Starting phenix.real_space_refine on Wed Mar 20 23:07:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk6_34847/03_2024/8hk6_34847.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk6_34847/03_2024/8hk6_34847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk6_34847/03_2024/8hk6_34847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk6_34847/03_2024/8hk6_34847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk6_34847/03_2024/8hk6_34847.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk6_34847/03_2024/8hk6_34847.pdb" } resolution = 2.64 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.051 sd= 0.187 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: 6 Type Number sf(0) Gaussians K 20 8.98 5 Zn 4 6.06 5 S 212 5.16 5 C 18588 2.51 5 N 4772 2.21 5 O 5108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "A GLU 808": "OE1" <-> "OE2" Residue "A GLU 830": "OE1" <-> "OE2" Residue "A TYR 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 878": "OD1" <-> "OD2" Residue "A PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1151": "OE1" <-> "OE2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B ASP 388": "OD1" <-> "OD2" Residue "B PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 601": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B GLU 808": "OE1" <-> "OE2" Residue "B GLU 830": "OE1" <-> "OE2" Residue "B TYR 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 951": "OE1" <-> "OE2" Residue "B PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1151": "OE1" <-> "OE2" Residue "B ASP 1187": "OD1" <-> "OD2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 388": "OD1" <-> "OD2" Residue "C PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 509": "OE1" <-> "OE2" Residue "C GLU 576": "OE1" <-> "OE2" Residue "C TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 601": "OE1" <-> "OE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C ASP 782": "OD1" <-> "OD2" Residue "C GLU 808": "OE1" <-> "OE2" Residue "C ASP 884": "OD1" <-> "OD2" Residue "C PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1151": "OE1" <-> "OE2" Residue "C ASP 1187": "OD1" <-> "OD2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 293": "OE1" <-> "OE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 355": "OE1" <-> "OE2" Residue "D ASP 388": "OD1" <-> "OD2" Residue "D ASP 413": "OD1" <-> "OD2" Residue "D PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 544": "OE1" <-> "OE2" Residue "D GLU 547": "OE1" <-> "OE2" Residue "D GLU 576": "OE1" <-> "OE2" Residue "D TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 748": "OE1" <-> "OE2" Residue "D GLU 808": "OE1" <-> "OE2" Residue "D GLU 848": "OE1" <-> "OE2" Residue "D GLU 946": "OE1" <-> "OE2" Residue "D PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1035": "OE1" <-> "OE2" Residue "D TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1151": "OE1" <-> "OE2" Residue "D ASP 1187": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28704 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "D" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' K': 8, ' ZN': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 4, ' ZN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 4, ' ZN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 4, ' ZN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4448 SG CYS A 777 85.572 96.078 128.620 1.00 74.69 S ATOM 4454 SG CYS A 778 86.057 99.913 128.438 1.00 82.67 S ATOM 4508 SG CYS A 785 82.677 98.393 129.556 1.00105.48 S ATOM 11618 SG CYS B 777 53.556 85.575 128.703 1.00 75.07 S ATOM 11624 SG CYS B 778 49.929 85.993 128.505 1.00 82.61 S ATOM 11678 SG CYS B 785 51.410 82.824 129.668 1.00105.30 S ATOM 18788 SG CYS C 777 64.165 53.688 128.607 1.00 73.24 S ATOM 18794 SG CYS C 778 63.708 49.848 128.422 1.00 82.57 S ATOM 18848 SG CYS C 785 67.054 51.395 129.583 1.00106.68 S ATOM 25958 SG CYS D 777 96.044 64.149 128.595 1.00 77.59 S ATOM 25964 SG CYS D 778 99.891 63.713 128.419 1.00 82.97 S ATOM 26018 SG CYS D 785 98.311 67.055 129.542 1.00106.54 S Time building chain proxies: 15.64, per 1000 atoms: 0.54 Number of scatterers: 28704 At special positions: 0 Unit cell: (150.8, 150.8, 144.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 K 20 19.00 S 212 16.00 O 5108 8.00 N 4772 7.00 C 18588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 11.26 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" ND1 HIS A 787 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 777 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 778 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 785 " pdb=" ZN B1303 " pdb="ZN ZN B1303 " - pdb=" ND1 HIS B 787 " pdb="ZN ZN B1303 " - pdb=" SG CYS B 777 " pdb="ZN ZN B1303 " - pdb=" SG CYS B 778 " pdb="ZN ZN B1303 " - pdb=" SG CYS B 785 " pdb=" ZN C1303 " pdb="ZN ZN C1303 " - pdb=" ND1 HIS C 787 " pdb="ZN ZN C1303 " - pdb=" SG CYS C 777 " pdb="ZN ZN C1303 " - pdb=" SG CYS C 785 " pdb="ZN ZN C1303 " - pdb=" SG CYS C 778 " pdb=" ZN D1303 " pdb="ZN ZN D1303 " - pdb=" ND1 HIS D 787 " pdb="ZN ZN D1303 " - pdb=" SG CYS D 777 " pdb="ZN ZN D1303 " - pdb=" SG CYS D 785 " pdb="ZN ZN D1303 " - pdb=" SG CYS D 778 " Number of angles added : 12 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6888 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 21 sheets defined 53.8% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'A' and resid 110 through 136 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 173 through 198 removed outlier: 3.608A pdb=" N ALA A 178 " --> pdb=" O MET A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 228 Proline residue: A 221 - end of helix removed outlier: 3.858A pdb=" N ILE A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.934A pdb=" N ASN A 233 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 234 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 254 removed outlier: 4.044A pdb=" N LEU A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 293 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 324 through 357 Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 382 through 394 Processing helix chain 'A' and resid 395 through 400 removed outlier: 6.701A pdb=" N ARG A 398 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 400 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 removed outlier: 3.564A pdb=" N VAL A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 427 removed outlier: 4.457A pdb=" N GLN A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 463 through 482 Processing helix chain 'A' and resid 493 through 500 removed outlier: 4.717A pdb=" N PHE A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS A 499 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 removed outlier: 3.551A pdb=" N CYS A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 547 through 557 Processing helix chain 'A' and resid 572 through 576 Processing helix chain 'A' and resid 579 through 592 Processing helix chain 'A' and resid 633 through 644 removed outlier: 3.612A pdb=" N PHE A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 780 Processing helix chain 'A' and resid 792 through 797 removed outlier: 3.523A pdb=" N TYR A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 792 through 797' Processing helix chain 'A' and resid 811 through 823 Proline residue: A 820 - end of helix Processing helix chain 'A' and resid 843 through 851 Processing helix chain 'A' and resid 865 through 873 Processing helix chain 'A' and resid 893 through 897 Processing helix chain 'A' and resid 898 through 912 Processing helix chain 'A' and resid 923 through 930 removed outlier: 4.053A pdb=" N ARG A 928 " --> pdb=" O SER A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 952 removed outlier: 3.681A pdb=" N SER A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 960 removed outlier: 3.966A pdb=" N PHE A 960 " --> pdb=" O ALA A 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 957 through 960' Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 972 through 982 removed outlier: 3.586A pdb=" N ASP A 976 " --> pdb=" O ILE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 996 Processing helix chain 'A' and resid 1013 through 1017 removed outlier: 3.630A pdb=" N LEU A1017 " --> pdb=" O GLU A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1033 Processing helix chain 'A' and resid 1129 through 1143 Processing helix chain 'A' and resid 1144 through 1161 Processing helix chain 'B' and resid 111 through 136 Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 173 through 198 Processing helix chain 'B' and resid 211 through 218 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 226 through 227 No H-bonds generated for 'chain 'B' and resid 226 through 227' Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 240 through 254 removed outlier: 4.033A pdb=" N LEU B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 293 Processing helix chain 'B' and resid 300 through 313 Processing helix chain 'B' and resid 324 through 357 Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 382 through 394 Processing helix chain 'B' and resid 395 through 400 removed outlier: 6.664A pdb=" N ARG B 398 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 400 " --> pdb=" O PRO B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 422 removed outlier: 3.582A pdb=" N VAL B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 removed outlier: 4.418A pdb=" N GLN B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 463 through 482 Processing helix chain 'B' and resid 493 through 500 removed outlier: 4.719A pdb=" N PHE B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS B 499 " --> pdb=" O ASN B 496 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 removed outlier: 3.552A pdb=" N CYS B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 534 Processing helix chain 'B' and resid 547 through 557 Processing helix chain 'B' and resid 572 through 576 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.606A pdb=" N PHE B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 638 " --> pdb=" O ALA B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 792 through 797 removed outlier: 3.612A pdb=" N TYR B 796 " --> pdb=" O ASP B 792 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 792 through 797' Processing helix chain 'B' and resid 811 through 823 Proline residue: B 820 - end of helix Processing helix chain 'B' and resid 843 through 851 Processing helix chain 'B' and resid 865 through 873 Processing helix chain 'B' and resid 893 through 897 Processing helix chain 'B' and resid 898 through 912 Processing helix chain 'B' and resid 923 through 930 removed outlier: 4.055A pdb=" N ARG B 928 " --> pdb=" O SER B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 952 removed outlier: 3.658A pdb=" N SER B 943 " --> pdb=" O SER B 939 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 960 removed outlier: 3.926A pdb=" N PHE B 960 " --> pdb=" O ALA B 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 957 through 960' Processing helix chain 'B' and resid 961 through 966 Processing helix chain 'B' and resid 972 through 982 removed outlier: 3.621A pdb=" N ASP B 976 " --> pdb=" O ILE B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 996 Processing helix chain 'B' and resid 1013 through 1017 removed outlier: 3.631A pdb=" N LEU B1017 " --> pdb=" O GLU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1033 Processing helix chain 'B' and resid 1129 through 1143 Processing helix chain 'B' and resid 1144 through 1161 Processing helix chain 'C' and resid 111 through 136 Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 173 through 198 removed outlier: 3.517A pdb=" N ALA C 178 " --> pdb=" O MET C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 225 Proline residue: C 221 - end of helix Processing helix chain 'C' and resid 226 through 227 No H-bonds generated for 'chain 'C' and resid 226 through 227' Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 240 through 254 removed outlier: 4.038A pdb=" N LEU C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 293 Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 324 through 357 Proline residue: C 343 - end of helix Processing helix chain 'C' and resid 382 through 394 Processing helix chain 'C' and resid 395 through 400 removed outlier: 6.724A pdb=" N ARG C 398 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN C 400 " --> pdb=" O PRO C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 422 removed outlier: 3.623A pdb=" N VAL C 419 " --> pdb=" O GLN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 427 removed outlier: 4.406A pdb=" N GLN C 427 " --> pdb=" O PRO C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 463 through 482 Processing helix chain 'C' and resid 493 through 500 removed outlier: 4.723A pdb=" N PHE C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS C 499 " --> pdb=" O ASN C 496 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 500 " --> pdb=" O LYS C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 523 removed outlier: 3.554A pdb=" N CYS C 521 " --> pdb=" O LEU C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 534 Processing helix chain 'C' and resid 547 through 557 Processing helix chain 'C' and resid 572 through 576 Processing helix chain 'C' and resid 579 through 592 Processing helix chain 'C' and resid 633 through 644 removed outlier: 3.607A pdb=" N PHE C 637 " --> pdb=" O SER C 633 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 638 " --> pdb=" O ALA C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 Processing helix chain 'C' and resid 792 through 797 removed outlier: 3.535A pdb=" N TYR C 796 " --> pdb=" O ASP C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 823 Proline residue: C 820 - end of helix Processing helix chain 'C' and resid 843 through 851 Processing helix chain 'C' and resid 865 through 873 Processing helix chain 'C' and resid 893 through 897 Processing helix chain 'C' and resid 898 through 912 Processing helix chain 'C' and resid 923 through 930 removed outlier: 4.042A pdb=" N ARG C 928 " --> pdb=" O SER C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 952 removed outlier: 3.663A pdb=" N SER C 943 " --> pdb=" O SER C 939 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 960 removed outlier: 4.077A pdb=" N PHE C 960 " --> pdb=" O ALA C 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 957 through 960' Processing helix chain 'C' and resid 961 through 966 Processing helix chain 'C' and resid 972 through 982 removed outlier: 3.637A pdb=" N ASP C 976 " --> pdb=" O ILE C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 996 Processing helix chain 'C' and resid 1013 through 1017 removed outlier: 3.622A pdb=" N LEU C1017 " --> pdb=" O GLU C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1033 Processing helix chain 'C' and resid 1129 through 1143 Processing helix chain 'C' and resid 1144 through 1161 Processing helix chain 'D' and resid 111 through 137 Processing helix chain 'D' and resid 164 through 169 Processing helix chain 'D' and resid 173 through 198 removed outlier: 3.626A pdb=" N ALA D 178 " --> pdb=" O MET D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 219 through 226 removed outlier: 3.544A pdb=" N ILE D 223 " --> pdb=" O THR D 219 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 254 removed outlier: 4.060A pdb=" N LEU D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN D 254 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 293 Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 324 through 357 Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 382 through 394 Processing helix chain 'D' and resid 395 through 400 removed outlier: 6.762A pdb=" N ARG D 398 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN D 400 " --> pdb=" O PRO D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 421 Processing helix chain 'D' and resid 422 through 427 removed outlier: 4.421A pdb=" N GLN D 427 " --> pdb=" O PRO D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 446 through 450 Processing helix chain 'D' and resid 463 through 482 Processing helix chain 'D' and resid 493 through 500 removed outlier: 4.713A pdb=" N PHE D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS D 499 " --> pdb=" O ASN D 496 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL D 500 " --> pdb=" O LYS D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 523 removed outlier: 3.545A pdb=" N CYS D 521 " --> pdb=" O LEU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 534 Processing helix chain 'D' and resid 547 through 557 Processing helix chain 'D' and resid 572 through 576 Processing helix chain 'D' and resid 579 through 592 Processing helix chain 'D' and resid 633 through 644 removed outlier: 3.616A pdb=" N PHE D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS D 638 " --> pdb=" O ALA D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 780 Processing helix chain 'D' and resid 792 through 797 removed outlier: 3.520A pdb=" N TYR D 796 " --> pdb=" O ASP D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 823 Proline residue: D 820 - end of helix Processing helix chain 'D' and resid 843 through 851 Processing helix chain 'D' and resid 865 through 873 Processing helix chain 'D' and resid 893 through 897 Processing helix chain 'D' and resid 898 through 912 Processing helix chain 'D' and resid 923 through 930 removed outlier: 4.046A pdb=" N ARG D 928 " --> pdb=" O SER D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 936 through 952 removed outlier: 3.713A pdb=" N SER D 943 " --> pdb=" O SER D 939 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS D 944 " --> pdb=" O LEU D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 957 through 960 removed outlier: 4.113A pdb=" N PHE D 960 " --> pdb=" O ALA D 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 957 through 960' Processing helix chain 'D' and resid 961 through 966 Processing helix chain 'D' and resid 972 through 982 removed outlier: 3.621A pdb=" N ASP D 976 " --> pdb=" O ILE D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 996 Processing helix chain 'D' and resid 1013 through 1017 removed outlier: 3.622A pdb=" N LEU D1017 " --> pdb=" O GLU D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1033 Processing helix chain 'D' and resid 1129 through 1143 Processing helix chain 'D' and resid 1144 through 1161 Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 144 Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 432 removed outlier: 6.164A pdb=" N VAL A 404 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU A 432 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE A 406 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N PHE A 454 " --> pdb=" O HIS A 373 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL A 375 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LEU A 456 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N CYS A 377 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS A 453 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLN A 490 " --> pdb=" O CYS A 453 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE A 455 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 560 through 565 removed outlier: 6.579A pdb=" N ILE A 625 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU A 595 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 750 through 752 Processing sheet with id=AA5, first strand: chain 'A' and resid 856 through 860 removed outlier: 6.129A pdb=" N ILE A 834 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N MET A 859 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU A 836 " --> pdb=" O MET A 859 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE A 803 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU A 837 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 805 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU A 802 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 916 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 920 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1006 through 1012 removed outlier: 3.913A pdb=" N ASP A1194 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A1039 " --> pdb=" O TYR A1197 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE A1199 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 429 through 432 removed outlier: 6.171A pdb=" N VAL B 404 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU B 432 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE B 406 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N PHE B 454 " --> pdb=" O HIS B 373 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 375 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU B 456 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS B 377 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N CYS B 453 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLN B 490 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE B 455 " --> pdb=" O GLN B 490 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 560 through 565 removed outlier: 6.586A pdb=" N ILE B 625 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU B 595 " --> pdb=" O ILE B 625 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 750 through 752 Processing sheet with id=AB1, first strand: chain 'B' and resid 856 through 860 removed outlier: 6.125A pdb=" N ILE B 834 " --> pdb=" O TYR B 857 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N MET B 859 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU B 836 " --> pdb=" O MET B 859 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE B 803 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU B 837 " --> pdb=" O ILE B 803 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B 805 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU B 802 " --> pdb=" O ALA B 877 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER B 916 " --> pdb=" O ASP B 878 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 920 " --> pdb=" O VAL B 882 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1006 through 1012 removed outlier: 3.918A pdb=" N ASP B1194 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B1039 " --> pdb=" O TYR B1197 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B1199 " --> pdb=" O PRO B1037 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 429 through 432 removed outlier: 6.152A pdb=" N VAL C 404 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU C 432 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE C 406 " --> pdb=" O LEU C 432 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N PHE C 454 " --> pdb=" O HIS C 373 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL C 375 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU C 456 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N CYS C 377 " --> pdb=" O LEU C 456 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS C 453 " --> pdb=" O TYR C 488 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLN C 490 " --> pdb=" O CYS C 453 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE C 455 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 560 through 565 removed outlier: 6.583A pdb=" N ILE C 625 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU C 595 " --> pdb=" O ILE C 625 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 750 through 752 Processing sheet with id=AB6, first strand: chain 'C' and resid 856 through 860 removed outlier: 6.132A pdb=" N ILE C 834 " --> pdb=" O TYR C 857 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N MET C 859 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU C 836 " --> pdb=" O MET C 859 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE C 803 " --> pdb=" O VAL C 835 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU C 837 " --> pdb=" O ILE C 803 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 805 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU C 802 " --> pdb=" O ALA C 877 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER C 916 " --> pdb=" O ASP C 878 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 920 " --> pdb=" O VAL C 882 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1006 through 1012 removed outlier: 3.917A pdb=" N ASP C1194 " --> pdb=" O ILE C1012 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY C1039 " --> pdb=" O TYR C1197 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE C1199 " --> pdb=" O PRO C1037 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 429 through 432 removed outlier: 6.165A pdb=" N VAL D 404 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU D 432 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE D 406 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N CYS D 453 " --> pdb=" O TYR D 488 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLN D 490 " --> pdb=" O CYS D 453 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE D 455 " --> pdb=" O GLN D 490 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 560 through 565 removed outlier: 6.584A pdb=" N ILE D 625 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU D 595 " --> pdb=" O ILE D 625 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 750 through 752 Processing sheet with id=AC2, first strand: chain 'D' and resid 856 through 860 removed outlier: 6.119A pdb=" N ILE D 834 " --> pdb=" O TYR D 857 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N MET D 859 " --> pdb=" O ILE D 834 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU D 836 " --> pdb=" O MET D 859 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE D 803 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU D 837 " --> pdb=" O ILE D 803 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL D 805 " --> pdb=" O LEU D 837 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU D 802 " --> pdb=" O ALA D 877 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER D 916 " --> pdb=" O ASP D 878 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU D 920 " --> pdb=" O VAL D 882 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1006 through 1012 removed outlier: 3.907A pdb=" N ASP D1194 " --> pdb=" O ILE D1012 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY D1039 " --> pdb=" O TYR D1197 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE D1199 " --> pdb=" O PRO D1037 " (cutoff:3.500A) 1401 hydrogen bonds defined for protein. 3903 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: 10.27 Time building geometry restraints manager: 12.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 2 1.22 - 1.37: 9990 1.37 - 1.53: 16059 1.53 - 1.68: 2981 1.68 - 1.83: 312 Bond restraints: 29344 Sorted by residual: bond pdb=" CB PRO C 139 " pdb=" CG PRO C 139 " ideal model delta sigma weight residual 1.492 1.065 0.427 5.00e-02 4.00e+02 7.28e+01 bond pdb=" CG PRO C 139 " pdb=" CD PRO C 139 " ideal model delta sigma weight residual 1.503 1.237 0.266 3.40e-02 8.65e+02 6.11e+01 bond pdb=" C ASP C 138 " pdb=" N PRO C 139 " ideal model delta sigma weight residual 1.335 1.264 0.071 1.30e-02 5.92e+03 2.98e+01 bond pdb=" N PRO C 139 " pdb=" CA PRO C 139 " ideal model delta sigma weight residual 1.473 1.525 -0.051 1.32e-02 5.74e+03 1.51e+01 bond pdb=" CG PRO C 423 " pdb=" CD PRO C 423 " ideal model delta sigma weight residual 1.503 1.393 0.110 3.40e-02 8.65e+02 1.05e+01 ... (remaining 29339 not shown) Histogram of bond angle deviations from ideal: 73.90 - 95.12: 4 95.12 - 116.33: 19591 116.33 - 137.55: 20216 137.55 - 158.76: 0 158.76 - 179.97: 1 Bond angle restraints: 39812 Sorted by residual: angle pdb=" CB PRO C 139 " pdb=" CG PRO C 139 " pdb=" CD PRO C 139 " ideal model delta sigma weight residual 106.10 179.97 -73.87 3.20e+00 9.77e-02 5.33e+02 angle pdb=" N PRO C 139 " pdb=" CD PRO C 139 " pdb=" CG PRO C 139 " ideal model delta sigma weight residual 103.20 73.90 29.30 1.50e+00 4.44e-01 3.81e+02 angle pdb=" CA PRO C 139 " pdb=" CB PRO C 139 " pdb=" CG PRO C 139 " ideal model delta sigma weight residual 104.50 74.99 29.51 1.90e+00 2.77e-01 2.41e+02 angle pdb=" N PRO C 423 " pdb=" CD PRO C 423 " pdb=" CG PRO C 423 " ideal model delta sigma weight residual 103.20 94.23 8.97 1.50e+00 4.44e-01 3.58e+01 angle pdb=" N PRO A 229 " pdb=" CA PRO A 229 " pdb=" C PRO A 229 " ideal model delta sigma weight residual 110.70 117.43 -6.73 1.22e+00 6.72e-01 3.04e+01 ... (remaining 39807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 15426 17.83 - 35.66: 1633 35.66 - 53.49: 403 53.49 - 71.32: 113 71.32 - 89.15: 29 Dihedral angle restraints: 17604 sinusoidal: 6992 harmonic: 10612 Sorted by residual: dihedral pdb=" CA PRO D 149 " pdb=" C PRO D 149 " pdb=" N LYS D 150 " pdb=" CA LYS D 150 " ideal model delta harmonic sigma weight residual 180.00 152.78 27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA PRO B 149 " pdb=" C PRO B 149 " pdb=" N LYS B 150 " pdb=" CA LYS B 150 " ideal model delta harmonic sigma weight residual 180.00 154.66 25.34 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA PRO A 149 " pdb=" C PRO A 149 " pdb=" N LYS A 150 " pdb=" CA LYS A 150 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 17601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4043 0.066 - 0.132: 463 0.132 - 0.198: 30 0.198 - 0.264: 3 0.264 - 0.330: 9 Chirality restraints: 4548 Sorted by residual: chirality pdb=" CA TRP C 146 " pdb=" N TRP C 146 " pdb=" C TRP C 146 " pdb=" CB TRP C 146 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA TRP D 146 " pdb=" N TRP D 146 " pdb=" C TRP D 146 " pdb=" CB TRP D 146 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA PRO D 149 " pdb=" N PRO D 149 " pdb=" C PRO D 149 " pdb=" CB PRO D 149 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 4545 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 169 " 0.032 2.00e-02 2.50e+03 3.87e-02 3.74e+01 pdb=" CG TRP A 169 " -0.095 2.00e-02 2.50e+03 pdb=" CD1 TRP A 169 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP A 169 " 0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP A 169 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP A 169 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 169 " 0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 169 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 169 " -0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP A 169 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 148 " -0.092 5.00e-02 4.00e+02 1.39e-01 3.07e+01 pdb=" N PRO A 149 " 0.240 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 148 " 0.092 5.00e-02 4.00e+02 1.38e-01 3.06e+01 pdb=" N PRO C 149 " -0.239 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.073 5.00e-02 4.00e+02 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.21: 23 2.21 - 2.94: 12399 2.94 - 3.67: 49918 3.67 - 4.41: 86827 4.41 - 5.14: 142549 Nonbonded interactions: 291716 Sorted by model distance: nonbonded pdb=" OE1 GLN B 415 " pdb=" NZ LYS C 438 " model vdw 1.477 2.520 nonbonded pdb=" NH1 ARG A1137 " pdb=" CD2 LEU B1204 " model vdw 1.836 3.540 nonbonded pdb=" CE1 HIS B1159 " pdb=" OE2 GLU C 848 " model vdw 2.024 3.260 nonbonded pdb=" CE1 HIS A1159 " pdb=" OE2 GLU B 848 " model vdw 2.033 3.260 nonbonded pdb=" O ASN B 163 " pdb=" OD1 ASN B 163 " model vdw 2.094 3.040 ... (remaining 291711 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 110 through 1205 or resid 1301 through 1305)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 5.250 Check model and map are aligned: 0.430 Set scattering table: 0.290 Process input model: 82.840 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.160 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:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.427 29344 Z= 0.383 Angle : 0.799 73.874 39812 Z= 0.398 Chirality : 0.046 0.330 4548 Planarity : 0.007 0.139 4992 Dihedral : 16.467 89.152 10716 Min Nonbonded Distance : 1.477 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.80 % Favored : 96.97 % Rotamer: Outliers : 1.62 % Allowed : 21.54 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.13), residues: 3532 helix: -0.40 (0.12), residues: 1684 sheet: -0.81 (0.24), residues: 356 loop : -0.38 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.002 TRP A 169 HIS 0.013 0.001 HIS D 291 PHE 0.032 0.002 PHE A 268 TYR 0.019 0.002 TYR D 351 ARG 0.009 0.001 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 532 time to evaluate : 3.241 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 232 ARG cc_start: 0.7958 (ttm170) cc_final: 0.7417 (ttm110) REVERT: A 275 PHE cc_start: 0.7159 (t80) cc_final: 0.6876 (t80) REVERT: B 604 LYS cc_start: 0.8043 (mttt) cc_final: 0.7799 (tptp) REVERT: B 794 LYS cc_start: 0.7698 (tptt) cc_final: 0.7399 (mmtm) REVERT: C 179 ILE cc_start: 0.7849 (mt) cc_final: 0.7618 (mp) REVERT: D 232 ARG cc_start: 0.7581 (mmm-85) cc_final: 0.7361 (mmm-85) REVERT: D 252 MET cc_start: 0.6810 (mtp) cc_final: 0.6539 (tmt) REVERT: D 603 ASN cc_start: 0.7574 (m-40) cc_final: 0.7056 (m110) REVERT: D 794 LYS cc_start: 0.8097 (tttp) cc_final: 0.7298 (mppt) outliers start: 51 outliers final: 36 residues processed: 571 average time/residue: 1.4913 time to fit residues: 982.8637 Evaluate side-chains 534 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 498 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1159 HIS Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 627 ILE Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 975 LEU Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1176 THR Chi-restraints excluded: chain C residue 1187 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 438 LYS Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 627 ILE Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 1176 THR Chi-restraints excluded: chain D residue 1204 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 7.9990 chunk 269 optimal weight: 9.9990 chunk 149 optimal weight: 0.2980 chunk 92 optimal weight: 3.9990 chunk 182 optimal weight: 30.0000 chunk 144 optimal weight: 0.0470 chunk 279 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 323 optimal weight: 9.9990 overall best weight: 1.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 218 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 GLN A 490 GLN A 505 HIS A 535 HIS A 603 ASN A 632 ASN A 981 GLN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 218 ASN B 298 ASN B 440 GLN B 490 GLN B 505 HIS B 535 HIS B 548 GLN B 952 ASN B 981 GLN B1046 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 218 ASN ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN C 505 HIS C 535 HIS C 632 ASN C 952 ASN C 981 GLN ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN D 218 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN D 415 GLN D 470 GLN D 490 GLN D 505 HIS D 535 HIS D 548 GLN D 632 ASN D 981 GLN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 29344 Z= 0.273 Angle : 0.596 11.370 39812 Z= 0.308 Chirality : 0.044 0.291 4548 Planarity : 0.006 0.135 4992 Dihedral : 5.788 58.735 3971 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.92 % Favored : 96.86 % Rotamer: Outliers : 4.61 % Allowed : 20.33 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.14), residues: 3532 helix: 0.43 (0.13), residues: 1692 sheet: -0.71 (0.24), residues: 348 loop : -0.18 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 228 HIS 0.008 0.001 HIS B 291 PHE 0.017 0.002 PHE A 283 TYR 0.018 0.002 TYR A 403 ARG 0.004 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 527 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8614 (mp) REVERT: A 200 LYS cc_start: 0.4206 (OUTLIER) cc_final: 0.3814 (tppt) REVERT: A 232 ARG cc_start: 0.8143 (ttm170) cc_final: 0.7570 (ttm110) REVERT: A 275 PHE cc_start: 0.7230 (t80) cc_final: 0.6952 (t80) REVERT: A 415 GLN cc_start: 0.8291 (mt0) cc_final: 0.7946 (mp10) REVERT: A 516 MET cc_start: 0.9117 (mtm) cc_final: 0.8489 (mtm) REVERT: A 548 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7842 (tp40) REVERT: A 604 LYS cc_start: 0.7849 (ptmm) cc_final: 0.7490 (tptp) REVERT: A 843 ASP cc_start: 0.8048 (p0) cc_final: 0.7839 (p0) REVERT: A 883 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7940 (m) REVERT: B 180 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7392 (tp40) REVERT: B 231 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7310 (tp) REVERT: B 413 ASP cc_start: 0.7848 (t0) cc_final: 0.7553 (t0) REVERT: B 415 GLN cc_start: 0.8278 (mt0) cc_final: 0.7799 (mp10) REVERT: B 428 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7755 (mtt180) REVERT: B 516 MET cc_start: 0.9108 (mtm) cc_final: 0.8485 (mtm) REVERT: B 604 LYS cc_start: 0.8012 (mttt) cc_final: 0.7594 (tptp) REVERT: B 794 LYS cc_start: 0.7767 (tptt) cc_final: 0.7414 (mppt) REVERT: B 859 MET cc_start: 0.8683 (ttm) cc_final: 0.8453 (ttm) REVERT: B 883 VAL cc_start: 0.8237 (OUTLIER) cc_final: 0.7993 (m) REVERT: C 200 LYS cc_start: 0.3593 (OUTLIER) cc_final: 0.3164 (tptp) REVERT: C 305 PHE cc_start: 0.8662 (t80) cc_final: 0.8398 (t80) REVERT: C 413 ASP cc_start: 0.8081 (t0) cc_final: 0.7874 (t0) REVERT: C 415 GLN cc_start: 0.8171 (mt0) cc_final: 0.7795 (mp10) REVERT: C 516 MET cc_start: 0.9131 (mtm) cc_final: 0.8543 (mtm) REVERT: C 604 LYS cc_start: 0.7933 (ptmm) cc_final: 0.7504 (tptp) REVERT: C 883 VAL cc_start: 0.8359 (OUTLIER) cc_final: 0.8146 (m) REVERT: C 988 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8765 (mmm) REVERT: D 200 LYS cc_start: 0.2805 (OUTLIER) cc_final: 0.2510 (tppp) REVERT: D 228 TRP cc_start: 0.5110 (OUTLIER) cc_final: 0.3854 (m100) REVERT: D 415 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7813 (mp10) REVERT: D 516 MET cc_start: 0.9101 (mtm) cc_final: 0.8482 (mtm) REVERT: D 548 GLN cc_start: 0.8107 (tp40) cc_final: 0.7867 (tp-100) REVERT: D 604 LYS cc_start: 0.7915 (ptmm) cc_final: 0.7279 (tptp) REVERT: D 783 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7163 (ptmm) REVERT: D 794 LYS cc_start: 0.8183 (tttp) cc_final: 0.7465 (mppt) REVERT: D 883 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7934 (m) outliers start: 145 outliers final: 71 residues processed: 609 average time/residue: 1.3808 time to fit residues: 980.1423 Evaluate side-chains 592 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 505 time to evaluate : 3.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 1016 ASP Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain B residue 1159 HIS Chi-restraints excluded: chain B residue 1204 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1016 ASP Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 600 ARG Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 840 ASN Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 1016 ASP Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1038 ILE Chi-restraints excluded: chain D residue 1204 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 269 optimal weight: 0.3980 chunk 220 optimal weight: 0.5980 chunk 89 optimal weight: 20.0000 chunk 323 optimal weight: 0.8980 chunk 349 optimal weight: 9.9990 chunk 288 optimal weight: 2.9990 chunk 321 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 GLN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 298 ASN B 952 ASN B 981 GLN B1046 HIS B1159 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C 632 ASN C 952 ASN C 981 GLN C1046 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN D 415 GLN D 632 ASN D 952 ASN D 981 GLN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 29344 Z= 0.298 Angle : 0.590 10.173 39812 Z= 0.301 Chirality : 0.044 0.278 4548 Planarity : 0.005 0.132 4992 Dihedral : 5.387 57.882 3926 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.77 % Favored : 97.00 % Rotamer: Outliers : 4.99 % Allowed : 21.06 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.14), residues: 3532 helix: 0.64 (0.13), residues: 1696 sheet: -0.97 (0.24), residues: 356 loop : -0.11 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 228 HIS 0.008 0.001 HIS B 291 PHE 0.014 0.002 PHE A 798 TYR 0.016 0.002 TYR B 351 ARG 0.005 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 532 time to evaluate : 3.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.4240 (OUTLIER) cc_final: 0.3801 (tppt) REVERT: A 232 ARG cc_start: 0.8152 (ttm170) cc_final: 0.7413 (ttm170) REVERT: A 267 MET cc_start: 0.8165 (ttm) cc_final: 0.7580 (ttm) REVERT: A 275 PHE cc_start: 0.7259 (t80) cc_final: 0.6837 (t80) REVERT: A 415 GLN cc_start: 0.8257 (mt0) cc_final: 0.7932 (mp10) REVERT: A 604 LYS cc_start: 0.7874 (ptmm) cc_final: 0.7463 (tptp) REVERT: A 859 MET cc_start: 0.8722 (ttm) cc_final: 0.8484 (ttm) REVERT: A 883 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.7959 (m) REVERT: B 180 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7291 (tp40) REVERT: B 231 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7309 (tp) REVERT: B 413 ASP cc_start: 0.7688 (t0) cc_final: 0.7325 (t0) REVERT: B 415 GLN cc_start: 0.8224 (mt0) cc_final: 0.7736 (mp10) REVERT: B 428 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7671 (mtt180) REVERT: B 461 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6737 (mt-10) REVERT: B 604 LYS cc_start: 0.7997 (mttt) cc_final: 0.7516 (tptp) REVERT: B 794 LYS cc_start: 0.7847 (tptt) cc_final: 0.7403 (mppt) REVERT: B 883 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7994 (m) REVERT: B 950 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7273 (ttp-170) REVERT: C 174 MET cc_start: 0.7059 (tpp) cc_final: 0.6806 (tpt) REVERT: C 200 LYS cc_start: 0.3604 (OUTLIER) cc_final: 0.3106 (tptp) REVERT: C 215 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6531 (tm-30) REVERT: C 267 MET cc_start: 0.7788 (ttp) cc_final: 0.7263 (ttm) REVERT: C 275 PHE cc_start: 0.7223 (t80) cc_final: 0.7004 (t80) REVERT: C 415 GLN cc_start: 0.8104 (mt0) cc_final: 0.7761 (mp10) REVERT: C 604 LYS cc_start: 0.7950 (ptmm) cc_final: 0.7372 (tptp) REVERT: C 883 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.8153 (m) REVERT: C 1137 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7191 (ttt-90) REVERT: D 200 LYS cc_start: 0.2799 (OUTLIER) cc_final: 0.2507 (tppp) REVERT: D 228 TRP cc_start: 0.5291 (OUTLIER) cc_final: 0.4036 (m100) REVERT: D 267 MET cc_start: 0.8211 (ttm) cc_final: 0.7758 (tpp) REVERT: D 334 MET cc_start: 0.8255 (tpp) cc_final: 0.8001 (mmm) REVERT: D 415 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7737 (mp10) REVERT: D 548 GLN cc_start: 0.8063 (tp40) cc_final: 0.7784 (tp-100) REVERT: D 604 LYS cc_start: 0.7926 (ptmm) cc_final: 0.7302 (tptp) REVERT: D 783 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.7149 (ptmm) REVERT: D 794 LYS cc_start: 0.8122 (tttp) cc_final: 0.7413 (mppt) REVERT: D 883 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7937 (m) outliers start: 157 outliers final: 84 residues processed: 620 average time/residue: 1.4024 time to fit residues: 1013.4256 Evaluate side-chains 615 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 515 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 950 ARG Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 981 GLN Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1016 ASP Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain B residue 1204 LEU Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1016 ASP Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1137 ARG Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1152 LEU Chi-restraints excluded: chain C residue 1187 ASP Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 600 ARG Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 840 ASN Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1016 ASP Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1152 LEU Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1204 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 0.8980 chunk 243 optimal weight: 4.9990 chunk 168 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 325 optimal weight: 0.7980 chunk 344 optimal weight: 0.8980 chunk 169 optimal weight: 0.9980 chunk 308 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 490 GLN B 548 GLN B 952 ASN B1046 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN C 981 GLN C1046 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 GLN D 490 GLN D 632 ASN D 952 ASN D 981 GLN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 29344 Z= 0.187 Angle : 0.535 9.986 39812 Z= 0.274 Chirality : 0.041 0.271 4548 Planarity : 0.005 0.128 4992 Dihedral : 5.158 56.657 3924 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.77 % Favored : 97.00 % Rotamer: Outliers : 4.51 % Allowed : 21.63 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.14), residues: 3532 helix: 0.93 (0.13), residues: 1696 sheet: -0.78 (0.24), residues: 348 loop : 0.01 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 228 HIS 0.006 0.001 HIS A 291 PHE 0.021 0.001 PHE C 188 TYR 0.017 0.001 TYR B 351 ARG 0.006 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 529 time to evaluate : 3.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 TRP cc_start: 0.7867 (m100) cc_final: 0.7609 (m100) REVERT: A 171 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: A 200 LYS cc_start: 0.4283 (OUTLIER) cc_final: 0.3837 (tppt) REVERT: A 228 TRP cc_start: 0.6118 (m-90) cc_final: 0.5440 (t60) REVERT: A 232 ARG cc_start: 0.8108 (ttm170) cc_final: 0.7842 (ttm170) REVERT: A 267 MET cc_start: 0.8041 (ttm) cc_final: 0.7376 (ttm) REVERT: A 275 PHE cc_start: 0.7189 (t80) cc_final: 0.6827 (t80) REVERT: A 415 GLN cc_start: 0.8227 (mt0) cc_final: 0.7937 (mp10) REVERT: A 548 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7786 (tp40) REVERT: A 604 LYS cc_start: 0.7880 (ptmm) cc_final: 0.7325 (tptp) REVERT: A 859 MET cc_start: 0.8655 (ttm) cc_final: 0.8384 (ttm) REVERT: A 883 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7954 (m) REVERT: A 1162 LEU cc_start: 0.8105 (mt) cc_final: 0.7903 (mt) REVERT: B 136 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8308 (mp) REVERT: B 180 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7269 (tp40) REVERT: B 413 ASP cc_start: 0.7632 (t0) cc_final: 0.7256 (t0) REVERT: B 415 GLN cc_start: 0.8206 (mt0) cc_final: 0.7729 (mp10) REVERT: B 565 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7722 (ttp80) REVERT: B 604 LYS cc_start: 0.8003 (mttt) cc_final: 0.7524 (tptp) REVERT: B 794 LYS cc_start: 0.7861 (tptt) cc_final: 0.7340 (mppt) REVERT: B 883 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7961 (m) REVERT: B 988 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8794 (mmm) REVERT: B 1137 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7080 (ttt-90) REVERT: C 200 LYS cc_start: 0.3437 (OUTLIER) cc_final: 0.2951 (tptp) REVERT: C 216 MET cc_start: 0.7214 (mmt) cc_final: 0.6942 (mpt) REVERT: C 252 MET cc_start: 0.5739 (OUTLIER) cc_final: 0.5022 (tpt) REVERT: C 267 MET cc_start: 0.7851 (ttp) cc_final: 0.7405 (ttm) REVERT: C 275 PHE cc_start: 0.7154 (t80) cc_final: 0.6913 (t80) REVERT: C 566 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.6929 (ttp) REVERT: C 604 LYS cc_start: 0.7954 (ptmm) cc_final: 0.7427 (tptp) REVERT: C 883 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.8107 (m) REVERT: C 988 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8761 (mmm) REVERT: C 1137 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7237 (ttt-90) REVERT: D 136 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8546 (mp) REVERT: D 200 LYS cc_start: 0.2794 (OUTLIER) cc_final: 0.2503 (tppp) REVERT: D 228 TRP cc_start: 0.5281 (OUTLIER) cc_final: 0.4063 (m100) REVERT: D 267 MET cc_start: 0.8131 (ttm) cc_final: 0.7852 (tpp) REVERT: D 275 PHE cc_start: 0.7310 (t80) cc_final: 0.6926 (t80) REVERT: D 294 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8348 (ttp80) REVERT: D 334 MET cc_start: 0.8174 (tpp) cc_final: 0.7946 (mmm) REVERT: D 415 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7761 (mp10) REVERT: D 548 GLN cc_start: 0.8010 (tp40) cc_final: 0.7733 (tp-100) REVERT: D 604 LYS cc_start: 0.7908 (ptmm) cc_final: 0.7273 (tptp) REVERT: D 794 LYS cc_start: 0.8059 (tttp) cc_final: 0.7397 (mppt) REVERT: D 883 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7907 (m) REVERT: D 988 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8816 (mmm) outliers start: 142 outliers final: 77 residues processed: 606 average time/residue: 1.4367 time to fit residues: 1013.6164 Evaluate side-chains 619 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 519 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1016 ASP Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1137 ARG Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain B residue 1204 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 490 GLN Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1016 ASP Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain C residue 1137 ARG Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1176 THR Chi-restraints excluded: chain C residue 1187 ASP Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 294 ARG Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 840 ASN Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1038 ILE Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1176 THR Chi-restraints excluded: chain D residue 1187 ASP Chi-restraints excluded: chain D residue 1204 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 256 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 293 optimal weight: 0.7980 chunk 237 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 175 optimal weight: 10.0000 chunk 308 optimal weight: 10.0000 chunk 86 optimal weight: 0.1980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B 952 ASN B1046 HIS ** B1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN C 981 GLN C1046 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 GLN D 490 GLN D 632 ASN D 788 ASN D 952 ASN D 981 GLN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 29344 Z= 0.246 Angle : 0.557 11.164 39812 Z= 0.283 Chirality : 0.042 0.267 4548 Planarity : 0.005 0.125 4992 Dihedral : 5.168 56.378 3924 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.69 % Favored : 97.08 % Rotamer: Outliers : 4.61 % Allowed : 22.01 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.14), residues: 3532 helix: 0.99 (0.13), residues: 1696 sheet: -0.75 (0.24), residues: 348 loop : 0.08 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS A 291 PHE 0.021 0.001 PHE D 235 TYR 0.017 0.001 TYR B 351 ARG 0.007 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 526 time to evaluate : 3.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 TRP cc_start: 0.7896 (m100) cc_final: 0.7680 (m100) REVERT: A 171 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: A 174 MET cc_start: 0.6081 (tpp) cc_final: 0.5636 (mmm) REVERT: A 200 LYS cc_start: 0.3999 (OUTLIER) cc_final: 0.3581 (tppt) REVERT: A 210 VAL cc_start: 0.4614 (OUTLIER) cc_final: 0.4253 (p) REVERT: A 232 ARG cc_start: 0.8172 (ttm170) cc_final: 0.7664 (ttm110) REVERT: A 267 MET cc_start: 0.8082 (ttm) cc_final: 0.7308 (tpp) REVERT: A 275 PHE cc_start: 0.7078 (t80) cc_final: 0.6664 (t80) REVERT: A 415 GLN cc_start: 0.8197 (mt0) cc_final: 0.7921 (mp10) REVERT: A 548 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7787 (tp40) REVERT: A 604 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7290 (tptp) REVERT: A 883 VAL cc_start: 0.8208 (OUTLIER) cc_final: 0.7964 (m) REVERT: A 1162 LEU cc_start: 0.8148 (mt) cc_final: 0.7936 (mt) REVERT: B 136 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8348 (mp) REVERT: B 180 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7208 (tp40) REVERT: B 231 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7230 (tp) REVERT: B 413 ASP cc_start: 0.7660 (t0) cc_final: 0.7153 (t0) REVERT: B 415 GLN cc_start: 0.8214 (mt0) cc_final: 0.7725 (mp10) REVERT: B 428 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7079 (mtm180) REVERT: B 548 GLN cc_start: 0.8041 (tp-100) cc_final: 0.7785 (tp-100) REVERT: B 604 LYS cc_start: 0.8079 (mttt) cc_final: 0.7532 (tptp) REVERT: B 794 LYS cc_start: 0.7875 (tptt) cc_final: 0.7365 (mppt) REVERT: B 844 HIS cc_start: 0.7506 (p-80) cc_final: 0.7173 (p-80) REVERT: B 859 MET cc_start: 0.8680 (ttm) cc_final: 0.8454 (ttm) REVERT: B 883 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7969 (m) REVERT: B 950 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7234 (ttp-170) REVERT: B 1137 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7147 (ttt-90) REVERT: C 200 LYS cc_start: 0.3351 (OUTLIER) cc_final: 0.2811 (tptp) REVERT: C 216 MET cc_start: 0.7149 (mmt) cc_final: 0.6861 (mpt) REVERT: C 252 MET cc_start: 0.5754 (OUTLIER) cc_final: 0.5057 (tpt) REVERT: C 267 MET cc_start: 0.7878 (ttp) cc_final: 0.7486 (ttm) REVERT: C 275 PHE cc_start: 0.7163 (t80) cc_final: 0.6925 (t80) REVERT: C 415 GLN cc_start: 0.8101 (mt0) cc_final: 0.7736 (mp10) REVERT: C 604 LYS cc_start: 0.7969 (ptmm) cc_final: 0.7406 (tptp) REVERT: C 794 LYS cc_start: 0.8118 (ttpp) cc_final: 0.7782 (tmmt) REVERT: C 876 TYR cc_start: 0.7991 (OUTLIER) cc_final: 0.7347 (p90) REVERT: C 883 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8109 (m) REVERT: C 1137 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7232 (ttt-90) REVERT: D 136 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8589 (mp) REVERT: D 200 LYS cc_start: 0.2777 (OUTLIER) cc_final: 0.2482 (tppp) REVERT: D 267 MET cc_start: 0.8123 (ttm) cc_final: 0.7764 (tpp) REVERT: D 275 PHE cc_start: 0.7339 (t80) cc_final: 0.6942 (t80) REVERT: D 334 MET cc_start: 0.8187 (tpp) cc_final: 0.7974 (mmm) REVERT: D 428 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7210 (mtm180) REVERT: D 548 GLN cc_start: 0.8001 (tp40) cc_final: 0.7743 (tp-100) REVERT: D 604 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7264 (tptp) REVERT: D 876 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.7421 (p90) REVERT: D 883 VAL cc_start: 0.8152 (OUTLIER) cc_final: 0.7908 (m) outliers start: 145 outliers final: 83 residues processed: 606 average time/residue: 1.4042 time to fit residues: 991.7970 Evaluate side-chains 616 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 509 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1016 ASP Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain B residue 1137 ARG Chi-restraints excluded: chain B residue 1143 ARG Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain B residue 1204 LEU Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 490 GLN Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 981 GLN Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1016 ASP Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain C residue 1137 ARG Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1187 ASP Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 428 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 604 LYS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 840 ASN Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 981 GLN Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1016 ASP Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1038 ILE Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain D residue 1187 ASP Chi-restraints excluded: chain D residue 1204 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 4.9990 chunk 309 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 344 optimal weight: 5.9990 chunk 285 optimal weight: 5.9990 chunk 159 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 270 GLN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B 952 ASN B1046 HIS ** B1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN C 981 GLN C1046 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 GLN D 632 ASN D 952 ASN D 981 GLN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 29344 Z= 0.235 Angle : 0.557 12.454 39812 Z= 0.282 Chirality : 0.042 0.264 4548 Planarity : 0.005 0.123 4992 Dihedral : 5.066 56.664 3922 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.77 % Favored : 97.00 % Rotamer: Outliers : 4.70 % Allowed : 22.33 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 3532 helix: 1.02 (0.13), residues: 1720 sheet: -0.73 (0.25), residues: 348 loop : 0.15 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.006 0.001 HIS A 291 PHE 0.025 0.001 PHE D 235 TYR 0.018 0.001 TYR B 351 ARG 0.007 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 520 time to evaluate : 3.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 TRP cc_start: 0.7911 (m100) cc_final: 0.7710 (m100) REVERT: A 200 LYS cc_start: 0.4031 (OUTLIER) cc_final: 0.3609 (tppt) REVERT: A 210 VAL cc_start: 0.4677 (OUTLIER) cc_final: 0.4308 (p) REVERT: A 232 ARG cc_start: 0.8188 (ttm170) cc_final: 0.7676 (ttm110) REVERT: A 267 MET cc_start: 0.8137 (ttm) cc_final: 0.7266 (tpp) REVERT: A 275 PHE cc_start: 0.7043 (t80) cc_final: 0.6582 (t80) REVERT: A 415 GLN cc_start: 0.8201 (mt0) cc_final: 0.7917 (mp10) REVERT: A 417 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7863 (mtt90) REVERT: A 461 GLU cc_start: 0.7398 (tt0) cc_final: 0.7158 (tm-30) REVERT: A 548 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7793 (tp40) REVERT: A 604 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7275 (tptp) REVERT: A 883 VAL cc_start: 0.8203 (OUTLIER) cc_final: 0.7961 (m) REVERT: B 136 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8396 (mp) REVERT: B 180 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7174 (tp40) REVERT: B 220 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7775 (pt) REVERT: B 413 ASP cc_start: 0.7722 (t0) cc_final: 0.7213 (t0) REVERT: B 415 GLN cc_start: 0.8223 (mt0) cc_final: 0.7714 (mp10) REVERT: B 428 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7083 (mtm180) REVERT: B 461 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6783 (mt-10) REVERT: B 548 GLN cc_start: 0.8032 (tp-100) cc_final: 0.7778 (tp-100) REVERT: B 604 LYS cc_start: 0.8075 (mttt) cc_final: 0.7529 (tptp) REVERT: B 783 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6725 (ptmm) REVERT: B 794 LYS cc_start: 0.7919 (tptt) cc_final: 0.7337 (mppt) REVERT: B 844 HIS cc_start: 0.7478 (p-80) cc_final: 0.7130 (p-80) REVERT: B 859 MET cc_start: 0.8664 (ttm) cc_final: 0.8432 (ttm) REVERT: B 883 VAL cc_start: 0.8206 (OUTLIER) cc_final: 0.7966 (m) REVERT: B 950 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7211 (ttp-170) REVERT: B 1137 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7141 (ttt-90) REVERT: C 200 LYS cc_start: 0.3362 (OUTLIER) cc_final: 0.2807 (tptp) REVERT: C 216 MET cc_start: 0.7312 (mmt) cc_final: 0.7059 (mpt) REVERT: C 252 MET cc_start: 0.5710 (OUTLIER) cc_final: 0.5020 (tpt) REVERT: C 267 MET cc_start: 0.7909 (ttp) cc_final: 0.7524 (ttm) REVERT: C 275 PHE cc_start: 0.7166 (t80) cc_final: 0.6900 (t80) REVERT: C 604 LYS cc_start: 0.7965 (ptmm) cc_final: 0.7324 (tptp) REVERT: C 794 LYS cc_start: 0.8133 (ttpp) cc_final: 0.7791 (tmmt) REVERT: C 876 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7401 (p90) REVERT: C 883 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.8109 (m) REVERT: C 950 ARG cc_start: 0.7457 (ttm170) cc_final: 0.7210 (mtm180) REVERT: D 136 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8552 (mp) REVERT: D 176 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8036 (mm) REVERT: D 200 LYS cc_start: 0.2816 (OUTLIER) cc_final: 0.2545 (tppp) REVERT: D 267 MET cc_start: 0.8148 (ttm) cc_final: 0.7832 (tpp) REVERT: D 275 PHE cc_start: 0.7224 (t80) cc_final: 0.6776 (t80) REVERT: D 334 MET cc_start: 0.8188 (tpp) cc_final: 0.7978 (mmm) REVERT: D 428 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7215 (mtm180) REVERT: D 461 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6785 (tm-30) REVERT: D 548 GLN cc_start: 0.7991 (tp40) cc_final: 0.7721 (tp-100) REVERT: D 604 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7220 (tptp) REVERT: D 844 HIS cc_start: 0.7481 (p-80) cc_final: 0.7086 (p-80) REVERT: D 859 MET cc_start: 0.8666 (ttm) cc_final: 0.8436 (ttm) REVERT: D 876 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7387 (p90) REVERT: D 883 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7908 (m) outliers start: 148 outliers final: 89 residues processed: 606 average time/residue: 1.3714 time to fit residues: 970.8292 Evaluate side-chains 629 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 513 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain B residue 1137 ARG Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain B residue 1204 LEU Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 490 GLN Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 981 GLN Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1016 ASP Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1152 LEU Chi-restraints excluded: chain C residue 1176 THR Chi-restraints excluded: chain C residue 1187 ASP Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 428 ARG Chi-restraints excluded: chain D residue 461 GLU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 600 ARG Chi-restraints excluded: chain D residue 604 LYS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 840 ASN Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 981 GLN Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1016 ASP Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1033 SER Chi-restraints excluded: chain D residue 1038 ILE Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain D residue 1176 THR Chi-restraints excluded: chain D residue 1187 ASP Chi-restraints excluded: chain D residue 1204 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 251 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 289 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 343 optimal weight: 1.9990 chunk 214 optimal weight: 0.3980 chunk 209 optimal weight: 0.8980 chunk 158 optimal weight: 0.0570 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 270 GLN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B 952 ASN B1046 HIS ** B1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN C 981 GLN C1046 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 GLN D 632 ASN D 952 ASN D 981 GLN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 29344 Z= 0.210 Angle : 0.553 14.407 39812 Z= 0.280 Chirality : 0.042 0.277 4548 Planarity : 0.005 0.120 4992 Dihedral : 5.012 57.527 3922 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.86 % Favored : 96.91 % Rotamer: Outliers : 4.45 % Allowed : 22.55 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.14), residues: 3532 helix: 1.08 (0.13), residues: 1724 sheet: -0.68 (0.25), residues: 348 loop : 0.17 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS D 291 PHE 0.029 0.001 PHE D 235 TYR 0.019 0.001 TYR B 351 ARG 0.004 0.000 ARG B 968 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 522 time to evaluate : 3.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.4038 (OUTLIER) cc_final: 0.3622 (tppt) REVERT: A 210 VAL cc_start: 0.4668 (OUTLIER) cc_final: 0.4300 (p) REVERT: A 232 ARG cc_start: 0.8196 (ttm170) cc_final: 0.7660 (ttm110) REVERT: A 267 MET cc_start: 0.8136 (ttm) cc_final: 0.7381 (tpp) REVERT: A 275 PHE cc_start: 0.7068 (t80) cc_final: 0.6609 (t80) REVERT: A 415 GLN cc_start: 0.8206 (mt0) cc_final: 0.7907 (mp10) REVERT: A 548 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7783 (tp40) REVERT: A 604 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7233 (tptp) REVERT: A 794 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6554 (mmtm) REVERT: A 883 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7951 (m) REVERT: B 180 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7227 (tp40) REVERT: B 220 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7788 (pt) REVERT: B 413 ASP cc_start: 0.7655 (t0) cc_final: 0.7173 (t0) REVERT: B 415 GLN cc_start: 0.8206 (mt0) cc_final: 0.7703 (mp10) REVERT: B 428 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7154 (mtm180) REVERT: B 461 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6791 (mt-10) REVERT: B 548 GLN cc_start: 0.8015 (tp-100) cc_final: 0.7756 (tp-100) REVERT: B 604 LYS cc_start: 0.8076 (mttt) cc_final: 0.7536 (tptp) REVERT: B 783 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.6707 (ptmm) REVERT: B 794 LYS cc_start: 0.7917 (tptt) cc_final: 0.7341 (mppt) REVERT: B 844 HIS cc_start: 0.7467 (p-80) cc_final: 0.7118 (p-80) REVERT: B 859 MET cc_start: 0.8653 (ttm) cc_final: 0.8427 (ttm) REVERT: B 883 VAL cc_start: 0.8199 (OUTLIER) cc_final: 0.7962 (m) REVERT: B 950 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7181 (ttp-170) REVERT: B 1137 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7134 (ttt-90) REVERT: C 174 MET cc_start: 0.6894 (OUTLIER) cc_final: 0.6488 (tpt) REVERT: C 200 LYS cc_start: 0.3369 (OUTLIER) cc_final: 0.2800 (tptp) REVERT: C 216 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.7055 (mpt) REVERT: C 231 LEU cc_start: 0.7702 (mt) cc_final: 0.7260 (tt) REVERT: C 252 MET cc_start: 0.5610 (OUTLIER) cc_final: 0.4961 (tpt) REVERT: C 267 MET cc_start: 0.7913 (ttp) cc_final: 0.7551 (ttm) REVERT: C 275 PHE cc_start: 0.7172 (t80) cc_final: 0.6898 (t80) REVERT: C 604 LYS cc_start: 0.7970 (ptmm) cc_final: 0.7310 (tptp) REVERT: C 794 LYS cc_start: 0.8065 (ttpp) cc_final: 0.7702 (tmmt) REVERT: C 876 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7347 (p90) REVERT: C 950 ARG cc_start: 0.7440 (ttm170) cc_final: 0.7206 (mtm180) REVERT: C 988 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8757 (mmm) REVERT: C 1137 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6423 (ttt-90) REVERT: D 200 LYS cc_start: 0.2906 (OUTLIER) cc_final: 0.2670 (tppp) REVERT: D 267 MET cc_start: 0.8118 (ttm) cc_final: 0.7829 (tpp) REVERT: D 275 PHE cc_start: 0.7226 (t80) cc_final: 0.6786 (t80) REVERT: D 548 GLN cc_start: 0.7972 (tp40) cc_final: 0.7695 (tp-100) REVERT: D 604 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7205 (tptp) REVERT: D 799 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8277 (mmtp) REVERT: D 844 HIS cc_start: 0.7470 (p-80) cc_final: 0.7071 (p-80) REVERT: D 859 MET cc_start: 0.8646 (ttm) cc_final: 0.8421 (ttm) REVERT: D 876 TYR cc_start: 0.7991 (OUTLIER) cc_final: 0.7402 (p90) REVERT: D 883 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7898 (m) REVERT: D 950 ARG cc_start: 0.7610 (ttm170) cc_final: 0.7341 (ttm170) outliers start: 140 outliers final: 82 residues processed: 596 average time/residue: 1.4006 time to fit residues: 973.6521 Evaluate side-chains 620 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 513 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain B residue 1137 ARG Chi-restraints excluded: chain B residue 1143 ARG Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain B residue 1204 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 490 GLN Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1016 ASP Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain C residue 1137 ARG Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1176 THR Chi-restraints excluded: chain C residue 1187 ASP Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 604 LYS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 840 ASN Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1038 ILE Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain D residue 1176 THR Chi-restraints excluded: chain D residue 1187 ASP Chi-restraints excluded: chain D residue 1204 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 204 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 218 optimal weight: 0.6980 chunk 233 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 269 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 298 ASN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B 952 ASN B1046 HIS ** B1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN C 981 GLN C1046 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 GLN D 632 ASN D 952 ASN D 981 GLN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 29344 Z= 0.191 Angle : 0.551 12.122 39812 Z= 0.278 Chirality : 0.042 0.260 4548 Planarity : 0.005 0.118 4992 Dihedral : 4.840 58.711 3920 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.66 % Favored : 97.11 % Rotamer: Outliers : 4.07 % Allowed : 23.00 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.14), residues: 3532 helix: 1.21 (0.13), residues: 1700 sheet: -0.58 (0.25), residues: 348 loop : 0.16 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 169 HIS 0.005 0.001 HIS D 291 PHE 0.030 0.001 PHE D 235 TYR 0.019 0.001 TYR B 351 ARG 0.004 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 524 time to evaluate : 3.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ILE cc_start: 0.7251 (tp) cc_final: 0.6706 (pt) REVERT: A 171 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: A 200 LYS cc_start: 0.4034 (OUTLIER) cc_final: 0.3609 (tppt) REVERT: A 210 VAL cc_start: 0.4768 (OUTLIER) cc_final: 0.4414 (p) REVERT: A 228 TRP cc_start: 0.6183 (m-90) cc_final: 0.5444 (t60) REVERT: A 232 ARG cc_start: 0.8176 (ttm170) cc_final: 0.7627 (ttm170) REVERT: A 267 MET cc_start: 0.8120 (ttm) cc_final: 0.7468 (tpp) REVERT: A 275 PHE cc_start: 0.7065 (t80) cc_final: 0.6585 (t80) REVERT: A 415 GLN cc_start: 0.8195 (mt0) cc_final: 0.7892 (mp10) REVERT: A 428 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7058 (mtm180) REVERT: A 461 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7155 (tm-30) REVERT: A 548 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7762 (tp40) REVERT: A 604 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7272 (tptp) REVERT: A 794 LYS cc_start: 0.7282 (mppt) cc_final: 0.6763 (mmtm) REVERT: A 844 HIS cc_start: 0.7445 (p-80) cc_final: 0.7025 (p-80) REVERT: A 859 MET cc_start: 0.8645 (ttm) cc_final: 0.8438 (ttm) REVERT: A 883 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7934 (m) REVERT: A 988 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8792 (mmm) REVERT: B 129 LEU cc_start: 0.8652 (tp) cc_final: 0.8286 (tt) REVERT: B 131 ILE cc_start: 0.8008 (mm) cc_final: 0.7713 (OUTLIER) REVERT: B 180 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7312 (tp40) REVERT: B 220 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7603 (pt) REVERT: B 291 HIS cc_start: 0.8528 (t70) cc_final: 0.8269 (t70) REVERT: B 349 LEU cc_start: 0.8471 (mt) cc_final: 0.8225 (mt) REVERT: B 352 LEU cc_start: 0.7915 (mt) cc_final: 0.7706 (mm) REVERT: B 413 ASP cc_start: 0.7606 (t0) cc_final: 0.7115 (t0) REVERT: B 415 GLN cc_start: 0.8193 (mt0) cc_final: 0.7682 (mp10) REVERT: B 428 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7161 (mtm180) REVERT: B 461 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6807 (mt-10) REVERT: B 548 GLN cc_start: 0.8004 (tp-100) cc_final: 0.7751 (tp-100) REVERT: B 604 LYS cc_start: 0.8012 (mttt) cc_final: 0.7513 (tptp) REVERT: B 786 LYS cc_start: 0.7759 (mppt) cc_final: 0.7303 (mmmm) REVERT: B 794 LYS cc_start: 0.7928 (tptt) cc_final: 0.7358 (mppt) REVERT: B 844 HIS cc_start: 0.7442 (p-80) cc_final: 0.7073 (p-80) REVERT: B 859 MET cc_start: 0.8622 (ttm) cc_final: 0.8411 (ttm) REVERT: B 883 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7955 (m) REVERT: B 930 MET cc_start: 0.6243 (tmm) cc_final: 0.5872 (mmm) REVERT: B 950 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7166 (ttp-170) REVERT: B 988 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8805 (mmm) REVERT: C 174 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6616 (tpt) REVERT: C 200 LYS cc_start: 0.3160 (OUTLIER) cc_final: 0.2693 (tptp) REVERT: C 216 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.7040 (mpt) REVERT: C 231 LEU cc_start: 0.7677 (mt) cc_final: 0.7221 (tt) REVERT: C 252 MET cc_start: 0.5707 (OUTLIER) cc_final: 0.5126 (tpt) REVERT: C 267 MET cc_start: 0.7791 (ttp) cc_final: 0.7417 (ttm) REVERT: C 275 PHE cc_start: 0.7224 (t80) cc_final: 0.6925 (t80) REVERT: C 604 LYS cc_start: 0.7958 (ptmm) cc_final: 0.7335 (tptp) REVERT: C 794 LYS cc_start: 0.8056 (ttpp) cc_final: 0.7685 (tmmt) REVERT: C 876 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7295 (p90) REVERT: C 950 ARG cc_start: 0.7413 (ttm170) cc_final: 0.7199 (mtm180) REVERT: C 988 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8765 (mmm) REVERT: C 1137 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6465 (ttt-90) REVERT: D 200 LYS cc_start: 0.2851 (OUTLIER) cc_final: 0.2631 (tppp) REVERT: D 294 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7967 (ttp80) REVERT: D 355 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7317 (mm-30) REVERT: D 428 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7265 (mtm180) REVERT: D 461 GLU cc_start: 0.6969 (tt0) cc_final: 0.6748 (tm-30) REVERT: D 548 GLN cc_start: 0.7931 (tp40) cc_final: 0.7675 (tp-100) REVERT: D 604 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7187 (tptp) REVERT: D 783 LYS cc_start: 0.7546 (ptmm) cc_final: 0.7318 (pptt) REVERT: D 799 LYS cc_start: 0.8641 (mmmt) cc_final: 0.8279 (mmtp) REVERT: D 844 HIS cc_start: 0.7432 (p-80) cc_final: 0.7023 (p-80) REVERT: D 859 MET cc_start: 0.8605 (ttm) cc_final: 0.8399 (ttm) REVERT: D 876 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7350 (p90) REVERT: D 883 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7878 (m) REVERT: D 988 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8822 (mmm) outliers start: 128 outliers final: 77 residues processed: 598 average time/residue: 1.4293 time to fit residues: 993.3462 Evaluate side-chains 618 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 513 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain B residue 1143 ARG Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain B residue 1204 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 490 GLN Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain C residue 1137 ARG Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1176 THR Chi-restraints excluded: chain C residue 1187 ASP Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 294 ARG Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 428 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 604 LYS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 840 ASN Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1038 ILE Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain D residue 1176 THR Chi-restraints excluded: chain D residue 1187 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 6.9990 chunk 328 optimal weight: 3.9990 chunk 299 optimal weight: 4.9990 chunk 319 optimal weight: 0.9980 chunk 192 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 288 optimal weight: 0.7980 chunk 302 optimal weight: 0.1980 chunk 318 optimal weight: 9.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A 952 ASN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 270 GLN B 298 ASN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B 952 ASN B1046 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN C1046 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 GLN D 952 ASN D 981 GLN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 29344 Z= 0.308 Angle : 0.607 12.927 39812 Z= 0.304 Chirality : 0.044 0.262 4548 Planarity : 0.005 0.119 4992 Dihedral : 4.879 59.638 3916 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.75 % Favored : 97.03 % Rotamer: Outliers : 4.03 % Allowed : 23.25 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.14), residues: 3532 helix: 1.11 (0.13), residues: 1700 sheet: -0.66 (0.25), residues: 348 loop : 0.11 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 169 HIS 0.006 0.001 HIS D 291 PHE 0.030 0.002 PHE D 235 TYR 0.015 0.002 TYR D 351 ARG 0.004 0.000 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 516 time to evaluate : 3.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ILE cc_start: 0.7257 (tp) cc_final: 0.6822 (pt) REVERT: A 200 LYS cc_start: 0.4054 (OUTLIER) cc_final: 0.3608 (tppt) REVERT: A 210 VAL cc_start: 0.4783 (OUTLIER) cc_final: 0.4435 (p) REVERT: A 232 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7604 (ttm170) REVERT: A 267 MET cc_start: 0.8124 (ttm) cc_final: 0.7512 (tpp) REVERT: A 275 PHE cc_start: 0.7079 (t80) cc_final: 0.6585 (t80) REVERT: A 348 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: A 415 GLN cc_start: 0.8218 (mt0) cc_final: 0.7895 (mp10) REVERT: A 428 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.6983 (mtm180) REVERT: A 461 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7136 (tm-30) REVERT: A 604 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7261 (tptp) REVERT: A 794 LYS cc_start: 0.7109 (mppt) cc_final: 0.6577 (mmtm) REVERT: A 883 VAL cc_start: 0.8208 (OUTLIER) cc_final: 0.7946 (m) REVERT: B 129 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8236 (tt) REVERT: B 131 ILE cc_start: 0.8018 (mm) cc_final: 0.7729 (OUTLIER) REVERT: B 180 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7323 (tp40) REVERT: B 220 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7608 (pt) REVERT: B 228 TRP cc_start: 0.6908 (t-100) cc_final: 0.6551 (t60) REVERT: B 291 HIS cc_start: 0.8579 (t70) cc_final: 0.8242 (t70) REVERT: B 349 LEU cc_start: 0.8522 (mt) cc_final: 0.8292 (mt) REVERT: B 352 LEU cc_start: 0.7901 (mt) cc_final: 0.7678 (mm) REVERT: B 356 ARG cc_start: 0.7640 (tmm-80) cc_final: 0.7324 (tmm-80) REVERT: B 413 ASP cc_start: 0.7620 (t0) cc_final: 0.7127 (t0) REVERT: B 415 GLN cc_start: 0.8221 (mt0) cc_final: 0.7697 (mp10) REVERT: B 428 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7050 (mtm180) REVERT: B 461 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6763 (mt-10) REVERT: B 548 GLN cc_start: 0.8018 (tp-100) cc_final: 0.7750 (tp-100) REVERT: B 604 LYS cc_start: 0.8033 (mttt) cc_final: 0.7471 (tptp) REVERT: B 786 LYS cc_start: 0.7763 (mppt) cc_final: 0.7305 (mmmm) REVERT: B 794 LYS cc_start: 0.7932 (tptt) cc_final: 0.7350 (mppt) REVERT: B 844 HIS cc_start: 0.7495 (p-80) cc_final: 0.7158 (p-80) REVERT: B 859 MET cc_start: 0.8685 (ttm) cc_final: 0.8437 (ttm) REVERT: B 883 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.8008 (m) REVERT: B 950 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7171 (ttp-170) REVERT: C 174 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6577 (tpt) REVERT: C 200 LYS cc_start: 0.3260 (OUTLIER) cc_final: 0.2776 (tptp) REVERT: C 216 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7003 (mpt) REVERT: C 231 LEU cc_start: 0.7700 (mt) cc_final: 0.7243 (tt) REVERT: C 252 MET cc_start: 0.5713 (OUTLIER) cc_final: 0.5141 (tpt) REVERT: C 267 MET cc_start: 0.7776 (ttp) cc_final: 0.7427 (ttm) REVERT: C 275 PHE cc_start: 0.7234 (t80) cc_final: 0.6944 (t80) REVERT: C 349 LEU cc_start: 0.8450 (tp) cc_final: 0.8180 (mt) REVERT: C 604 LYS cc_start: 0.7973 (ptmm) cc_final: 0.7450 (tptp) REVERT: C 794 LYS cc_start: 0.8099 (ttpp) cc_final: 0.7725 (tmmt) REVERT: C 876 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7422 (p90) REVERT: C 950 ARG cc_start: 0.7429 (ttm170) cc_final: 0.7216 (mtm180) REVERT: D 136 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8507 (mp) REVERT: D 200 LYS cc_start: 0.2689 (OUTLIER) cc_final: 0.2328 (tppt) REVERT: D 252 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.6084 (tmt) REVERT: D 428 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7196 (mtm180) REVERT: D 461 GLU cc_start: 0.6994 (tt0) cc_final: 0.6633 (tm-30) REVERT: D 548 GLN cc_start: 0.7970 (tp40) cc_final: 0.7697 (tp-100) REVERT: D 604 LYS cc_start: 0.7900 (ptmm) cc_final: 0.7213 (tptp) REVERT: D 799 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8278 (mmtt) REVERT: D 859 MET cc_start: 0.8649 (ttm) cc_final: 0.8427 (ttm) REVERT: D 876 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.7414 (p90) REVERT: D 883 VAL cc_start: 0.8179 (OUTLIER) cc_final: 0.7923 (m) REVERT: D 930 MET cc_start: 0.6559 (tmm) cc_final: 0.6080 (mmm) outliers start: 127 outliers final: 85 residues processed: 588 average time/residue: 1.4118 time to fit residues: 966.9543 Evaluate side-chains 610 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 502 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain B residue 1143 ARG Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain B residue 1204 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 490 GLN Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 981 GLN Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1016 ASP Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1152 LEU Chi-restraints excluded: chain C residue 1187 ASP Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 428 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 840 ASN Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 981 GLN Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1038 ILE Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain D residue 1152 LEU Chi-restraints excluded: chain D residue 1176 THR Chi-restraints excluded: chain D residue 1187 ASP Chi-restraints excluded: chain D residue 1204 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 0.8980 chunk 338 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 235 optimal weight: 0.9980 chunk 354 optimal weight: 0.6980 chunk 326 optimal weight: 0.6980 chunk 282 optimal weight: 0.1980 chunk 29 optimal weight: 8.9990 chunk 218 optimal weight: 0.9990 chunk 173 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 952 ASN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 298 ASN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B 952 ASN B1046 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN C1046 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 GLN D 632 ASN D 952 ASN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 29344 Z= 0.182 Angle : 0.568 15.260 39812 Z= 0.284 Chirality : 0.041 0.258 4548 Planarity : 0.005 0.117 4992 Dihedral : 4.699 58.692 3916 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.69 % Favored : 97.08 % Rotamer: Outliers : 3.24 % Allowed : 24.27 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.14), residues: 3532 helix: 1.26 (0.13), residues: 1700 sheet: -0.49 (0.25), residues: 352 loop : 0.22 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 169 HIS 0.005 0.001 HIS D 291 PHE 0.033 0.001 PHE D 235 TYR 0.019 0.001 TYR C 351 ARG 0.006 0.000 ARG A 444 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 510 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ILE cc_start: 0.7205 (tp) cc_final: 0.6723 (pt) REVERT: A 200 LYS cc_start: 0.4307 (OUTLIER) cc_final: 0.3831 (tppt) REVERT: A 210 VAL cc_start: 0.4787 (OUTLIER) cc_final: 0.4435 (p) REVERT: A 232 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7592 (ttm170) REVERT: A 267 MET cc_start: 0.8101 (ttm) cc_final: 0.7408 (tpp) REVERT: A 275 PHE cc_start: 0.7120 (t80) cc_final: 0.6603 (t80) REVERT: A 415 GLN cc_start: 0.8193 (mt0) cc_final: 0.7877 (mp10) REVERT: A 604 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7155 (tptp) REVERT: A 794 LYS cc_start: 0.7251 (mppt) cc_final: 0.6777 (mmtm) REVERT: A 844 HIS cc_start: 0.7452 (p-80) cc_final: 0.7043 (p-80) REVERT: A 883 VAL cc_start: 0.8165 (OUTLIER) cc_final: 0.7928 (m) REVERT: A 988 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8802 (mmm) REVERT: B 129 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8214 (tt) REVERT: B 131 ILE cc_start: 0.7992 (mm) cc_final: 0.7760 (OUTLIER) REVERT: B 179 ILE cc_start: 0.7757 (tt) cc_final: 0.7540 (tp) REVERT: B 220 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7578 (pt) REVERT: B 349 LEU cc_start: 0.8511 (mt) cc_final: 0.8287 (mt) REVERT: B 352 LEU cc_start: 0.7865 (mt) cc_final: 0.7641 (mm) REVERT: B 356 ARG cc_start: 0.7637 (tmm-80) cc_final: 0.7318 (tmm-80) REVERT: B 413 ASP cc_start: 0.7543 (t0) cc_final: 0.7068 (t0) REVERT: B 415 GLN cc_start: 0.8189 (mt0) cc_final: 0.7683 (mp10) REVERT: B 548 GLN cc_start: 0.7976 (tp-100) cc_final: 0.7715 (tp-100) REVERT: B 604 LYS cc_start: 0.8038 (mttt) cc_final: 0.7445 (tptp) REVERT: B 786 LYS cc_start: 0.7761 (mppt) cc_final: 0.7273 (mmmm) REVERT: B 794 LYS cc_start: 0.7921 (tptt) cc_final: 0.7337 (mppt) REVERT: B 844 HIS cc_start: 0.7412 (p-80) cc_final: 0.7020 (p-80) REVERT: B 859 MET cc_start: 0.8602 (ttm) cc_final: 0.8392 (ttm) REVERT: B 883 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7975 (m) REVERT: B 950 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7155 (ttp-170) REVERT: C 174 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6565 (tpt) REVERT: C 200 LYS cc_start: 0.3462 (OUTLIER) cc_final: 0.2938 (tptp) REVERT: C 216 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6967 (mpt) REVERT: C 231 LEU cc_start: 0.7676 (mt) cc_final: 0.7213 (tt) REVERT: C 252 MET cc_start: 0.5833 (OUTLIER) cc_final: 0.5276 (tpt) REVERT: C 275 PHE cc_start: 0.7198 (t80) cc_final: 0.6867 (t80) REVERT: C 349 LEU cc_start: 0.8466 (tp) cc_final: 0.8210 (mt) REVERT: C 604 LYS cc_start: 0.7943 (ptmm) cc_final: 0.7414 (tptp) REVERT: C 794 LYS cc_start: 0.8071 (ttpp) cc_final: 0.7688 (tmmt) REVERT: C 876 TYR cc_start: 0.8051 (OUTLIER) cc_final: 0.7263 (p90) REVERT: C 950 ARG cc_start: 0.7441 (ttm170) cc_final: 0.7162 (mtm180) REVERT: C 988 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8756 (mmm) REVERT: C 1137 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6475 (ttt-90) REVERT: D 173 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7684 (mmmt) REVERT: D 200 LYS cc_start: 0.2895 (OUTLIER) cc_final: 0.2528 (tppt) REVERT: D 232 ARG cc_start: 0.7754 (mmm-85) cc_final: 0.7479 (mtt-85) REVERT: D 351 TYR cc_start: 0.7225 (t80) cc_final: 0.6772 (t80) REVERT: D 461 GLU cc_start: 0.6995 (tt0) cc_final: 0.6645 (tm-30) REVERT: D 538 ARG cc_start: 0.7738 (mpt180) cc_final: 0.7511 (mmp80) REVERT: D 548 GLN cc_start: 0.7911 (tp40) cc_final: 0.7656 (tp-100) REVERT: D 604 LYS cc_start: 0.7881 (ptmm) cc_final: 0.7213 (tptp) REVERT: D 783 LYS cc_start: 0.7545 (ptmm) cc_final: 0.7329 (pptt) REVERT: D 799 LYS cc_start: 0.8641 (mmmt) cc_final: 0.8276 (mmtt) REVERT: D 844 HIS cc_start: 0.7432 (p-80) cc_final: 0.7050 (p-80) REVERT: D 876 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7326 (p90) REVERT: D 883 VAL cc_start: 0.8133 (OUTLIER) cc_final: 0.7893 (m) REVERT: D 930 MET cc_start: 0.6207 (tmm) cc_final: 0.5890 (mmm) REVERT: D 988 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8820 (mmm) outliers start: 102 outliers final: 65 residues processed: 568 average time/residue: 1.4138 time to fit residues: 934.8721 Evaluate side-chains 590 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 505 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain B residue 1204 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 490 GLN Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 981 GLN Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1137 ARG Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1187 ASP Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 840 ASN Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain D residue 1176 THR Chi-restraints excluded: chain D residue 1187 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 5.9990 chunk 300 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 282 optimal weight: 9.9990 chunk 118 optimal weight: 0.0270 chunk 290 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.0870 overall best weight: 1.0218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A 952 ASN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 298 ASN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B 952 ASN B1046 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN C1046 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 GLN D 952 ASN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.130599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098568 restraints weight = 50975.085| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.11 r_work: 0.3179 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 29344 Z= 0.209 Angle : 0.574 15.896 39812 Z= 0.285 Chirality : 0.042 0.257 4548 Planarity : 0.005 0.116 4992 Dihedral : 4.641 57.446 3914 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.63 % Favored : 97.14 % Rotamer: Outliers : 3.18 % Allowed : 24.40 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.14), residues: 3532 helix: 1.25 (0.13), residues: 1700 sheet: -0.51 (0.25), residues: 356 loop : 0.22 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 169 HIS 0.005 0.001 HIS D 291 PHE 0.031 0.001 PHE C 268 TYR 0.021 0.001 TYR A 351 ARG 0.008 0.000 ARG A 600 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13882.56 seconds wall clock time: 244 minutes 31.21 seconds (14671.21 seconds total)