G 151 LYS cc_start: 0.8610 (mttm) cc_final: 0.8381 (mttm) REVERT: G 177 LEU cc_start: 0.8342 (tp) cc_final: 0.8076 (tm) REVERT: G 201 LYS cc_start: 0.8290 (mtpt) cc_final: 0.7972 (mtpt) REVERT: G 204 ILE cc_start: 0.8959 (pt) cc_final: 0.8715 (pp) REVERT: G 237 ASP cc_start: 0.7788 (t0) cc_final: 0.7552 (m-30) REVERT: G 260 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6863 (mt-10) REVERT: G 310 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8123 (mt0) REVERT: G 335 GLU cc_start: 0.7708 (tt0) cc_final: 0.7205 (tt0) REVERT: G 350 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: G 375 ASN cc_start: 0.7818 (m110) cc_final: 0.7481 (m110) REVERT: G 393 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7327 (mt-10) REVERT: G 396 GLU cc_start: 0.7783 (tp30) cc_final: 0.7498 (tp30) REVERT: G 401 ILE cc_start: 0.8534 (mm) cc_final: 0.8276 (mp) REVERT: G 426 ASN cc_start: 0.8649 (t0) cc_final: 0.8393 (t0) REVERT: G 473 GLU cc_start: 0.7772 (tp30) cc_final: 0.7523 (tp30) REVERT: G 511 ASP cc_start: 0.7893 (t0) cc_final: 0.7662 (t0) REVERT: G 532 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8431 (ttpp) REVERT: G 536 LYS cc_start: 0.8104 (ttpp) cc_final: 0.7825 (ttpp) REVERT: G 549 GLN cc_start: 0.8087 (tp40) cc_final: 0.7594 (tp40) REVERT: I 40 ILE cc_start: 0.8551 (mt) cc_final: 0.8319 (mp) REVERT: I 88 ASP cc_start: 0.7788 (t0) cc_final: 0.7541 (t0) REVERT: I 89 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8239 (ttmt) REVERT: I 96 MET cc_start: 0.7976 (mpp) cc_final: 0.6459 (ppp) REVERT: I 100 ASP cc_start: 0.7190 (m-30) cc_final: 0.6908 (m-30) REVERT: I 193 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7297 (mt-10) REVERT: I 249 SER cc_start: 0.8548 (t) cc_final: 0.8086 (p) REVERT: I 303 PHE cc_start: 0.8320 (m-80) cc_final: 0.8022 (m-10) REVERT: I 312 LYS cc_start: 0.8588 (mttt) cc_final: 0.8252 (mttt) REVERT: I 380 PHE cc_start: 0.8654 (p90) cc_final: 0.8415 (p90) REVERT: I 387 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8383 (mtpp) REVERT: I 436 ILE cc_start: 0.8642 (mm) cc_final: 0.8399 (mp) REVERT: I 439 LYS cc_start: 0.4134 (mmtt) cc_final: 0.2601 (mmmt) REVERT: I 450 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8248 (p) REVERT: I 501 LYS cc_start: 0.8552 (tttt) cc_final: 0.8289 (tttm) REVERT: I 518 MET cc_start: 0.6957 (ptp) cc_final: 0.6559 (ptp) REVERT: I 546 ASN cc_start: 0.8541 (p0) cc_final: 0.8335 (p0) outliers start: 154 outliers final: 90 residues processed: 1125 average time/residue: 1.2846 time to fit residues: 1733.7096 Evaluate side-chains 1152 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1048 time to evaluate : 3.413 ------------------------------------------------------------------------------- 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 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 582 LYS Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 492 ASN Chi-restraints excluded: chain D residue 493 ASN Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 310 GLN Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 350 GLN Chi-restraints excluded: chain G residue 354 LYS Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 168 ASP Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 387 LYS Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain I residue 526 ASP Chi-restraints excluded: chain I residue 553 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 134 optimal weight: 2.9990 chunk 359 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 234 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 399 optimal weight: 0.3980 chunk 331 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 GLN A 468 GLN B 48 GLN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN B 404 GLN B 468 GLN B 565 ASN D 248 ASN D 350 GLN D 383 GLN D 459 ASN E 47 ASN E 102 HIS E 137 HIS E 180 ASN E 181 ASN E 483 HIS F 180 ASN F 505 ASN G 310 GLN I 72 ASN I 147 ASN I 234 HIS I 302 ASN I 459 ASN I 549 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 33478 Z= 0.362 Angle : 0.575 15.636 45788 Z= 0.286 Chirality : 0.044 0.185 4980 Planarity : 0.004 0.052 6021 Dihedral : 5.501 89.617 4446 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.53 % Allowed : 18.56 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.49 (0.13), residues: 3895 helix: -0.36 (0.43), residues: 116 sheet: -0.22 (0.16), residues: 1042 loop : -0.32 (0.11), residues: 2737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 545 HIS 0.008 0.001 HIS B 70 PHE 0.025 0.002 PHE F 380 TYR 0.025 0.002 TYR A 444 ARG 0.010 0.001 ARG C 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1228 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1071 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8241 (t0) REVERT: A 48 GLN cc_start: 0.8097 (mt0) cc_final: 0.7831 (mt0) REVERT: A 52 LYS cc_start: 0.8215 (ttmt) cc_final: 0.7898 (ttmt) REVERT: A 77 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7388 (mm-30) REVERT: A 87 MET cc_start: 0.7333 (ttm) cc_final: 0.7109 (ttt) REVERT: A 142 GLU cc_start: 0.8009 (pt0) cc_final: 0.7749 (pt0) REVERT: A 144 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7366 (mt-10) REVERT: A 221 SER cc_start: 0.8707 (m) cc_final: 0.8437 (t) REVERT: A 239 ASP cc_start: 0.7824 (t0) cc_final: 0.7532 (t0) REVERT: A 245 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7822 (m) REVERT: A 296 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7645 (mm-40) REVERT: A 302 ASN cc_start: 0.7479 (m110) cc_final: 0.6942 (m110) REVERT: A 313 ARG cc_start: 0.8745 (mtt180) cc_final: 0.8405 (mtt-85) REVERT: A 339 SER cc_start: 0.8740 (m) cc_final: 0.8087 (p) REVERT: A 401 ILE cc_start: 0.8448 (mm) cc_final: 0.8120 (pp) REVERT: A 439 LYS cc_start: 0.8597 (mmtp) cc_final: 0.8299 (mmtt) REVERT: A 460 VAL cc_start: 0.8829 (m) cc_final: 0.8532 (p) REVERT: A 511 ASP cc_start: 0.7516 (t0) cc_final: 0.7149 (t0) REVERT: A 519 SER cc_start: 0.8611 (t) cc_final: 0.8387 (t) REVERT: A 530 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8449 (ttmt) REVERT: A 549 GLN cc_start: 0.8142 (tp-100) cc_final: 0.7868 (tp40) REVERT: B 51 PHE cc_start: 0.8376 (m-80) cc_final: 0.8091 (m-80) REVERT: B 77 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7096 (tm-30) REVERT: B 87 MET cc_start: 0.7685 (ptm) cc_final: 0.7357 (ptm) REVERT: B 101 ILE cc_start: 0.8629 (mt) cc_final: 0.8166 (mt) REVERT: B 113 ASP cc_start: 0.7793 (t0) cc_final: 0.7502 (t0) REVERT: B 154 SER cc_start: 0.8709 (m) cc_final: 0.8273 (t) REVERT: B 172 SER cc_start: 0.8593 (p) cc_final: 0.8330 (p) REVERT: B 180 ASN cc_start: 0.8066 (m-40) cc_final: 0.7841 (m-40) REVERT: B 221 SER cc_start: 0.8653 (p) cc_final: 0.8350 (p) REVERT: B 271 LYS cc_start: 0.8294 (ptmt) cc_final: 0.7974 (ptmt) REVERT: B 408 ARG cc_start: 0.4855 (mtm180) cc_final: 0.3990 (mtt-85) REVERT: B 411 GLU cc_start: 0.7971 (tt0) cc_final: 0.7425 (tt0) REVERT: B 439 LYS cc_start: 0.8628 (mmtm) cc_final: 0.8332 (mmtt) REVERT: B 479 LYS cc_start: 0.8585 (mmtm) cc_final: 0.7982 (mmtm) REVERT: B 549 GLN cc_start: 0.8041 (tt0) cc_final: 0.7841 (tt0) REVERT: B 553 ILE cc_start: 0.6350 (mp) cc_final: 0.5805 (tt) REVERT: B 576 SER cc_start: 0.8500 (t) cc_final: 0.8022 (p) REVERT: B 582 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7917 (mtmm) REVERT: C 52 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7738 (ttpt) REVERT: C 71 LEU cc_start: 0.8399 (tp) cc_final: 0.8117 (tm) REVERT: C 77 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7276 (tm-30) REVERT: C 133 MET cc_start: 0.8041 (mmt) cc_final: 0.7507 (mmm) REVERT: C 155 GLU cc_start: 0.7165 (pp20) cc_final: 0.6828 (pp20) REVERT: C 186 THR cc_start: 0.8189 (m) cc_final: 0.7963 (p) REVERT: C 193 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7209 (mt-10) REVERT: C 204 ILE cc_start: 0.8982 (pt) cc_final: 0.8706 (pp) REVERT: C 221 SER cc_start: 0.8741 (p) cc_final: 0.8511 (t) REVERT: C 237 ASP cc_start: 0.7494 (t0) cc_final: 0.7233 (t0) REVERT: C 349 THR cc_start: 0.8318 (p) cc_final: 0.8031 (t) REVERT: C 382 ARG cc_start: 0.8490 (mtt90) cc_final: 0.8258 (mtt90) REVERT: C 397 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7417 (mtm-85) REVERT: C 404 GLN cc_start: 0.7623 (pp30) cc_final: 0.7333 (pp30) REVERT: C 479 LYS cc_start: 0.8579 (mttm) cc_final: 0.8340 (mttm) REVERT: C 501 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8413 (tttt) REVERT: C 509 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6917 (mm-30) REVERT: C 511 ASP cc_start: 0.7668 (t0) cc_final: 0.7310 (t0) REVERT: C 550 GLN cc_start: 0.4456 (mm-40) cc_final: 0.4184 (tp40) REVERT: C 574 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6951 (mm-30) REVERT: D 51 PHE cc_start: 0.8334 (m-80) cc_final: 0.7813 (m-80) REVERT: D 77 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7135 (mm-30) REVERT: D 82 VAL cc_start: 0.8370 (t) cc_final: 0.8031 (m) REVERT: D 101 ILE cc_start: 0.8647 (mt) cc_final: 0.8317 (mp) REVERT: D 122 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.7754 (p0) REVERT: D 125 ASP cc_start: 0.7840 (m-30) cc_final: 0.7522 (m-30) REVERT: D 142 GLU cc_start: 0.7995 (pt0) cc_final: 0.7787 (pt0) REVERT: D 257 THR cc_start: 0.7856 (t) cc_final: 0.7449 (m) REVERT: D 387 LYS cc_start: 0.8138 (tptm) cc_final: 0.7880 (tppp) REVERT: D 396 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7324 (mm-30) REVERT: D 400 TYR cc_start: 0.8641 (t80) cc_final: 0.8366 (t80) REVERT: D 511 ASP cc_start: 0.7859 (t0) cc_final: 0.7538 (t0) REVERT: D 532 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8364 (ttpp) REVERT: D 574 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7322 (mm-30) REVERT: D 583 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7761 (mt) REVERT: E 50 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7087 (mt-10) REVERT: E 60 GLU cc_start: 0.7298 (tt0) cc_final: 0.7076 (tt0) REVERT: E 77 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6984 (mm-30) REVERT: E 96 MET cc_start: 0.8121 (pmm) cc_final: 0.6544 (ptt) REVERT: E 101 ILE cc_start: 0.8496 (mt) cc_final: 0.8142 (mt) REVERT: E 133 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7803 (mpp) REVERT: E 135 GLU cc_start: 0.7832 (pt0) cc_final: 0.7540 (pt0) REVERT: E 149 VAL cc_start: 0.8948 (t) cc_final: 0.8391 (p) REVERT: E 163 LYS cc_start: 0.8082 (mttp) cc_final: 0.7852 (mttp) REVERT: E 179 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8262 (t) REVERT: E 193 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7305 (mt-10) REVERT: E 255 LEU cc_start: 0.8351 (mp) cc_final: 0.8066 (mm) REVERT: E 296 GLN cc_start: 0.8270 (mm-40) cc_final: 0.8010 (mm-40) REVERT: E 305 ASP cc_start: 0.8409 (m-30) cc_final: 0.5743 (m-30) REVERT: E 312 LYS cc_start: 0.5533 (tptp) cc_final: 0.4745 (tptp) REVERT: E 314 ARG cc_start: 0.8144 (mtt90) cc_final: 0.7227 (mtp180) REVERT: E 325 ILE cc_start: 0.8779 (mt) cc_final: 0.8464 (mp) REVERT: E 411 GLU cc_start: 0.7773 (mp0) cc_final: 0.7227 (mp0) REVERT: E 497 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8120 (mt0) REVERT: E 526 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7206 (p0) REVERT: E 570 LYS cc_start: 0.8711 (ptmt) cc_final: 0.8491 (ptmm) REVERT: F 40 ILE cc_start: 0.8407 (mt) cc_final: 0.8015 (tp) REVERT: F 77 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7420 (mm-30) REVERT: F 89 LYS cc_start: 0.8386 (tppt) cc_final: 0.8026 (tppt) REVERT: F 163 LYS cc_start: 0.8238 (mttt) cc_final: 0.7968 (mttt) REVERT: F 173 LEU cc_start: 0.8768 (tp) cc_final: 0.8458 (tt) REVERT: F 192 SER cc_start: 0.8462 (t) cc_final: 0.8017 (p) REVERT: F 239 ASP cc_start: 0.7945 (m-30) cc_final: 0.7562 (m-30) REVERT: F 244 TYR cc_start: 0.8481 (m-80) cc_final: 0.8213 (m-80) REVERT: F 265 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8307 (p) REVERT: F 293 SER cc_start: 0.8477 (t) cc_final: 0.8108 (p) REVERT: F 346 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7271 (mt-10) REVERT: F 413 ASP cc_start: 0.7535 (t70) cc_final: 0.7151 (t0) REVERT: F 434 ASP cc_start: 0.7747 (m-30) cc_final: 0.7475 (m-30) REVERT: F 566 ILE cc_start: 0.9084 (pt) cc_final: 0.8796 (pp) REVERT: G 60 GLU cc_start: 0.7622 (tt0) cc_final: 0.7359 (tt0) REVERT: G 87 MET cc_start: 0.6927 (ptm) cc_final: 0.6717 (ptm) REVERT: G 89 LYS cc_start: 0.8648 (tttt) cc_final: 0.8291 (ttmm) REVERT: G 133 MET cc_start: 0.8292 (mmt) cc_final: 0.7971 (mmt) REVERT: G 135 GLU cc_start: 0.7929 (pt0) cc_final: 0.7456 (pt0) REVERT: G 151 LYS cc_start: 0.8612 (mttm) cc_final: 0.8387 (mttm) REVERT: G 172 SER cc_start: 0.8620 (p) cc_final: 0.8208 (m) REVERT: G 177 LEU cc_start: 0.8350 (tp) cc_final: 0.8086 (tm) REVERT: G 201 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7989 (mtpt) REVERT: G 204 ILE cc_start: 0.8868 (pt) cc_final: 0.8634 (pp) REVERT: G 237 ASP cc_start: 0.7820 (t0) cc_final: 0.7559 (m-30) REVERT: G 260 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6852 (mt-10) REVERT: G 274 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7204 (mtp-110) REVERT: G 310 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8076 (mt0) REVERT: G 335 GLU cc_start: 0.7715 (tt0) cc_final: 0.7201 (tt0) REVERT: G 350 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8316 (mt0) REVERT: G 375 ASN cc_start: 0.7802 (m110) cc_final: 0.7476 (m110) REVERT: G 393 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7311 (mt-10) REVERT: G 396 GLU cc_start: 0.7774 (tp30) cc_final: 0.7496 (tp30) REVERT: G 401 ILE cc_start: 0.8540 (mm) cc_final: 0.8294 (mp) REVERT: G 426 ASN cc_start: 0.8642 (t0) cc_final: 0.8398 (t0) REVERT: G 473 GLU cc_start: 0.7735 (tp30) cc_final: 0.7479 (tp30) REVERT: G 511 ASP cc_start: 0.7904 (t0) cc_final: 0.7667 (t0) REVERT: G 532 LYS cc_start: 0.8838 (ttmt) cc_final: 0.8418 (ttpp) REVERT: G 536 LYS cc_start: 0.8116 (ttpp) cc_final: 0.7819 (ttpp) REVERT: G 549 GLN cc_start: 0.8085 (tp40) cc_final: 0.7596 (tp40) REVERT: I 40 ILE cc_start: 0.8545 (mt) cc_final: 0.8316 (mp) REVERT: I 76 SER cc_start: 0.8405 (p) cc_final: 0.8197 (t) REVERT: I 88 ASP cc_start: 0.7794 (t0) cc_final: 0.7547 (t0) REVERT: I 89 LYS cc_start: 0.8528 (ttmt) cc_final: 0.8241 (ttmt) REVERT: I 96 MET cc_start: 0.7983 (mpp) cc_final: 0.6447 (ppp) REVERT: I 100 ASP cc_start: 0.7175 (m-30) cc_final: 0.6907 (m-30) REVERT: I 183 MET cc_start: 0.8317 (mmm) cc_final: 0.8063 (mmm) REVERT: I 193 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7292 (mt-10) REVERT: I 249 SER cc_start: 0.8553 (t) cc_final: 0.8104 (p) REVERT: I 303 PHE cc_start: 0.8317 (m-80) cc_final: 0.8020 (m-10) REVERT: I 312 LYS cc_start: 0.8622 (mttt) cc_final: 0.8278 (mttt) REVERT: I 380 PHE cc_start: 0.8656 (p90) cc_final: 0.8433 (p90) REVERT: I 387 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8382 (mtpp) REVERT: I 436 ILE cc_start: 0.8625 (mm) cc_final: 0.8391 (mp) REVERT: I 439 LYS cc_start: 0.4170 (mmtt) cc_final: 0.2618 (mmmt) REVERT: I 450 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8220 (p) REVERT: I 501 LYS cc_start: 0.8550 (tttt) cc_final: 0.8292 (tttm) REVERT: I 518 MET cc_start: 0.6996 (ptp) cc_final: 0.6601 (ptp) outliers start: 157 outliers final: 101 residues processed: 1125 average time/residue: 1.2977 time to fit residues: 1751.3168 Evaluate side-chains 1172 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1054 time to evaluate : 3.868 ------------------------------------------------------------------------------- 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 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 403 HIS Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 582 LYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 493 ASN Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 403 HIS Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 497 GLN Chi-restraints excluded: chain E residue 526 ASP Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 274 ARG Chi-restraints excluded: chain G residue 310 GLN Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 350 GLN Chi-restraints excluded: chain G residue 354 LYS Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 168 ASP Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 387 LYS Chi-restraints excluded: chain I residue 429 VAL Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain I residue 526 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 385 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 227 optimal weight: 9.9990 chunk 291 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 336 optimal weight: 0.7980 chunk 223 optimal weight: 10.0000 chunk 398 optimal weight: 0.0070 chunk 249 optimal weight: 6.9990 chunk 242 optimal weight: 0.0070 chunk 183 optimal weight: 5.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN A 558 GLN B 48 GLN B 234 HIS ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN B 404 GLN C 383 GLN D 350 GLN D 383 GLN E 47 ASN E 102 HIS E 137 HIS E 180 ASN E 483 HIS E 497 GLN F 180 ASN F 505 ASN G 242 GLN G 310 GLN G 318 GLN I 72 ASN I 147 ASN I 302 ASN I 459 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 33478 Z= 0.129 Angle : 0.514 15.546 45788 Z= 0.253 Chirality : 0.041 0.182 4980 Planarity : 0.004 0.048 6021 Dihedral : 5.003 89.273 4445 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.37 % Allowed : 20.47 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.27 (0.13), residues: 3895 helix: -0.35 (0.43), residues: 111 sheet: -0.15 (0.16), residues: 1030 loop : -0.12 (0.12), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 414 HIS 0.007 0.001 HIS B 70 PHE 0.018 0.001 PHE C 268 TYR 0.025 0.001 TYR A 444 ARG 0.012 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1212 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1095 time to evaluate : 3.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8278 (t0) REVERT: A 48 GLN cc_start: 0.8015 (mt0) cc_final: 0.7718 (mt0) REVERT: A 52 LYS cc_start: 0.8158 (ttmt) cc_final: 0.7831 (ttmt) REVERT: A 77 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7343 (mm-30) REVERT: A 87 MET cc_start: 0.7336 (ttm) cc_final: 0.7073 (ttm) REVERT: A 144 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7289 (mt-10) REVERT: A 239 ASP cc_start: 0.7885 (t0) cc_final: 0.7481 (t0) REVERT: A 249 SER cc_start: 0.8068 (p) cc_final: 0.7841 (p) REVERT: A 280 GLN cc_start: 0.8496 (mt0) cc_final: 0.8287 (mt0) REVERT: A 296 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7651 (mm-40) REVERT: A 302 ASN cc_start: 0.7511 (m110) cc_final: 0.6990 (m110) REVERT: A 339 SER cc_start: 0.8654 (m) cc_final: 0.7984 (p) REVERT: A 439 LYS cc_start: 0.8489 (mmtp) cc_final: 0.8215 (mmtt) REVERT: A 460 VAL cc_start: 0.8833 (m) cc_final: 0.8531 (p) REVERT: A 511 ASP cc_start: 0.7338 (t0) cc_final: 0.7057 (t0) REVERT: A 519 SER cc_start: 0.8619 (t) cc_final: 0.8410 (t) REVERT: A 530 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8396 (ttpp) REVERT: B 53 PHE cc_start: 0.8503 (m-80) cc_final: 0.8159 (m-80) REVERT: B 77 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7039 (tm-30) REVERT: B 87 MET cc_start: 0.7619 (ptm) cc_final: 0.7293 (ptm) REVERT: B 101 ILE cc_start: 0.8652 (mt) cc_final: 0.8165 (mt) REVERT: B 113 ASP cc_start: 0.7782 (t0) cc_final: 0.7468 (t0) REVERT: B 135 GLU cc_start: 0.8087 (pt0) cc_final: 0.7759 (pt0) REVERT: B 154 SER cc_start: 0.8677 (m) cc_final: 0.8241 (t) REVERT: B 180 ASN cc_start: 0.8044 (m-40) cc_final: 0.7813 (m-40) REVERT: B 216 ARG cc_start: 0.8135 (ttt-90) cc_final: 0.7864 (ttt-90) REVERT: B 221 SER cc_start: 0.8668 (p) cc_final: 0.8331 (p) REVERT: B 271 LYS cc_start: 0.8255 (ptmt) cc_final: 0.7928 (ptmt) REVERT: B 408 ARG cc_start: 0.4710 (mtm180) cc_final: 0.3833 (mtt-85) REVERT: B 411 GLU cc_start: 0.7927 (tt0) cc_final: 0.7440 (tt0) REVERT: B 479 LYS cc_start: 0.8591 (mmtm) cc_final: 0.8004 (mmtm) REVERT: B 549 GLN cc_start: 0.8089 (tt0) cc_final: 0.7861 (tt0) REVERT: B 576 SER cc_start: 0.8440 (t) cc_final: 0.8004 (p) REVERT: C 48 GLN cc_start: 0.8099 (mt0) cc_final: 0.7790 (mt0) REVERT: C 52 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7766 (ttpt) REVERT: C 71 LEU cc_start: 0.8457 (tp) cc_final: 0.8177 (tm) REVERT: C 77 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7225 (tm-30) REVERT: C 133 MET cc_start: 0.7982 (mmt) cc_final: 0.7483 (mmm) REVERT: C 155 GLU cc_start: 0.7120 (pp20) cc_final: 0.6771 (pp20) REVERT: C 183 MET cc_start: 0.8414 (mmm) cc_final: 0.8059 (mmm) REVERT: C 193 GLU cc_start: 0.7433 (mm-30) cc_final: 0.6964 (mt-10) REVERT: C 204 ILE cc_start: 0.8965 (pt) cc_final: 0.8712 (pp) REVERT: C 221 SER cc_start: 0.8733 (p) cc_final: 0.8447 (t) REVERT: C 260 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6984 (mt-10) REVERT: C 349 THR cc_start: 0.8312 (p) cc_final: 0.8031 (t) REVERT: C 397 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7378 (mtm-85) REVERT: C 404 GLN cc_start: 0.7560 (pp30) cc_final: 0.7254 (pp30) REVERT: C 479 LYS cc_start: 0.8555 (mttm) cc_final: 0.8289 (mttm) REVERT: C 501 LYS cc_start: 0.8595 (tttp) cc_final: 0.8345 (tttt) REVERT: C 509 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6876 (mm-30) REVERT: C 511 ASP cc_start: 0.7649 (t0) cc_final: 0.7321 (t0) REVERT: C 513 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: C 574 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6928 (mm-30) REVERT: C 575 LYS cc_start: 0.8193 (mmtp) cc_final: 0.7820 (mmtp) REVERT: D 51 PHE cc_start: 0.8316 (m-80) cc_final: 0.7749 (m-80) REVERT: D 77 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7144 (mm-30) REVERT: D 82 VAL cc_start: 0.8319 (t) cc_final: 0.8034 (m) REVERT: D 101 ILE cc_start: 0.8527 (mt) cc_final: 0.8182 (mp) REVERT: D 122 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7739 (p0) REVERT: D 125 ASP cc_start: 0.7751 (m-30) cc_final: 0.7420 (m-30) REVERT: D 257 THR cc_start: 0.7397 (t) cc_final: 0.6967 (m) REVERT: D 387 LYS cc_start: 0.8046 (tptm) cc_final: 0.7790 (tppp) REVERT: D 400 TYR cc_start: 0.8597 (t80) cc_final: 0.8325 (t80) REVERT: D 511 ASP cc_start: 0.7778 (t0) cc_final: 0.7369 (t0) REVERT: D 573 TYR cc_start: 0.8170 (p90) cc_final: 0.7528 (p90) REVERT: D 583 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7733 (mt) REVERT: E 44 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.8019 (t) REVERT: E 50 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6998 (mm-30) REVERT: E 60 GLU cc_start: 0.7261 (tt0) cc_final: 0.7032 (tt0) REVERT: E 96 MET cc_start: 0.8062 (pmm) cc_final: 0.6483 (ptt) REVERT: E 133 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7793 (mpp) REVERT: E 135 GLU cc_start: 0.7789 (pt0) cc_final: 0.7512 (pt0) REVERT: E 149 VAL cc_start: 0.8968 (t) cc_final: 0.8441 (p) REVERT: E 163 LYS cc_start: 0.8094 (mttp) cc_final: 0.7857 (mttp) REVERT: E 178 ASP cc_start: 0.7367 (t0) cc_final: 0.6974 (t0) REVERT: E 179 SER cc_start: 0.8433 (p) cc_final: 0.8173 (t) REVERT: E 193 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7316 (mt-10) REVERT: E 255 LEU cc_start: 0.8306 (mp) cc_final: 0.8038 (mm) REVERT: E 296 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7993 (mm-40) REVERT: E 312 LYS cc_start: 0.5309 (tptp) cc_final: 0.4776 (tptp) REVERT: E 314 ARG cc_start: 0.8124 (mtt90) cc_final: 0.7261 (mtt-85) REVERT: E 325 ILE cc_start: 0.8681 (mt) cc_final: 0.8374 (mp) REVERT: E 353 PHE cc_start: 0.8413 (p90) cc_final: 0.8128 (p90) REVERT: E 411 GLU cc_start: 0.7758 (mp0) cc_final: 0.7215 (mp0) REVERT: E 526 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7154 (p0) REVERT: E 558 GLN cc_start: 0.8178 (pt0) cc_final: 0.7962 (pt0) REVERT: F 40 ILE cc_start: 0.8381 (mt) cc_final: 0.8009 (tp) REVERT: F 77 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7371 (mm-30) REVERT: F 79 TYR cc_start: 0.8697 (m-80) cc_final: 0.8439 (m-80) REVERT: F 89 LYS cc_start: 0.8379 (tppt) cc_final: 0.8041 (tppt) REVERT: F 163 LYS cc_start: 0.8217 (mttt) cc_final: 0.7956 (mttt) REVERT: F 173 LEU cc_start: 0.8656 (tp) cc_final: 0.8345 (tt) REVERT: F 192 SER cc_start: 0.8407 (t) cc_final: 0.8003 (p) REVERT: F 239 ASP cc_start: 0.7877 (m-30) cc_final: 0.7426 (m-30) REVERT: F 265 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8133 (p) REVERT: F 413 ASP cc_start: 0.7449 (t70) cc_final: 0.7045 (t0) REVERT: F 434 ASP cc_start: 0.7732 (m-30) cc_final: 0.7468 (m-30) REVERT: G 49 THR cc_start: 0.8519 (m) cc_final: 0.8150 (t) REVERT: G 60 GLU cc_start: 0.7596 (tt0) cc_final: 0.7336 (tt0) REVERT: G 133 MET cc_start: 0.8260 (mmt) cc_final: 0.7925 (mmt) REVERT: G 135 GLU cc_start: 0.7899 (pt0) cc_final: 0.7441 (pt0) REVERT: G 151 LYS cc_start: 0.8597 (mttm) cc_final: 0.8372 (mttm) REVERT: G 177 LEU cc_start: 0.8332 (tp) cc_final: 0.8072 (tm) REVERT: G 187 PRO cc_start: 0.8665 (Cg_endo) cc_final: 0.8381 (Cg_exo) REVERT: G 201 LYS cc_start: 0.8344 (mtpt) cc_final: 0.8139 (mtpt) REVERT: G 204 ILE cc_start: 0.8938 (pt) cc_final: 0.8680 (pp) REVERT: G 237 ASP cc_start: 0.7811 (t0) cc_final: 0.7514 (m-30) REVERT: G 260 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6745 (mt-10) REVERT: G 274 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7201 (mtp-110) REVERT: G 303 PHE cc_start: 0.8700 (m-80) cc_final: 0.8455 (m-80) REVERT: G 335 GLU cc_start: 0.7657 (tt0) cc_final: 0.7178 (tt0) REVERT: G 375 ASN cc_start: 0.7912 (m110) cc_final: 0.7557 (m110) REVERT: G 393 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7290 (mt-10) REVERT: G 396 GLU cc_start: 0.7762 (tp30) cc_final: 0.7488 (tp30) REVERT: G 401 ILE cc_start: 0.8541 (mm) cc_final: 0.8279 (mp) REVERT: G 426 ASN cc_start: 0.8608 (t0) cc_final: 0.8369 (t0) REVERT: G 439 LYS cc_start: 0.8706 (mmmm) cc_final: 0.8319 (mttt) REVERT: G 473 GLU cc_start: 0.7749 (tp30) cc_final: 0.7527 (tp30) REVERT: G 484 VAL cc_start: 0.8809 (m) cc_final: 0.8484 (t) REVERT: G 536 LYS cc_start: 0.8030 (ttpp) cc_final: 0.7752 (ttpp) REVERT: G 549 GLN cc_start: 0.8081 (tp40) cc_final: 0.7474 (tp40) REVERT: I 40 ILE cc_start: 0.8493 (mt) cc_final: 0.8282 (mp) REVERT: I 89 LYS cc_start: 0.8525 (ttmt) cc_final: 0.8231 (ttmt) REVERT: I 96 MET cc_start: 0.7963 (mpp) cc_final: 0.6453 (ptt) REVERT: I 100 ASP cc_start: 0.7159 (m-30) cc_final: 0.6882 (m-30) REVERT: I 233 TYR cc_start: 0.7985 (t80) cc_final: 0.7606 (t80) REVERT: I 249 SER cc_start: 0.8503 (t) cc_final: 0.8016 (p) REVERT: I 303 PHE cc_start: 0.8260 (m-80) cc_final: 0.7968 (m-10) REVERT: I 312 LYS cc_start: 0.8561 (mttt) cc_final: 0.8191 (mttt) REVERT: I 436 ILE cc_start: 0.8561 (mm) cc_final: 0.8332 (mp) REVERT: I 439 LYS cc_start: 0.3990 (mmtt) cc_final: 0.2524 (mmmt) REVERT: I 501 LYS cc_start: 0.8500 (tttt) cc_final: 0.8218 (tttm) REVERT: I 518 MET cc_start: 0.7014 (ptp) cc_final: 0.6610 (ptp) REVERT: I 526 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7167 (p0) REVERT: I 530 LYS cc_start: 0.8626 (ttpp) cc_final: 0.8399 (ttpp) REVERT: I 561 TYR cc_start: 0.8652 (m-80) cc_final: 0.8381 (m-80) outliers start: 117 outliers final: 62 residues processed: 1132 average time/residue: 1.3028 time to fit residues: 1766.6707 Evaluate side-chains 1134 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1060 time to evaluate : 3.374 ------------------------------------------------------------------------------- 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 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 403 HIS Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 493 ASN Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 403 HIS Chi-restraints excluded: chain E residue 526 ASP Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 274 ARG Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 354 LYS Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain I residue 168 ASP Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 526 ASP Chi-restraints excluded: chain I residue 569 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 246 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 253 optimal weight: 9.9990 chunk 271 optimal weight: 8.9990 chunk 196 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 312 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN A 403 HIS A 468 GLN A 558 GLN B 48 GLN ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN B 404 GLN B 497 GLN B 565 ASN C 497 GLN C 550 GLN D 383 GLN D 466 ASN E 47 ASN E 78 ASN E 102 HIS E 137 HIS E 180 ASN E 181 ASN E 483 HIS E 497 GLN F 180 ASN F 505 ASN F 549 GLN G 383 GLN I 72 ASN ** I 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 ASN I 416 GLN I 459 ASN I 549 GLN ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.142 33478 Z= 0.658 Angle : 0.674 16.124 45788 Z= 0.341 Chirality : 0.050 0.257 4980 Planarity : 0.005 0.067 6021 Dihedral : 5.655 89.605 4445 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.92 % Allowed : 21.16 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.64 (0.13), residues: 3895 helix: -0.82 (0.38), residues: 147 sheet: -0.31 (0.16), residues: 1049 loop : -0.42 (0.11), residues: 2699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP G 545 HIS 0.010 0.002 HIS B 70 PHE 0.037 0.003 PHE I 266 TYR 0.032 0.003 TYR I 524 ARG 0.017 0.001 ARG C 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1225 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1089 time to evaluate : 3.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLN cc_start: 0.8172 (mt0) cc_final: 0.7882 (mt0) REVERT: A 52 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7957 (ttmt) REVERT: A 77 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7393 (mm-30) REVERT: A 87 MET cc_start: 0.7310 (ttm) cc_final: 0.7080 (ttt) REVERT: A 142 GLU cc_start: 0.8043 (pt0) cc_final: 0.7776 (pt0) REVERT: A 144 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7416 (mt-10) REVERT: A 221 SER cc_start: 0.8486 (m) cc_final: 0.8209 (t) REVERT: A 239 ASP cc_start: 0.7886 (t0) cc_final: 0.7621 (t0) REVERT: A 245 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7849 (m) REVERT: A 296 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7648 (mm-40) REVERT: A 302 ASN cc_start: 0.7553 (m110) cc_final: 0.6995 (m110) REVERT: A 400 TYR cc_start: 0.8507 (t80) cc_final: 0.7885 (t80) REVERT: A 439 LYS cc_start: 0.8607 (mmtp) cc_final: 0.8301 (mmtt) REVERT: A 460 VAL cc_start: 0.8834 (m) cc_final: 0.8523 (p) REVERT: A 511 ASP cc_start: 0.7524 (t0) cc_final: 0.7137 (t0) REVERT: A 519 SER cc_start: 0.8637 (t) cc_final: 0.8414 (t) REVERT: A 530 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8486 (ttmt) REVERT: A 549 GLN cc_start: 0.8282 (tp40) cc_final: 0.8029 (tt0) REVERT: B 51 PHE cc_start: 0.8414 (m-80) cc_final: 0.8136 (m-80) REVERT: B 77 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7052 (tm-30) REVERT: B 87 MET cc_start: 0.7698 (ptm) cc_final: 0.7389 (ptm) REVERT: B 101 ILE cc_start: 0.8677 (mt) cc_final: 0.8116 (mt) REVERT: B 113 ASP cc_start: 0.7782 (t0) cc_final: 0.7477 (t0) REVERT: B 135 GLU cc_start: 0.8108 (pt0) cc_final: 0.7805 (pt0) REVERT: B 154 SER cc_start: 0.8703 (m) cc_final: 0.8288 (t) REVERT: B 172 SER cc_start: 0.8598 (p) cc_final: 0.8366 (p) REVERT: B 180 ASN cc_start: 0.8066 (m-40) cc_final: 0.7848 (m-40) REVERT: B 216 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7835 (ttt-90) REVERT: B 221 SER cc_start: 0.8806 (p) cc_final: 0.8521 (p) REVERT: B 271 LYS cc_start: 0.8314 (ptmt) cc_final: 0.8032 (ptmt) REVERT: B 408 ARG cc_start: 0.4917 (mtm180) cc_final: 0.4178 (mtm180) REVERT: B 411 GLU cc_start: 0.7990 (tt0) cc_final: 0.7459 (tt0) REVERT: B 439 LYS cc_start: 0.8705 (mmtm) cc_final: 0.8390 (mmtt) REVERT: B 479 LYS cc_start: 0.8536 (mmtm) cc_final: 0.7922 (mmtm) REVERT: B 553 ILE cc_start: 0.6416 (mp) cc_final: 0.5852 (tt) REVERT: C 50 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7255 (mt-10) REVERT: C 52 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7782 (ttpt) REVERT: C 71 LEU cc_start: 0.8388 (tp) cc_final: 0.8125 (tm) REVERT: C 77 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7267 (tm-30) REVERT: C 140 SER cc_start: 0.8948 (OUTLIER) cc_final: 0.8701 (t) REVERT: C 144 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7620 (mt-10) REVERT: C 155 GLU cc_start: 0.7165 (pp20) cc_final: 0.6844 (pp20) REVERT: C 192 SER cc_start: 0.8599 (m) cc_final: 0.8358 (p) REVERT: C 193 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7121 (mt-10) REVERT: C 204 ILE cc_start: 0.8986 (pt) cc_final: 0.8713 (pp) REVERT: C 221 SER cc_start: 0.8757 (p) cc_final: 0.8546 (t) REVERT: C 260 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7225 (mt-10) REVERT: C 349 THR cc_start: 0.8324 (p) cc_final: 0.8055 (t) REVERT: C 397 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7403 (mtm-85) REVERT: C 404 GLN cc_start: 0.7682 (pp30) cc_final: 0.7402 (pp30) REVERT: C 479 LYS cc_start: 0.8597 (mttm) cc_final: 0.8336 (mttm) REVERT: C 501 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8451 (tttt) REVERT: C 509 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6981 (mm-30) REVERT: C 511 ASP cc_start: 0.7678 (t0) cc_final: 0.7347 (t0) REVERT: C 513 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7675 (m-30) REVERT: D 51 PHE cc_start: 0.8365 (m-80) cc_final: 0.7871 (m-80) REVERT: D 77 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7167 (mm-30) REVERT: D 101 ILE cc_start: 0.8745 (mt) cc_final: 0.8437 (mp) REVERT: D 178 ASP cc_start: 0.7864 (t0) cc_final: 0.7328 (t0) REVERT: D 400 TYR cc_start: 0.8664 (t80) cc_final: 0.8384 (t80) REVERT: D 492 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.8001 (p0) REVERT: D 511 ASP cc_start: 0.7906 (t0) cc_final: 0.7490 (t0) REVERT: D 530 LYS cc_start: 0.8843 (ttpt) cc_final: 0.8635 (ttpt) REVERT: D 532 LYS cc_start: 0.8639 (ttpt) cc_final: 0.8283 (ttpp) REVERT: D 583 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7865 (mt) REVERT: E 60 GLU cc_start: 0.7303 (tt0) cc_final: 0.7082 (tt0) REVERT: E 135 GLU cc_start: 0.7874 (pt0) cc_final: 0.7588 (pt0) REVERT: E 149 VAL cc_start: 0.8916 (t) cc_final: 0.8405 (p) REVERT: E 163 LYS cc_start: 0.8089 (mttp) cc_final: 0.7853 (mttp) REVERT: E 193 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7321 (mt-10) REVERT: E 255 LEU cc_start: 0.8429 (mp) cc_final: 0.8128 (mm) REVERT: E 260 GLU cc_start: 0.7418 (tt0) cc_final: 0.6923 (tm-30) REVERT: E 261 PHE cc_start: 0.8525 (t80) cc_final: 0.8099 (t80) REVERT: E 296 GLN cc_start: 0.8289 (mm-40) cc_final: 0.8005 (mm-40) REVERT: E 305 ASP cc_start: 0.8452 (m-30) cc_final: 0.5853 (m-30) REVERT: E 312 LYS cc_start: 0.5773 (tptp) cc_final: 0.4937 (mtpp) REVERT: E 314 ARG cc_start: 0.8160 (mtt90) cc_final: 0.7218 (mtp180) REVERT: E 319 MET cc_start: 0.5680 (mmt) cc_final: 0.5089 (mmt) REVERT: E 411 GLU cc_start: 0.7796 (mp0) cc_final: 0.7262 (mp0) REVERT: E 570 LYS cc_start: 0.8712 (ptmt) cc_final: 0.8469 (ptmm) REVERT: F 53 PHE cc_start: 0.8417 (m-80) cc_final: 0.8201 (m-80) REVERT: F 77 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7424 (mm-30) REVERT: F 89 LYS cc_start: 0.8379 (tppt) cc_final: 0.8041 (tppt) REVERT: F 163 LYS cc_start: 0.8212 (mttt) cc_final: 0.7953 (mttt) REVERT: F 173 LEU cc_start: 0.8802 (tp) cc_final: 0.8508 (tt) REVERT: F 192 SER cc_start: 0.8496 (t) cc_final: 0.8170 (t) REVERT: F 239 ASP cc_start: 0.7964 (m-30) cc_final: 0.7539 (m-30) REVERT: F 265 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8428 (p) REVERT: F 293 SER cc_start: 0.8508 (t) cc_final: 0.8128 (p) REVERT: F 413 ASP cc_start: 0.7494 (t70) cc_final: 0.7119 (t0) REVERT: F 434 ASP cc_start: 0.7668 (m-30) cc_final: 0.7378 (m-30) REVERT: F 521 ILE cc_start: 0.8661 (mt) cc_final: 0.8427 (mm) REVERT: F 566 ILE cc_start: 0.9121 (pt) cc_final: 0.8817 (pp) REVERT: F 575 LYS cc_start: 0.8530 (mttp) cc_final: 0.8286 (mttp) REVERT: G 49 THR cc_start: 0.8501 (m) cc_final: 0.8120 (t) REVERT: G 60 GLU cc_start: 0.7632 (tt0) cc_final: 0.7401 (tt0) REVERT: G 89 LYS cc_start: 0.8672 (tttt) cc_final: 0.8362 (ttmm) REVERT: G 130 VAL cc_start: 0.8430 (m) cc_final: 0.8200 (p) REVERT: G 133 MET cc_start: 0.8294 (mmt) cc_final: 0.7744 (mmm) REVERT: G 135 GLU cc_start: 0.7919 (pt0) cc_final: 0.7414 (pt0) REVERT: G 151 LYS cc_start: 0.8607 (mttm) cc_final: 0.8367 (mttm) REVERT: G 172 SER cc_start: 0.8648 (p) cc_final: 0.8280 (m) REVERT: G 177 LEU cc_start: 0.8382 (tp) cc_final: 0.8065 (tm) REVERT: G 201 LYS cc_start: 0.8306 (mtpt) cc_final: 0.7989 (mtpt) REVERT: G 204 ILE cc_start: 0.8876 (pt) cc_final: 0.8585 (pp) REVERT: G 237 ASP cc_start: 0.7927 (t0) cc_final: 0.7654 (m-30) REVERT: G 260 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6888 (mt-10) REVERT: G 274 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7228 (mtp-110) REVERT: G 285 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8278 (mp) REVERT: G 335 GLU cc_start: 0.7747 (tt0) cc_final: 0.7281 (tt0) REVERT: G 350 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8319 (mt0) REVERT: G 375 ASN cc_start: 0.7867 (m110) cc_final: 0.7543 (m110) REVERT: G 393 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7284 (mt-10) REVERT: G 396 GLU cc_start: 0.7785 (tp30) cc_final: 0.7516 (tp30) REVERT: G 401 ILE cc_start: 0.8597 (mm) cc_final: 0.8350 (mp) REVERT: G 426 ASN cc_start: 0.8717 (t0) cc_final: 0.8482 (t0) REVERT: G 473 GLU cc_start: 0.7741 (tp30) cc_final: 0.7396 (tp30) REVERT: G 484 VAL cc_start: 0.8865 (m) cc_final: 0.8553 (t) REVERT: G 501 LYS cc_start: 0.8666 (tttp) cc_final: 0.8272 (ptmm) REVERT: G 532 LYS cc_start: 0.8828 (ttmt) cc_final: 0.8618 (ttpp) REVERT: G 536 LYS cc_start: 0.8191 (ttpp) cc_final: 0.7896 (ttpp) REVERT: G 549 GLN cc_start: 0.8053 (tp40) cc_final: 0.7524 (tp40) REVERT: G 552 SER cc_start: 0.8693 (p) cc_final: 0.8338 (t) REVERT: I 40 ILE cc_start: 0.8565 (mt) cc_final: 0.8330 (mp) REVERT: I 88 ASP cc_start: 0.7819 (t0) cc_final: 0.7564 (t0) REVERT: I 89 LYS cc_start: 0.8505 (ttmt) cc_final: 0.8225 (ttmt) REVERT: I 96 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.6512 (ptt) REVERT: I 100 ASP cc_start: 0.7200 (m-30) cc_final: 0.6920 (m-30) REVERT: I 193 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7333 (mt-10) REVERT: I 249 SER cc_start: 0.8595 (t) cc_final: 0.8126 (p) REVERT: I 303 PHE cc_start: 0.8338 (m-80) cc_final: 0.8041 (m-10) REVERT: I 312 LYS cc_start: 0.8632 (mttt) cc_final: 0.8318 (mttt) REVERT: I 387 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8336 (mtpp) REVERT: I 436 ILE cc_start: 0.8656 (mm) cc_final: 0.8435 (mp) REVERT: I 439 LYS cc_start: 0.4118 (mmtt) cc_final: 0.2686 (mmmt) REVERT: I 501 LYS cc_start: 0.8570 (tttt) cc_final: 0.8324 (tttm) REVERT: I 518 MET cc_start: 0.6997 (ptp) cc_final: 0.6578 (ptp) outliers start: 136 outliers final: 93 residues processed: 1131 average time/residue: 1.3037 time to fit residues: 1762.7272 Evaluate side-chains 1184 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1076 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 403 HIS Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 492 ASN Chi-restraints excluded: chain D residue 493 ASN Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 403 HIS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 274 ARG Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 350 GLN Chi-restraints excluded: chain G residue 354 LYS Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 526 ASP Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 128 LEU Chi-restraints excluded: chain I residue 168 ASP Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 387 LYS Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain I residue 526 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 362 optimal weight: 2.9990 chunk 381 optimal weight: 2.9990 chunk 347 optimal weight: 0.9980 chunk 370 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 335 optimal weight: 8.9990 chunk 350 optimal weight: 5.9990 chunk 369 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN A 558 GLN B 48 GLN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN B 404 GLN B 497 GLN C 550 GLN D 167 ASN D 383 GLN E 47 ASN E 78 ASN E 102 HIS E 137 HIS E 180 ASN E 483 HIS E 497 GLN E 558 GLN F 180 ASN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 ASN F 508 ASN G 550 GLN I 72 ASN ** I 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 ASN I 310 GLN I 459 ASN ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33478 Z= 0.175 Angle : 0.549 15.915 45788 Z= 0.271 Chirality : 0.042 0.210 4980 Planarity : 0.004 0.049 6021 Dihedral : 5.189 87.525 4443 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.80 % Allowed : 23.00 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.41 (0.13), residues: 3895 helix: -0.41 (0.42), residues: 117 sheet: -0.20 (0.16), residues: 1032 loop : -0.24 (0.12), residues: 2746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 58 HIS 0.009 0.001 HIS B 70 PHE 0.028 0.001 PHE A 53 TYR 0.025 0.001 TYR A 444 ARG 0.011 0.001 ARG C 520 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1089 time to evaluate : 3.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8597 (t0) cc_final: 0.8287 (t0) REVERT: A 48 GLN cc_start: 0.8087 (mt0) cc_final: 0.7794 (mt0) REVERT: A 52 LYS cc_start: 0.8191 (ttmt) cc_final: 0.7864 (ttmt) REVERT: A 77 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7352 (mm-30) REVERT: A 87 MET cc_start: 0.7290 (ttm) cc_final: 0.7045 (ttt) REVERT: A 142 GLU cc_start: 0.8003 (pt0) cc_final: 0.7746 (pt0) REVERT: A 144 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7267 (mt-10) REVERT: A 221 SER cc_start: 0.8585 (m) cc_final: 0.8307 (t) REVERT: A 239 ASP cc_start: 0.7829 (t0) cc_final: 0.7444 (t0) REVERT: A 245 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7598 (m) REVERT: A 249 SER cc_start: 0.7991 (p) cc_final: 0.7753 (p) REVERT: A 296 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7611 (mm-40) REVERT: A 302 ASN cc_start: 0.7527 (m110) cc_final: 0.7001 (m110) REVERT: A 339 SER cc_start: 0.8682 (m) cc_final: 0.8016 (p) REVERT: A 400 TYR cc_start: 0.8406 (t80) cc_final: 0.7744 (t80) REVERT: A 401 ILE cc_start: 0.8432 (mm) cc_final: 0.8142 (pp) REVERT: A 439 LYS cc_start: 0.8505 (mmtp) cc_final: 0.8244 (mmtt) REVERT: A 460 VAL cc_start: 0.8840 (m) cc_final: 0.8543 (p) REVERT: A 511 ASP cc_start: 0.7374 (t0) cc_final: 0.7063 (t0) REVERT: A 519 SER cc_start: 0.8647 (t) cc_final: 0.8415 (t) REVERT: A 549 GLN cc_start: 0.8272 (tp40) cc_final: 0.7984 (tt0) REVERT: B 51 PHE cc_start: 0.8334 (m-80) cc_final: 0.8015 (m-80) REVERT: B 53 PHE cc_start: 0.8530 (m-80) cc_final: 0.8142 (m-80) REVERT: B 77 GLU cc_start: 0.7536 (tm-30) cc_final: 0.6950 (tm-30) REVERT: B 87 MET cc_start: 0.7642 (ptm) cc_final: 0.7304 (ptm) REVERT: B 101 ILE cc_start: 0.8673 (mt) cc_final: 0.8072 (mt) REVERT: B 113 ASP cc_start: 0.7798 (t0) cc_final: 0.7450 (t0) REVERT: B 154 SER cc_start: 0.8667 (m) cc_final: 0.8268 (t) REVERT: B 172 SER cc_start: 0.8541 (p) cc_final: 0.8298 (p) REVERT: B 180 ASN cc_start: 0.8054 (m-40) cc_final: 0.7829 (m-40) REVERT: B 216 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7803 (ttt-90) REVERT: B 221 SER cc_start: 0.8615 (p) cc_final: 0.8317 (p) REVERT: B 271 LYS cc_start: 0.8297 (ptmt) cc_final: 0.7974 (ptmt) REVERT: B 408 ARG cc_start: 0.4790 (mtm180) cc_final: 0.3450 (mtm180) REVERT: B 411 GLU cc_start: 0.7945 (tt0) cc_final: 0.7515 (tt0) REVERT: B 439 LYS cc_start: 0.8596 (mmtm) cc_final: 0.8357 (mmtt) REVERT: B 479 LYS cc_start: 0.8595 (mmtm) cc_final: 0.7996 (mmtm) REVERT: C 48 GLN cc_start: 0.8100 (mt0) cc_final: 0.7878 (mt0) REVERT: C 50 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7197 (mt-10) REVERT: C 52 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7740 (ttpt) REVERT: C 71 LEU cc_start: 0.8372 (tp) cc_final: 0.8123 (tm) REVERT: C 77 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7258 (tm-30) REVERT: C 99 ASP cc_start: 0.7283 (t70) cc_final: 0.6824 (t70) REVERT: C 133 MET cc_start: 0.8046 (mmt) cc_final: 0.7838 (mmm) REVERT: C 155 GLU cc_start: 0.7137 (pp20) cc_final: 0.6806 (pp20) REVERT: C 193 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6983 (mt-10) REVERT: C 204 ILE cc_start: 0.8960 (pt) cc_final: 0.8718 (pp) REVERT: C 221 SER cc_start: 0.8763 (p) cc_final: 0.8512 (t) REVERT: C 260 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7159 (mt-10) REVERT: C 349 THR cc_start: 0.8329 (p) cc_final: 0.8053 (t) REVERT: C 382 ARG cc_start: 0.8491 (mtt90) cc_final: 0.8200 (mtt90) REVERT: C 397 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7381 (mtm-85) REVERT: C 404 GLN cc_start: 0.7619 (pp30) cc_final: 0.7342 (pp30) REVERT: C 479 LYS cc_start: 0.8582 (mttm) cc_final: 0.8373 (mttm) REVERT: C 501 LYS cc_start: 0.8604 (tttp) cc_final: 0.8360 (tttt) REVERT: C 509 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6895 (mm-30) REVERT: C 511 ASP cc_start: 0.7652 (t0) cc_final: 0.7326 (t0) REVERT: C 520 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.8389 (mtm110) REVERT: D 51 PHE cc_start: 0.8330 (m-80) cc_final: 0.7808 (m-80) REVERT: D 77 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7041 (mm-30) REVERT: D 82 VAL cc_start: 0.8367 (t) cc_final: 0.8070 (m) REVERT: D 101 ILE cc_start: 0.8606 (mt) cc_final: 0.8257 (mp) REVERT: D 122 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.7739 (p0) REVERT: D 125 ASP cc_start: 0.7789 (m-30) cc_final: 0.7441 (m-30) REVERT: D 178 ASP cc_start: 0.7797 (t0) cc_final: 0.7244 (t0) REVERT: D 209 ARG cc_start: 0.8622 (pmt170) cc_final: 0.5969 (pmt-80) REVERT: D 400 TYR cc_start: 0.8602 (t80) cc_final: 0.8332 (t80) REVERT: D 471 ASP cc_start: 0.7666 (t0) cc_final: 0.7238 (t0) REVERT: D 511 ASP cc_start: 0.7747 (t0) cc_final: 0.7303 (t0) REVERT: D 532 LYS cc_start: 0.8656 (ttpt) cc_final: 0.8271 (ttpp) REVERT: D 540 ARG cc_start: 0.8566 (ptm-80) cc_final: 0.8337 (ptt-90) REVERT: D 583 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7800 (mt) REVERT: E 60 GLU cc_start: 0.7302 (tt0) cc_final: 0.7086 (tt0) REVERT: E 96 MET cc_start: 0.7800 (pmm) cc_final: 0.6548 (ptt) REVERT: E 135 GLU cc_start: 0.7781 (pt0) cc_final: 0.7508 (pt0) REVERT: E 149 VAL cc_start: 0.8975 (t) cc_final: 0.8488 (p) REVERT: E 163 LYS cc_start: 0.8105 (mttp) cc_final: 0.7858 (mttp) REVERT: E 178 ASP cc_start: 0.7410 (t0) cc_final: 0.7002 (t0) REVERT: E 179 SER cc_start: 0.8442 (p) cc_final: 0.8193 (t) REVERT: E 193 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7301 (mt-10) REVERT: E 255 LEU cc_start: 0.8304 (mp) cc_final: 0.8025 (mm) REVERT: E 260 GLU cc_start: 0.7404 (tt0) cc_final: 0.6927 (tm-30) REVERT: E 296 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7985 (mm-40) REVERT: E 312 LYS cc_start: 0.5481 (tptp) cc_final: 0.4945 (mtpt) REVERT: E 314 ARG cc_start: 0.8139 (mtt90) cc_final: 0.7420 (mtt-85) REVERT: E 353 PHE cc_start: 0.8405 (p90) cc_final: 0.8171 (p90) REVERT: E 411 GLU cc_start: 0.7758 (mp0) cc_final: 0.7247 (mp0) REVERT: F 77 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7465 (mm-30) REVERT: F 79 TYR cc_start: 0.8718 (m-80) cc_final: 0.8347 (m-80) REVERT: F 89 LYS cc_start: 0.8381 (tppt) cc_final: 0.8069 (tppt) REVERT: F 163 LYS cc_start: 0.8235 (mttt) cc_final: 0.7973 (mttt) REVERT: F 173 LEU cc_start: 0.8755 (tp) cc_final: 0.8471 (tt) REVERT: F 192 SER cc_start: 0.8452 (t) cc_final: 0.8022 (p) REVERT: F 239 ASP cc_start: 0.7852 (m-30) cc_final: 0.7482 (m-30) REVERT: F 265 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8260 (p) REVERT: F 293 SER cc_start: 0.8461 (t) cc_final: 0.8099 (p) REVERT: F 413 ASP cc_start: 0.7464 (t70) cc_final: 0.7058 (t0) REVERT: F 434 ASP cc_start: 0.7716 (m-30) cc_final: 0.7446 (m-30) REVERT: F 575 LYS cc_start: 0.8469 (mttp) cc_final: 0.8237 (mttp) REVERT: G 49 THR cc_start: 0.8442 (m) cc_final: 0.8045 (t) REVERT: G 60 GLU cc_start: 0.7584 (tt0) cc_final: 0.7334 (tt0) REVERT: G 89 LYS cc_start: 0.8649 (tttt) cc_final: 0.8303 (ttmm) REVERT: G 133 MET cc_start: 0.8252 (mmt) cc_final: 0.7903 (mmt) REVERT: G 135 GLU cc_start: 0.7880 (pt0) cc_final: 0.7395 (pt0) REVERT: G 151 LYS cc_start: 0.8627 (mttm) cc_final: 0.8385 (mttm) REVERT: G 172 SER cc_start: 0.8662 (p) cc_final: 0.8268 (m) REVERT: G 177 LEU cc_start: 0.8341 (tp) cc_final: 0.8055 (tm) REVERT: G 187 PRO cc_start: 0.8695 (Cg_endo) cc_final: 0.8439 (Cg_exo) REVERT: G 201 LYS cc_start: 0.8342 (mtpt) cc_final: 0.8136 (mtpt) REVERT: G 204 ILE cc_start: 0.8941 (pt) cc_final: 0.8696 (pp) REVERT: G 237 ASP cc_start: 0.7868 (t0) cc_final: 0.7598 (m-30) REVERT: G 260 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6809 (mt-10) REVERT: G 285 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7794 (mt) REVERT: G 335 GLU cc_start: 0.7678 (tt0) cc_final: 0.7255 (tt0) REVERT: G 375 ASN cc_start: 0.7914 (m110) cc_final: 0.7565 (m110) REVERT: G 393 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7254 (mt-10) REVERT: G 396 GLU cc_start: 0.7765 (tp30) cc_final: 0.7505 (tp30) REVERT: G 400 TYR cc_start: 0.8217 (t80) cc_final: 0.7899 (t80) REVERT: G 401 ILE cc_start: 0.8549 (mm) cc_final: 0.8286 (mp) REVERT: G 426 ASN cc_start: 0.8625 (t0) cc_final: 0.8396 (t0) REVERT: G 473 GLU cc_start: 0.7750 (tp30) cc_final: 0.7470 (tp30) REVERT: G 484 VAL cc_start: 0.8805 (m) cc_final: 0.8499 (t) REVERT: G 501 LYS cc_start: 0.8599 (tttp) cc_final: 0.8270 (ptmm) REVERT: G 532 LYS cc_start: 0.8818 (ttmt) cc_final: 0.8413 (ttpp) REVERT: G 536 LYS cc_start: 0.8083 (ttpp) cc_final: 0.7783 (ttpp) REVERT: G 549 GLN cc_start: 0.8028 (tp40) cc_final: 0.7543 (tp40) REVERT: G 552 SER cc_start: 0.8552 (p) cc_final: 0.8247 (t) REVERT: I 40 ILE cc_start: 0.8531 (mt) cc_final: 0.8303 (mp) REVERT: I 88 ASP cc_start: 0.7807 (t0) cc_final: 0.7520 (t0) REVERT: I 89 LYS cc_start: 0.8507 (ttmt) cc_final: 0.8235 (ttmt) REVERT: I 96 MET cc_start: 0.7989 (mpp) cc_final: 0.6489 (ptt) REVERT: I 100 ASP cc_start: 0.7168 (m-30) cc_final: 0.6891 (m-30) REVERT: I 233 TYR cc_start: 0.7995 (t80) cc_final: 0.7777 (t80) REVERT: I 249 SER cc_start: 0.8517 (t) cc_final: 0.8046 (p) REVERT: I 293 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8288 (p) REVERT: I 303 PHE cc_start: 0.8290 (m-80) cc_final: 0.7982 (m-10) REVERT: I 312 LYS cc_start: 0.8608 (mttt) cc_final: 0.8256 (mttt) REVERT: I 387 LYS cc_start: 0.8593 (mmmm) cc_final: 0.8302 (mtpp) REVERT: I 436 ILE cc_start: 0.8609 (mm) cc_final: 0.8373 (mp) REVERT: I 439 LYS cc_start: 0.3910 (mmtt) cc_final: 0.2357 (mmmt) REVERT: I 501 LYS cc_start: 0.8523 (tttt) cc_final: 0.8114 (tttm) REVERT: I 518 MET cc_start: 0.7014 (ptp) cc_final: 0.6592 (ptp) REVERT: I 561 TYR cc_start: 0.8651 (m-80) cc_final: 0.8417 (m-80) outliers start: 97 outliers final: 71 residues processed: 1120 average time/residue: 1.3465 time to fit residues: 1802.2778 Evaluate side-chains 1148 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1069 time to evaluate : 3.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 403 HIS Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 493 ASN Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 383 GLN Chi-restraints excluded: chain E residue 403 HIS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 354 LYS Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain I residue 168 ASP Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 429 VAL Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 526 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 243 optimal weight: 4.9990 chunk 392 optimal weight: 10.0000 chunk 239 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 272 optimal weight: 3.9990 chunk 411 optimal weight: 4.9990 chunk 378 optimal weight: 1.9990 chunk 327 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 253 optimal weight: 2.9990 chunk 200 optimal weight: 0.0040 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 318 GLN ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN B 95 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN B 404 GLN B 497 GLN C 550 GLN D 167 ASN D 350 GLN D 383 GLN E 47 ASN E 102 HIS E 137 HIS E 180 ASN E 483 HIS E 558 GLN F 180 ASN ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 ASN G 310 GLN G 468 GLN G 550 GLN G 577 GLN I 72 ASN ** I 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 ASN I 416 GLN I 459 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33478 Z= 0.237 Angle : 0.569 16.183 45788 Z= 0.278 Chirality : 0.043 0.194 4980 Planarity : 0.004 0.050 6021 Dihedral : 5.145 88.010 4443 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.51 % Allowed : 23.75 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.37 (0.13), residues: 3895 helix: -0.31 (0.43), residues: 117 sheet: -0.05 (0.16), residues: 980 loop : -0.29 (0.12), residues: 2798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP I 414 HIS 0.009 0.001 HIS B 70 PHE 0.030 0.001 PHE I 266 TYR 0.029 0.001 TYR A 444 ARG 0.012 0.001 ARG C 520 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1089 time to evaluate : 3.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8651 (t0) cc_final: 0.8343 (t0) REVERT: A 48 GLN cc_start: 0.8099 (mt0) cc_final: 0.7810 (mt0) REVERT: A 52 LYS cc_start: 0.8213 (ttmt) cc_final: 0.7867 (ttmt) REVERT: A 77 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7371 (mm-30) REVERT: A 87 MET cc_start: 0.7280 (ttm) cc_final: 0.7009 (ttm) REVERT: A 142 GLU cc_start: 0.8001 (pt0) cc_final: 0.7746 (pt0) REVERT: A 144 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7309 (mt-10) REVERT: A 221 SER cc_start: 0.8644 (m) cc_final: 0.8350 (t) REVERT: A 239 ASP cc_start: 0.7953 (t0) cc_final: 0.7539 (t0) REVERT: A 245 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7595 (m) REVERT: A 249 SER cc_start: 0.8081 (p) cc_final: 0.7855 (p) REVERT: A 296 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7611 (mm-40) REVERT: A 302 ASN cc_start: 0.7547 (m110) cc_final: 0.7013 (m110) REVERT: A 339 SER cc_start: 0.8670 (m) cc_final: 0.7992 (p) REVERT: A 400 TYR cc_start: 0.8424 (t80) cc_final: 0.7841 (t80) REVERT: A 460 VAL cc_start: 0.8846 (m) cc_final: 0.8545 (p) REVERT: A 511 ASP cc_start: 0.7368 (t0) cc_final: 0.7055 (t0) REVERT: A 519 SER cc_start: 0.8648 (t) cc_final: 0.8423 (t) REVERT: A 549 GLN cc_start: 0.8253 (tp40) cc_final: 0.7944 (tt0) REVERT: B 51 PHE cc_start: 0.8325 (m-80) cc_final: 0.8003 (m-80) REVERT: B 53 PHE cc_start: 0.8522 (m-80) cc_final: 0.8142 (m-80) REVERT: B 77 GLU cc_start: 0.7467 (tm-30) cc_final: 0.6964 (tm-30) REVERT: B 87 MET cc_start: 0.7639 (ptm) cc_final: 0.7302 (ptm) REVERT: B 101 ILE cc_start: 0.8669 (mt) cc_final: 0.8058 (mt) REVERT: B 113 ASP cc_start: 0.7790 (t0) cc_final: 0.7445 (t0) REVERT: B 135 GLU cc_start: 0.8114 (pt0) cc_final: 0.7806 (pt0) REVERT: B 154 SER cc_start: 0.8657 (m) cc_final: 0.8269 (t) REVERT: B 172 SER cc_start: 0.8532 (p) cc_final: 0.8291 (p) REVERT: B 180 ASN cc_start: 0.8070 (m-40) cc_final: 0.7860 (m-40) REVERT: B 216 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7779 (ttt-90) REVERT: B 221 SER cc_start: 0.8688 (p) cc_final: 0.8449 (p) REVERT: B 271 LYS cc_start: 0.8299 (ptmt) cc_final: 0.7973 (ptmt) REVERT: B 408 ARG cc_start: 0.4799 (mtm180) cc_final: 0.3436 (mtm180) REVERT: B 411 GLU cc_start: 0.7936 (tt0) cc_final: 0.7511 (tt0) REVERT: B 439 LYS cc_start: 0.8590 (mmtm) cc_final: 0.8292 (mmtt) REVERT: B 479 LYS cc_start: 0.8588 (mmtm) cc_final: 0.7992 (mmtm) REVERT: C 48 GLN cc_start: 0.8037 (mt0) cc_final: 0.7830 (mt0) REVERT: C 50 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7178 (mt-10) REVERT: C 52 LYS cc_start: 0.8185 (ttpt) cc_final: 0.7754 (ttpt) REVERT: C 71 LEU cc_start: 0.8378 (tp) cc_final: 0.8116 (tm) REVERT: C 77 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7247 (tm-30) REVERT: C 133 MET cc_start: 0.8070 (mmt) cc_final: 0.7826 (mmm) REVERT: C 144 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7554 (mt-10) REVERT: C 155 GLU cc_start: 0.7136 (pp20) cc_final: 0.6804 (pp20) REVERT: C 193 GLU cc_start: 0.7462 (mm-30) cc_final: 0.6993 (mt-10) REVERT: C 204 ILE cc_start: 0.8964 (pt) cc_final: 0.8711 (pp) REVERT: C 221 SER cc_start: 0.8765 (p) cc_final: 0.8529 (t) REVERT: C 260 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7144 (mt-10) REVERT: C 349 THR cc_start: 0.8341 (p) cc_final: 0.8083 (t) REVERT: C 382 ARG cc_start: 0.8503 (mtt90) cc_final: 0.8245 (mtt90) REVERT: C 397 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7403 (mtm-85) REVERT: C 404 GLN cc_start: 0.7631 (pp30) cc_final: 0.7371 (pp30) REVERT: C 479 LYS cc_start: 0.8593 (mttm) cc_final: 0.8319 (mttm) REVERT: C 501 LYS cc_start: 0.8646 (tttp) cc_final: 0.8387 (tttt) REVERT: C 509 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6918 (mm-30) REVERT: C 511 ASP cc_start: 0.7650 (t0) cc_final: 0.7327 (t0) REVERT: D 51 PHE cc_start: 0.8334 (m-80) cc_final: 0.7768 (m-80) REVERT: D 77 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7049 (mm-30) REVERT: D 82 VAL cc_start: 0.8356 (t) cc_final: 0.8047 (m) REVERT: D 101 ILE cc_start: 0.8616 (mt) cc_final: 0.8272 (mp) REVERT: D 122 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7727 (p0) REVERT: D 125 ASP cc_start: 0.7801 (m-30) cc_final: 0.7448 (m-30) REVERT: D 178 ASP cc_start: 0.7848 (t0) cc_final: 0.7299 (t0) REVERT: D 209 ARG cc_start: 0.8595 (pmt170) cc_final: 0.5951 (pmt-80) REVERT: D 400 TYR cc_start: 0.8613 (t80) cc_final: 0.8337 (t80) REVERT: D 471 ASP cc_start: 0.7673 (t0) cc_final: 0.7232 (t0) REVERT: D 511 ASP cc_start: 0.7764 (t0) cc_final: 0.7297 (t0) REVERT: D 532 LYS cc_start: 0.8656 (ttpt) cc_final: 0.8262 (ttpp) REVERT: D 583 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7815 (mt) REVERT: E 60 GLU cc_start: 0.7304 (tt0) cc_final: 0.7087 (tt0) REVERT: E 96 MET cc_start: 0.7743 (pmm) cc_final: 0.6446 (ptt) REVERT: E 100 ASP cc_start: 0.7713 (t0) cc_final: 0.7319 (t0) REVERT: E 135 GLU cc_start: 0.7797 (pt0) cc_final: 0.7537 (pt0) REVERT: E 149 VAL cc_start: 0.8967 (t) cc_final: 0.8494 (p) REVERT: E 163 LYS cc_start: 0.8119 (mttp) cc_final: 0.7878 (mttp) REVERT: E 178 ASP cc_start: 0.7318 (t0) cc_final: 0.6935 (t0) REVERT: E 179 SER cc_start: 0.8476 (p) cc_final: 0.8238 (t) REVERT: E 193 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7296 (mt-10) REVERT: E 255 LEU cc_start: 0.8310 (mp) cc_final: 0.8026 (mm) REVERT: E 260 GLU cc_start: 0.7408 (tt0) cc_final: 0.6932 (tm-30) REVERT: E 261 PHE cc_start: 0.8407 (t80) cc_final: 0.8190 (t80) REVERT: E 296 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7972 (mm-40) REVERT: E 305 ASP cc_start: 0.8425 (m-30) cc_final: 0.5706 (m-30) REVERT: E 312 LYS cc_start: 0.5548 (tptp) cc_final: 0.4998 (mtpt) REVERT: E 314 ARG cc_start: 0.8142 (mtt90) cc_final: 0.7415 (mtt-85) REVERT: E 411 GLU cc_start: 0.7768 (mp0) cc_final: 0.7255 (mp0) REVERT: F 77 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7472 (mm-30) REVERT: F 79 TYR cc_start: 0.8727 (m-80) cc_final: 0.8345 (m-80) REVERT: F 89 LYS cc_start: 0.8361 (tppt) cc_final: 0.8091 (tppt) REVERT: F 163 LYS cc_start: 0.8228 (mttt) cc_final: 0.7966 (mttt) REVERT: F 173 LEU cc_start: 0.8751 (tp) cc_final: 0.8467 (tt) REVERT: F 192 SER cc_start: 0.8465 (t) cc_final: 0.8031 (p) REVERT: F 239 ASP cc_start: 0.7860 (m-30) cc_final: 0.7458 (m-30) REVERT: F 249 SER cc_start: 0.8939 (t) cc_final: 0.8522 (t) REVERT: F 265 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8276 (p) REVERT: F 293 SER cc_start: 0.8465 (t) cc_final: 0.8095 (p) REVERT: F 413 ASP cc_start: 0.7464 (t70) cc_final: 0.7073 (t0) REVERT: F 434 ASP cc_start: 0.7712 (m-30) cc_final: 0.7503 (m-30) REVERT: F 575 LYS cc_start: 0.8464 (mttp) cc_final: 0.8235 (mttp) REVERT: G 49 THR cc_start: 0.8427 (m) cc_final: 0.8039 (t) REVERT: G 60 GLU cc_start: 0.7579 (tt0) cc_final: 0.7331 (tt0) REVERT: G 89 LYS cc_start: 0.8659 (tttt) cc_final: 0.8314 (ttmm) REVERT: G 130 VAL cc_start: 0.8450 (m) cc_final: 0.8211 (p) REVERT: G 133 MET cc_start: 0.8261 (mmt) cc_final: 0.7930 (mmt) REVERT: G 135 GLU cc_start: 0.7885 (pt0) cc_final: 0.7407 (pt0) REVERT: G 151 LYS cc_start: 0.8625 (mttm) cc_final: 0.8384 (mttm) REVERT: G 172 SER cc_start: 0.8660 (p) cc_final: 0.8276 (m) REVERT: G 177 LEU cc_start: 0.8355 (tp) cc_final: 0.8065 (tm) REVERT: G 187 PRO cc_start: 0.8714 (Cg_endo) cc_final: 0.8435 (Cg_exo) REVERT: G 201 LYS cc_start: 0.8351 (mtpt) cc_final: 0.8139 (mtpt) REVERT: G 204 ILE cc_start: 0.8939 (pt) cc_final: 0.8696 (pp) REVERT: G 237 ASP cc_start: 0.7929 (t0) cc_final: 0.7613 (m-30) REVERT: G 260 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6783 (mt-10) REVERT: G 285 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7847 (mt) REVERT: G 335 GLU cc_start: 0.7711 (tt0) cc_final: 0.7239 (tt0) REVERT: G 375 ASN cc_start: 0.7920 (m110) cc_final: 0.7573 (m110) REVERT: G 393 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7257 (mt-10) REVERT: G 396 GLU cc_start: 0.7769 (tp30) cc_final: 0.7505 (tp30) REVERT: G 401 ILE cc_start: 0.8558 (mm) cc_final: 0.8301 (mp) REVERT: G 426 ASN cc_start: 0.8629 (t0) cc_final: 0.8406 (t0) REVERT: G 439 LYS cc_start: 0.8654 (mmmm) cc_final: 0.8290 (mmtp) REVERT: G 473 GLU cc_start: 0.7760 (tp30) cc_final: 0.7471 (tp30) REVERT: G 484 VAL cc_start: 0.8826 (m) cc_final: 0.8496 (t) REVERT: G 532 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8585 (ttpp) REVERT: G 536 LYS cc_start: 0.8113 (ttpp) cc_final: 0.7804 (ttpp) REVERT: G 549 GLN cc_start: 0.8039 (tp40) cc_final: 0.7493 (tp40) REVERT: G 552 SER cc_start: 0.8527 (p) cc_final: 0.8219 (t) REVERT: I 40 ILE cc_start: 0.8529 (mt) cc_final: 0.8307 (mp) REVERT: I 88 ASP cc_start: 0.7813 (t0) cc_final: 0.7529 (t0) REVERT: I 89 LYS cc_start: 0.8439 (ttmt) cc_final: 0.8188 (ttmt) REVERT: I 96 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.6464 (ptt) REVERT: I 100 ASP cc_start: 0.7170 (m-30) cc_final: 0.6888 (m-30) REVERT: I 233 TYR cc_start: 0.8021 (t80) cc_final: 0.7755 (t80) REVERT: I 245 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.8018 (m) REVERT: I 249 SER cc_start: 0.8515 (t) cc_final: 0.8058 (p) REVERT: I 293 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.8276 (p) REVERT: I 303 PHE cc_start: 0.8293 (m-80) cc_final: 0.8004 (m-10) REVERT: I 312 LYS cc_start: 0.8599 (mttt) cc_final: 0.8238 (mttt) REVERT: I 387 LYS cc_start: 0.8596 (mmmm) cc_final: 0.8310 (mtpp) REVERT: I 436 ILE cc_start: 0.8613 (mm) cc_final: 0.8385 (mp) REVERT: I 439 LYS cc_start: 0.3920 (mmtt) cc_final: 0.2286 (mmmt) REVERT: I 501 LYS cc_start: 0.8518 (tttt) cc_final: 0.8107 (tttm) REVERT: I 518 MET cc_start: 0.7027 (ptp) cc_final: 0.6602 (ptp) REVERT: I 526 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7161 (p0) outliers start: 87 outliers final: 62 residues processed: 1121 average time/residue: 1.3599 time to fit residues: 1830.0122 Evaluate side-chains 1154 residues out of total 3469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1081 time to evaluate : 3.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 403 HIS Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 493 ASN Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 403 HIS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 354 LYS Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 168 ASP Chi-restraints excluded: chain I residue 245 THR Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 429 VAL Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 ILE Chi-restraints excluded: chain I residue 526 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 260 optimal weight: 10.0000 chunk 349 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 302 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 328 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 336 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN B 95 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN B 404 GLN B 497 GLN C 550 GLN D 167 ASN D 350 GLN D 383 GLN E 47 ASN E 102 HIS E 137 HIS E 180 ASN E 181 ASN E 483 HIS E 558 GLN F 180 ASN ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 ASN G 318 GLN G 550 GLN G 577 GLN I 72 ASN I 147 ASN I 302 ASN I 416 GLN I 459 ASN ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.125940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110099 restraints weight = 46836.846| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.13 r_work: 0.3261 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 33478 Z= 0.158 Angle : 0.541 16.100 45788 Z= 0.263 Chirality : 0.042 0.190 4980 Planarity : 0.004 0.095 6021 Dihedral : 4.922 88.644 4443 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.36 % Allowed : 23.72 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.27 (0.13), residues: 3895 helix: -0.33 (0.42), residues: 118 sheet: -0.11 (0.16), residues: 996 loop : -0.14 (0.12), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 58 HIS 0.008 0.001 HIS B 70 PHE 0.028 0.001 PHE A 53 TYR 0.028 0.001 TYR A 444 ARG 0.028 0.001 ARG C 520 =============================================================================== Job complete usr+sys time: 21607.73 seconds wall clock time: 373 minutes 22.70 seconds (22402.70 seconds total)