Starting phenix.real_space_refine on Fri Mar 15 08:19:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a90_6995/03_2024/6a90_6995.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a90_6995/03_2024/6a90_6995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a90_6995/03_2024/6a90_6995.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a90_6995/03_2024/6a90_6995.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a90_6995/03_2024/6a90_6995.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a90_6995/03_2024/6a90_6995.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians S 74 5.16 5 Na 1 4.78 5 C 7319 2.51 5 N 1780 2.21 5 O 1911 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 552": "NH1" <-> "NH2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A ARG 883": "NH1" <-> "NH2" Residue "A ARG 957": "NH1" <-> "NH2" Residue "A ARG 1074": "NH1" <-> "NH2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "A ARG 1225": "NH1" <-> "NH2" Residue "A ARG 1274": "NH1" <-> "NH2" Residue "A ARG 1283": "NH1" <-> "NH2" Residue "A ARG 1297": "NH1" <-> "NH2" Residue "A ARG 1369": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11085 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 10537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1323, 10537 Classifications: {'peptide': 1323} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 1275} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 10, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 171 Chain: "B" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 449 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' NA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.44, per 1000 atoms: 0.58 Number of scatterers: 11085 At special positions: 0 Unit cell: (133.102, 134.193, 122.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 Na 1 11.00 O 1911 8.00 N 1780 7.00 C 7319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 343 " distance=2.02 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 717 " distance=2.05 Simple disulfide: pdb=" SG CYS A1011 " - pdb=" SG CYS A1030 " distance=2.03 Simple disulfide: pdb=" SG CYS A1368 " - pdb=" SG CYS A1381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 26 " distance=2.04 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 54 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 52 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1605 " - " ASN A1015 " " NAG A1606 " - " ASN A 312 " " NAG A1607 " - " ASN A 308 " " NAG C 1 " - " ASN A 330 " " NAG D 1 " - " ASN A1034 " Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 1.9 seconds 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2618 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 5 sheets defined 69.0% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.861A pdb=" N ARG A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 57' Processing helix chain 'A' and resid 97 through 110 removed outlier: 3.751A pdb=" N THR A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 removed outlier: 3.552A pdb=" N ALA A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 159 removed outlier: 3.939A pdb=" N MET A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 158 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.905A pdb=" N TYR A 166 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 167 " --> pdb=" O GLN A 163 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 170 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 removed outlier: 3.701A pdb=" N ARG A 198 " --> pdb=" O ALA A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 198' Processing helix chain 'A' and resid 199 through 217 removed outlier: 3.838A pdb=" N LEU A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 205 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 207 " --> pdb=" O TRP A 203 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 236 removed outlier: 3.544A pdb=" N ALA A 228 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 231 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 232 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.543A pdb=" N ILE A 240 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 258 removed outlier: 4.392A pdb=" N ILE A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 280 removed outlier: 3.866A pdb=" N LEU A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.672A pdb=" N THR A 285 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.689A pdb=" N ASN A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 360 through 374 Processing helix chain 'A' and resid 376 through 386 removed outlier: 3.921A pdb=" N LEU A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 392 through 404 removed outlier: 3.884A pdb=" N PHE A 396 " --> pdb=" O HIS A 392 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 435 removed outlier: 3.712A pdb=" N ILE A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 517 removed outlier: 3.575A pdb=" N LYS A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 509 " --> pdb=" O TRP A 505 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A 510 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 511 " --> pdb=" O LYS A 507 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 514 " --> pdb=" O GLY A 510 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 538 Processing helix chain 'A' and resid 545 through 571 removed outlier: 3.609A pdb=" N LEU A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 removed outlier: 4.263A pdb=" N PHE A 579 " --> pdb=" O PRO A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 600 removed outlier: 3.622A pdb=" N VAL A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 589 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 618 removed outlier: 3.645A pdb=" N PHE A 612 " --> pdb=" O PHE A 609 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 613 " --> pdb=" O ARG A 610 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 615 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 removed outlier: 4.443A pdb=" N PHE A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 619 through 624' Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.592A pdb=" N VAL A 633 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 663 removed outlier: 3.562A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 671 through 674 Processing helix chain 'A' and resid 686 through 699 removed outlier: 3.729A pdb=" N ALA A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 712 removed outlier: 3.765A pdb=" N ASP A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 729 removed outlier: 3.635A pdb=" N PHE A 720 " --> pdb=" O SER A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 736 Processing helix chain 'A' and resid 736 through 744 removed outlier: 3.672A pdb=" N ASN A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 854 removed outlier: 3.832A pdb=" N ARG A 840 " --> pdb=" O SER A 836 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N MET A 841 " --> pdb=" O SER A 837 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A 844 " --> pdb=" O ARG A 840 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 872 removed outlier: 3.746A pdb=" N GLN A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 876 removed outlier: 3.864A pdb=" N GLU A 876 " --> pdb=" O LEU A 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 873 through 876' Processing helix chain 'A' and resid 883 through 918 removed outlier: 3.669A pdb=" N ASN A 888 " --> pdb=" O PRO A 884 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 894 " --> pdb=" O THR A 890 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 895 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL A 902 " --> pdb=" O THR A 898 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE A 914 " --> pdb=" O PHE A 910 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N LYS A 915 " --> pdb=" O ALA A 911 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS A 916 " --> pdb=" O VAL A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 942 removed outlier: 3.571A pdb=" N VAL A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A 936 " --> pdb=" O ALA A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 952 removed outlier: 3.583A pdb=" N ARG A 951 " --> pdb=" O LEU A 947 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 952 " --> pdb=" O GLN A 948 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 947 through 952' Processing helix chain 'A' and resid 953 through 957 removed outlier: 3.562A pdb=" N ARG A 957 " --> pdb=" O ARG A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 963 removed outlier: 3.505A pdb=" N LEU A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 978 removed outlier: 4.279A pdb=" N VAL A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1005 removed outlier: 3.648A pdb=" N ASN A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 996 " --> pdb=" O PHE A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1033 removed outlier: 3.830A pdb=" N GLU A1033 " --> pdb=" O ASP A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1059 removed outlier: 3.693A pdb=" N LEU A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1073 removed outlier: 3.728A pdb=" N ILE A1066 " --> pdb=" O GLY A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1087 No H-bonds generated for 'chain 'A' and resid 1085 through 1087' Processing helix chain 'A' and resid 1088 through 1100 removed outlier: 3.790A pdb=" N PHE A1092 " --> pdb=" O MET A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1123 removed outlier: 4.170A pdb=" N VAL A1108 " --> pdb=" O LEU A1104 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A1117 " --> pdb=" O ASP A1113 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A1123 " --> pdb=" O ARG A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1142 removed outlier: 3.619A pdb=" N ARG A1142 " --> pdb=" O ARG A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1166 Processing helix chain 'A' and resid 1169 through 1186 removed outlier: 4.049A pdb=" N MET A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A1180 " --> pdb=" O MET A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1190 removed outlier: 3.616A pdb=" N ASP A1190 " --> pdb=" O MET A1187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1187 through 1190' Processing helix chain 'A' and resid 1197 through 1224 removed outlier: 3.665A pdb=" N LEU A1202 " --> pdb=" O PHE A1198 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A1211 " --> pdb=" O LEU A1207 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A1220 " --> pdb=" O GLU A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1230 removed outlier: 3.536A pdb=" N LYS A1230 " --> pdb=" O HIS A1227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1227 through 1230' Processing helix chain 'A' and resid 1231 through 1249 removed outlier: 3.623A pdb=" N ILE A1235 " --> pdb=" O ASP A1231 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A1236 " --> pdb=" O PRO A1232 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A1247 " --> pdb=" O LEU A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1270 removed outlier: 3.679A pdb=" N LEU A1264 " --> pdb=" O SER A1260 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A1267 " --> pdb=" O LEU A1263 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A1269 " --> pdb=" O ARG A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1278 removed outlier: 3.767A pdb=" N ARG A1274 " --> pdb=" O ARG A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1322 removed outlier: 3.780A pdb=" N LEU A1288 " --> pdb=" O GLY A1284 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A1291 " --> pdb=" O LEU A1287 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A1295 " --> pdb=" O ALA A1291 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ARG A1297 " --> pdb=" O ARG A1293 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N THR A1298 " --> pdb=" O LYS A1294 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1302 " --> pdb=" O THR A1298 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A1308 " --> pdb=" O PHE A1304 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A1319 " --> pdb=" O VAL A1315 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET A1322 " --> pdb=" O MET A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1349 removed outlier: 3.569A pdb=" N LEU A1345 " --> pdb=" O GLN A1341 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A1348 " --> pdb=" O ILE A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1352 No H-bonds generated for 'chain 'A' and resid 1350 through 1352' Processing helix chain 'A' and resid 1354 through 1363 removed outlier: 3.765A pdb=" N ALA A1361 " --> pdb=" O GLY A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1399 removed outlier: 4.253A pdb=" N SER A1393 " --> pdb=" O ALA A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1423 removed outlier: 3.966A pdb=" N ALA A1407 " --> pdb=" O ILE A1403 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A1416 " --> pdb=" O ASP A1412 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A1423 " --> pdb=" O GLU A1419 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1438 removed outlier: 3.809A pdb=" N TYR A1430 " --> pdb=" O THR A1426 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A1431 " --> pdb=" O ASP A1427 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET A1432 " --> pdb=" O ASP A1428 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A1433 " --> pdb=" O ASP A1429 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A1434 " --> pdb=" O TYR A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1460 removed outlier: 4.358A pdb=" N SER A1454 " --> pdb=" O TYR A1450 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU A1455 " --> pdb=" O ASP A1451 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A1458 " --> pdb=" O SER A1454 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A1459 " --> pdb=" O GLU A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1478 removed outlier: 3.656A pdb=" N SER A1476 " --> pdb=" O TYR A1472 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN A1478 " --> pdb=" O ILE A1474 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1505 removed outlier: 3.888A pdb=" N ASP A1499 " --> pdb=" O ALA A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1520 removed outlier: 3.607A pdb=" N ASP A1512 " --> pdb=" O VAL A1508 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A1513 " --> pdb=" O GLU A1509 " (cutoff:3.500A) Proline residue: A1516 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 287 through 290 Processing sheet with id=AA2, first strand: chain 'A' and resid 543 through 544 Processing sheet with id=AA3, first strand: chain 'A' and resid 1009 through 1012 Processing sheet with id=AA4, first strand: chain 'A' and resid 1447 through 1449 Processing sheet with id=AA5, first strand: chain 'B' and resid 7 through 8 removed outlier: 3.999A pdb=" N LYS B 28 " --> pdb=" O GLU B 8 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1605 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: 3.50 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2694 1.33 - 1.45: 2905 1.45 - 1.58: 5656 1.58 - 1.70: 0 1.70 - 1.83: 119 Bond restraints: 11374 Sorted by residual: bond pdb=" C1 NAG A1605 " pdb=" O5 NAG A1605 " ideal model delta sigma weight residual 1.406 1.503 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C1 NAG A1606 " pdb=" O5 NAG A1606 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.43e+00 bond pdb=" C PHE A 674 " pdb=" N PRO A 675 " ideal model delta sigma weight residual 1.335 1.368 -0.034 1.28e-02 6.10e+03 6.87e+00 bond pdb=" CB VAL A1057 " pdb=" CG2 VAL A1057 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.17e+00 bond pdb=" CB PRO A 980 " pdb=" CG PRO A 980 " ideal model delta sigma weight residual 1.492 1.379 0.113 5.00e-02 4.00e+02 5.10e+00 ... (remaining 11369 not shown) Histogram of bond angle deviations from ideal: 95.40 - 103.16: 101 103.16 - 110.93: 3673 110.93 - 118.69: 4999 118.69 - 126.45: 6496 126.45 - 134.21: 193 Bond angle restraints: 15462 Sorted by residual: angle pdb=" C PRO A 881 " pdb=" N GLN A 882 " pdb=" CA GLN A 882 " ideal model delta sigma weight residual 121.54 134.19 -12.65 1.91e+00 2.74e-01 4.38e+01 angle pdb=" C MET A1477 " pdb=" N ASN A1478 " pdb=" CA ASN A1478 " ideal model delta sigma weight residual 121.54 133.81 -12.27 1.91e+00 2.74e-01 4.12e+01 angle pdb=" N GLY A 335 " pdb=" CA GLY A 335 " pdb=" C GLY A 335 " ideal model delta sigma weight residual 113.24 120.76 -7.52 1.31e+00 5.83e-01 3.30e+01 angle pdb=" C LYS A1256 " pdb=" N TYR A1257 " pdb=" CA TYR A1257 " ideal model delta sigma weight residual 122.74 130.18 -7.44 1.44e+00 4.82e-01 2.67e+01 angle pdb=" N THR A1132 " pdb=" CA THR A1132 " pdb=" C THR A1132 " ideal model delta sigma weight residual 113.43 107.17 6.26 1.26e+00 6.30e-01 2.47e+01 ... (remaining 15457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.38: 6434 21.38 - 42.77: 228 42.77 - 64.15: 38 64.15 - 85.53: 8 85.53 - 106.92: 3 Dihedral angle restraints: 6711 sinusoidal: 2653 harmonic: 4058 Sorted by residual: dihedral pdb=" CB CYS B 25 " pdb=" SG CYS B 25 " pdb=" SG CYS B 54 " pdb=" CB CYS B 54 " ideal model delta sinusoidal sigma weight residual 93.00 169.68 -76.68 1 1.00e+01 1.00e-02 7.39e+01 dihedral pdb=" CB CYS A 328 " pdb=" SG CYS A 328 " pdb=" SG CYS A 343 " pdb=" CB CYS A 343 " ideal model delta sinusoidal sigma weight residual -86.00 -154.30 68.30 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CA ASP A 295 " pdb=" C ASP A 295 " pdb=" N GLY A 296 " pdb=" CA GLY A 296 " ideal model delta harmonic sigma weight residual 180.00 151.55 28.45 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 6708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1656 0.119 - 0.239: 103 0.239 - 0.358: 11 0.358 - 0.478: 3 0.478 - 0.597: 2 Chirality restraints: 1775 Sorted by residual: chirality pdb=" CG LEU A1054 " pdb=" CB LEU A1054 " pdb=" CD1 LEU A1054 " pdb=" CD2 LEU A1054 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.60 2.00e-01 2.50e+01 8.92e+00 chirality pdb=" C1 NAG A1607 " pdb=" ND2 ASN A 308 " pdb=" C2 NAG A1607 " pdb=" O5 NAG A1607 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.80e+00 ... (remaining 1772 not shown) Planarity restraints: 1913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 933 " 0.026 2.00e-02 2.50e+03 2.62e-02 1.37e+01 pdb=" CG TYR A 933 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR A 933 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 933 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 933 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A 933 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 933 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 933 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1313 " 0.018 2.00e-02 2.50e+03 2.25e-02 1.02e+01 pdb=" CG TYR A1313 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A1313 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A1313 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A1313 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A1313 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A1313 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A1313 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 624 " -0.030 2.00e-02 2.50e+03 1.93e-02 9.29e+00 pdb=" CG TRP A 624 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 624 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 624 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 624 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 624 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 624 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 624 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 624 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 624 " -0.002 2.00e-02 2.50e+03 ... (remaining 1910 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3456 2.82 - 3.34: 9812 3.34 - 3.86: 17322 3.86 - 4.38: 20755 4.38 - 4.90: 34959 Nonbonded interactions: 86304 Sorted by model distance: nonbonded pdb=" O LEU A1346 " pdb=" OH TYR A1394 " model vdw 2.302 2.440 nonbonded pdb=" O ALA A1146 " pdb=" OH TYR A1489 " model vdw 2.319 2.440 nonbonded pdb=" OD1 ASP A 686 " pdb=" ND1 HIS A 689 " model vdw 2.359 2.520 nonbonded pdb=" O LYS A1171 " pdb=" OG1 THR A1175 " model vdw 2.373 2.440 nonbonded pdb=" OG SER B 1 " pdb=" N ALA B 2 " model vdw 2.379 2.520 ... (remaining 86299 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 '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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.690 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.000 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:15.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.011 0.113 11374 Z= 0.709 Angle : 1.231 12.647 15462 Z= 0.653 Chirality : 0.072 0.597 1775 Planarity : 0.007 0.065 1908 Dihedral : 12.073 106.918 4069 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.58 % Favored : 92.13 % Rotamer: Outliers : 1.75 % Allowed : 5.15 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -5.83 (0.15), residues: 1372 helix: -4.25 (0.08), residues: 855 sheet: -4.54 (0.70), residues: 22 loop : -2.68 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP A 624 HIS 0.017 0.004 HIS A 153 PHE 0.041 0.005 PHE A 410 TYR 0.062 0.005 TYR A 933 ARG 0.017 0.002 ARG A1271 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 251 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.6753 (mmm160) cc_final: 0.6162 (mmm-85) REVERT: A 249 ASP cc_start: 0.8253 (m-30) cc_final: 0.8053 (m-30) REVERT: A 631 MET cc_start: 0.7881 (mmt) cc_final: 0.7674 (mtp) REVERT: A 636 LYS cc_start: 0.7814 (tmmt) cc_final: 0.7405 (ttmt) REVERT: A 886 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8406 (tt) REVERT: A 915 LYS cc_start: 0.7914 (tmtp) cc_final: 0.7454 (mttp) REVERT: A 922 TRP cc_start: 0.8269 (m100) cc_final: 0.7906 (m100) REVERT: A 1042 MET cc_start: 0.9099 (mmp) cc_final: 0.8861 (tpt) REVERT: A 1102 PHE cc_start: 0.8562 (t80) cc_final: 0.8225 (t80) REVERT: A 1164 TYR cc_start: 0.8121 (t80) cc_final: 0.7692 (t80) REVERT: A 1174 TYR cc_start: 0.7259 (m-10) cc_final: 0.6921 (m-80) REVERT: A 1218 VAL cc_start: 0.8022 (p) cc_final: 0.7721 (t) REVERT: A 1230 LYS cc_start: 0.7836 (mmmt) cc_final: 0.7094 (mmtt) REVERT: A 1300 PHE cc_start: 0.8135 (m-10) cc_final: 0.7110 (t80) REVERT: A 1422 LYS cc_start: 0.7668 (tttm) cc_final: 0.7431 (mttp) outliers start: 20 outliers final: 7 residues processed: 268 average time/residue: 1.1073 time to fit residues: 321.4316 Evaluate side-chains 182 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 124 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 291 HIS A 409 ASN A 421 HIS A 629 ASN A1486 HIS B 29 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11374 Z= 0.183 Angle : 0.692 10.682 15462 Z= 0.362 Chirality : 0.044 0.349 1775 Planarity : 0.005 0.066 1908 Dihedral : 8.512 87.859 1665 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.14 % Allowed : 11.87 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.29 (0.19), residues: 1372 helix: -1.93 (0.14), residues: 874 sheet: -4.32 (0.73), residues: 22 loop : -2.26 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 624 HIS 0.004 0.001 HIS A 392 PHE 0.018 0.001 PHE A1488 TYR 0.025 0.002 TYR A1313 ARG 0.008 0.001 ARG A1137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 201 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.6674 (mmm160) cc_final: 0.6195 (mmm-85) REVERT: A 236 ARG cc_start: 0.8172 (ptm160) cc_final: 0.7638 (ttt180) REVERT: A 419 TYR cc_start: 0.8846 (t80) cc_final: 0.8591 (t80) REVERT: A 597 GLU cc_start: 0.6484 (mt-10) cc_final: 0.6191 (mt-10) REVERT: A 628 ASN cc_start: 0.8561 (t0) cc_final: 0.8305 (t0) REVERT: A 631 MET cc_start: 0.7820 (mmt) cc_final: 0.7539 (mtp) REVERT: A 636 LYS cc_start: 0.7739 (tmmt) cc_final: 0.7360 (tppp) REVERT: A 739 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8881 (mt) REVERT: A 915 LYS cc_start: 0.7773 (tmtp) cc_final: 0.7415 (pmtt) REVERT: A 999 MET cc_start: 0.8239 (tpt) cc_final: 0.7838 (tpp) REVERT: A 1042 MET cc_start: 0.9079 (mmp) cc_final: 0.8782 (mmm) REVERT: A 1078 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8468 (mttt) REVERT: A 1164 TYR cc_start: 0.8125 (t80) cc_final: 0.7693 (t80) REVERT: A 1174 TYR cc_start: 0.7185 (m-10) cc_final: 0.6830 (m-80) REVERT: A 1218 VAL cc_start: 0.8103 (p) cc_final: 0.7822 (t) REVERT: A 1230 LYS cc_start: 0.7789 (mmmt) cc_final: 0.7021 (mmtt) REVERT: A 1283 ARG cc_start: 0.7663 (tpt90) cc_final: 0.6997 (tpp-160) REVERT: A 1300 PHE cc_start: 0.8059 (m-10) cc_final: 0.6982 (t80) REVERT: A 1396 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8499 (mt) REVERT: A 1416 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7626 (tt0) REVERT: A 1422 LYS cc_start: 0.7598 (tttm) cc_final: 0.7196 (mtmp) REVERT: A 1499 ASP cc_start: 0.7530 (t0) cc_final: 0.7038 (m-30) outliers start: 36 outliers final: 12 residues processed: 225 average time/residue: 0.9976 time to fit residues: 245.1990 Evaluate side-chains 181 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 124 optimal weight: 0.0270 chunk 134 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1234 ASN A1465 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11374 Z= 0.216 Angle : 0.643 11.241 15462 Z= 0.330 Chirality : 0.044 0.356 1775 Planarity : 0.004 0.053 1908 Dihedral : 7.732 74.451 1661 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 4.01 % Allowed : 13.87 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.22), residues: 1372 helix: -0.60 (0.17), residues: 884 sheet: -4.18 (0.72), residues: 22 loop : -2.07 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 624 HIS 0.005 0.001 HIS A 392 PHE 0.025 0.002 PHE A1279 TYR 0.025 0.002 TYR A1313 ARG 0.008 0.001 ARG A1137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 174 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7579 (mtt) cc_final: 0.7275 (mtp) REVERT: A 159 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6132 (mpp) REVERT: A 198 ARG cc_start: 0.6750 (mmm160) cc_final: 0.6311 (mmm-85) REVERT: A 236 ARG cc_start: 0.8247 (ptm160) cc_final: 0.7770 (ttt180) REVERT: A 419 TYR cc_start: 0.8897 (t80) cc_final: 0.8674 (t80) REVERT: A 628 ASN cc_start: 0.8541 (t0) cc_final: 0.8237 (t0) REVERT: A 631 MET cc_start: 0.7903 (mmt) cc_final: 0.7613 (mtp) REVERT: A 636 LYS cc_start: 0.7810 (tmmt) cc_final: 0.7050 (mppt) REVERT: A 649 PHE cc_start: 0.8384 (m-80) cc_final: 0.8161 (m-80) REVERT: A 665 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6735 (mpp) REVERT: A 915 LYS cc_start: 0.7874 (tmtp) cc_final: 0.7389 (pmtt) REVERT: A 999 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7811 (tpp) REVERT: A 1042 MET cc_start: 0.9106 (mmp) cc_final: 0.8784 (mmm) REVERT: A 1078 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8459 (mttt) REVERT: A 1164 TYR cc_start: 0.8147 (t80) cc_final: 0.7712 (t80) REVERT: A 1174 TYR cc_start: 0.7424 (m-10) cc_final: 0.7101 (m-80) REVERT: A 1230 LYS cc_start: 0.7850 (mmmt) cc_final: 0.7106 (mmtt) REVERT: A 1277 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.6091 (ptp90) REVERT: A 1300 PHE cc_start: 0.8060 (m-10) cc_final: 0.6993 (t80) REVERT: A 1396 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8505 (mt) REVERT: A 1416 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: A 1422 LYS cc_start: 0.7543 (tttm) cc_final: 0.7112 (mtmp) REVERT: A 1450 TYR cc_start: 0.7121 (t80) cc_final: 0.6845 (t80) REVERT: A 1499 ASP cc_start: 0.7266 (t0) cc_final: 0.6960 (m-30) outliers start: 46 outliers final: 20 residues processed: 204 average time/residue: 1.0429 time to fit residues: 232.5121 Evaluate side-chains 189 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1277 ARG Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 HIS ** A1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11374 Z= 0.190 Angle : 0.602 11.027 15462 Z= 0.308 Chirality : 0.043 0.383 1775 Planarity : 0.004 0.046 1908 Dihedral : 7.035 59.562 1659 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.36 % Allowed : 15.10 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.95 (0.23), residues: 1372 helix: 0.12 (0.18), residues: 883 sheet: -3.94 (0.67), residues: 22 loop : -1.83 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 PHE 0.019 0.001 PHE A1279 TYR 0.020 0.001 TYR A1313 ARG 0.007 0.001 ARG A1137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 180 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7559 (mtt) cc_final: 0.7238 (mtp) REVERT: A 198 ARG cc_start: 0.6750 (mmm160) cc_final: 0.6290 (mmm-85) REVERT: A 236 ARG cc_start: 0.8379 (ptm160) cc_final: 0.7938 (ttt180) REVERT: A 419 TYR cc_start: 0.8892 (t80) cc_final: 0.8678 (t80) REVERT: A 628 ASN cc_start: 0.8554 (t0) cc_final: 0.8233 (t0) REVERT: A 636 LYS cc_start: 0.7720 (tmmt) cc_final: 0.7000 (mppt) REVERT: A 708 ASP cc_start: 0.8103 (p0) cc_final: 0.7866 (m-30) REVERT: A 872 LEU cc_start: 0.8687 (mm) cc_final: 0.8435 (tm) REVERT: A 915 LYS cc_start: 0.7901 (tmtp) cc_final: 0.7393 (pmtt) REVERT: A 999 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7813 (tpp) REVERT: A 1033 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: A 1042 MET cc_start: 0.9104 (mmp) cc_final: 0.8799 (mmm) REVERT: A 1078 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8473 (mttt) REVERT: A 1083 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: A 1174 TYR cc_start: 0.7318 (m-10) cc_final: 0.7042 (m-80) REVERT: A 1230 LYS cc_start: 0.7954 (mmmt) cc_final: 0.7240 (mmtt) REVERT: A 1277 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.6028 (ptp90) REVERT: A 1300 PHE cc_start: 0.8021 (m-10) cc_final: 0.7019 (t80) REVERT: A 1369 ARG cc_start: 0.7935 (mtp180) cc_final: 0.7707 (mtm110) REVERT: A 1416 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: A 1422 LYS cc_start: 0.7560 (tttm) cc_final: 0.7082 (mtmp) REVERT: A 1450 TYR cc_start: 0.7260 (t80) cc_final: 0.6958 (t80) REVERT: A 1499 ASP cc_start: 0.7214 (t0) cc_final: 0.6936 (m-30) REVERT: A 1502 SER cc_start: 0.7018 (OUTLIER) cc_final: 0.6644 (m) outliers start: 50 outliers final: 19 residues processed: 209 average time/residue: 1.0741 time to fit residues: 245.0535 Evaluate side-chains 189 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1277 ARG Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1502 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 67 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 839 GLN A1118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11374 Z= 0.298 Angle : 0.649 11.949 15462 Z= 0.333 Chirality : 0.046 0.344 1775 Planarity : 0.004 0.047 1908 Dihedral : 6.770 59.893 1657 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.54 % Allowed : 15.62 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.74 (0.23), residues: 1372 helix: 0.31 (0.18), residues: 879 sheet: -3.90 (0.64), residues: 22 loop : -1.79 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 624 HIS 0.006 0.001 HIS A 153 PHE 0.025 0.002 PHE A1279 TYR 0.020 0.002 TYR A 381 ARG 0.005 0.001 ARG A1137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 161 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6417 (mpp) REVERT: A 198 ARG cc_start: 0.6840 (mmm160) cc_final: 0.6340 (mmm-85) REVERT: A 236 ARG cc_start: 0.8402 (ptm160) cc_final: 0.7917 (ttt180) REVERT: A 628 ASN cc_start: 0.8601 (t0) cc_final: 0.8268 (t0) REVERT: A 631 MET cc_start: 0.8021 (mtp) cc_final: 0.7771 (mtp) REVERT: A 636 LYS cc_start: 0.7750 (tmmt) cc_final: 0.6989 (mtpt) REVERT: A 665 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6859 (mpp) REVERT: A 915 LYS cc_start: 0.7903 (tmtp) cc_final: 0.7361 (pmtt) REVERT: A 999 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7859 (tpp) REVERT: A 1033 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: A 1042 MET cc_start: 0.9143 (mmp) cc_final: 0.8822 (mmm) REVERT: A 1078 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8663 (mttm) REVERT: A 1083 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: A 1174 TYR cc_start: 0.7253 (m-10) cc_final: 0.6917 (m-80) REVERT: A 1230 LYS cc_start: 0.7980 (mmmt) cc_final: 0.7265 (mmtt) REVERT: A 1300 PHE cc_start: 0.8214 (m-10) cc_final: 0.7143 (t80) REVERT: A 1346 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9029 (mt) REVERT: A 1369 ARG cc_start: 0.7957 (mtp180) cc_final: 0.7739 (mtm110) REVERT: A 1416 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: A 1422 LYS cc_start: 0.7613 (tttm) cc_final: 0.7080 (mtmp) REVERT: A 1450 TYR cc_start: 0.7361 (t80) cc_final: 0.7150 (t80) REVERT: A 1499 ASP cc_start: 0.7251 (t0) cc_final: 0.7022 (m-30) outliers start: 52 outliers final: 26 residues processed: 194 average time/residue: 1.0552 time to fit residues: 223.5512 Evaluate side-chains 191 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 157 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1346 LEU Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 132 optimal weight: 0.0870 chunk 110 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11374 Z= 0.173 Angle : 0.580 11.264 15462 Z= 0.297 Chirality : 0.042 0.306 1775 Planarity : 0.003 0.042 1908 Dihedral : 6.589 58.575 1657 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.66 % Allowed : 16.40 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.30 (0.24), residues: 1372 helix: 0.66 (0.18), residues: 881 sheet: -3.85 (0.66), residues: 22 loop : -1.63 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 624 HIS 0.003 0.001 HIS A1191 PHE 0.019 0.001 PHE A1279 TYR 0.019 0.001 TYR A 381 ARG 0.005 0.000 ARG A1137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 167 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7622 (mtt) cc_final: 0.7246 (mtp) REVERT: A 159 MET cc_start: 0.6689 (OUTLIER) cc_final: 0.6323 (mpp) REVERT: A 198 ARG cc_start: 0.6831 (mmm160) cc_final: 0.6389 (mmm-85) REVERT: A 236 ARG cc_start: 0.8384 (ptm160) cc_final: 0.7977 (ttt180) REVERT: A 543 MET cc_start: 0.8907 (mtm) cc_final: 0.8608 (mtm) REVERT: A 628 ASN cc_start: 0.8546 (t0) cc_final: 0.8218 (t0) REVERT: A 631 MET cc_start: 0.7977 (mtp) cc_final: 0.7530 (mtt) REVERT: A 636 LYS cc_start: 0.7800 (tmmt) cc_final: 0.7147 (mppt) REVERT: A 661 GLN cc_start: 0.8291 (mm-40) cc_final: 0.7888 (mm-40) REVERT: A 665 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.6774 (mpp) REVERT: A 708 ASP cc_start: 0.8092 (p0) cc_final: 0.7823 (m-30) REVERT: A 999 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7741 (tpp) REVERT: A 1042 MET cc_start: 0.9116 (mmp) cc_final: 0.8823 (mmm) REVERT: A 1078 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8424 (mttt) REVERT: A 1083 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: A 1196 MET cc_start: 0.6865 (tpt) cc_final: 0.6661 (pmm) REVERT: A 1230 LYS cc_start: 0.7867 (mmmt) cc_final: 0.7014 (mmtt) REVERT: A 1277 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.6118 (ptp90) REVERT: A 1300 PHE cc_start: 0.8184 (m-10) cc_final: 0.7114 (t80) REVERT: A 1416 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: A 1422 LYS cc_start: 0.7581 (tttm) cc_final: 0.7056 (mtmp) REVERT: A 1450 TYR cc_start: 0.7376 (t80) cc_final: 0.7141 (t80) REVERT: A 1499 ASP cc_start: 0.7454 (t0) cc_final: 0.7239 (m-30) REVERT: B 22 SER cc_start: 0.8056 (t) cc_final: 0.7698 (m) outliers start: 42 outliers final: 16 residues processed: 192 average time/residue: 1.1108 time to fit residues: 232.1027 Evaluate side-chains 179 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1277 ARG Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 96 optimal weight: 0.0040 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 80 optimal weight: 0.0470 chunk 60 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 overall best weight: 0.9694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 HIS A 839 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11374 Z= 0.205 Angle : 0.594 11.272 15462 Z= 0.303 Chirality : 0.043 0.305 1775 Planarity : 0.003 0.041 1908 Dihedral : 6.515 57.952 1657 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.32 % Allowed : 17.63 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.18 (0.24), residues: 1372 helix: 0.78 (0.18), residues: 879 sheet: -3.78 (0.65), residues: 22 loop : -1.63 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 PHE 0.022 0.001 PHE A1279 TYR 0.018 0.001 TYR A 381 ARG 0.006 0.000 ARG A1325 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.6328 (mpp) REVERT: A 198 ARG cc_start: 0.6741 (mmm160) cc_final: 0.6292 (mmm-85) REVERT: A 236 ARG cc_start: 0.8392 (ptm160) cc_final: 0.7999 (ttt180) REVERT: A 628 ASN cc_start: 0.8556 (t0) cc_final: 0.8222 (t0) REVERT: A 631 MET cc_start: 0.7986 (mtp) cc_final: 0.7533 (mtt) REVERT: A 636 LYS cc_start: 0.7795 (tmmt) cc_final: 0.7145 (mppt) REVERT: A 665 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6842 (mpp) REVERT: A 708 ASP cc_start: 0.8130 (p0) cc_final: 0.7857 (m-30) REVERT: A 999 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7773 (tpp) REVERT: A 1042 MET cc_start: 0.9114 (mmp) cc_final: 0.8809 (mmm) REVERT: A 1078 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8672 (mttm) REVERT: A 1083 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: A 1147 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7570 (mtpp) REVERT: A 1196 MET cc_start: 0.6977 (tpt) cc_final: 0.6545 (pmm) REVERT: A 1200 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6922 (mp0) REVERT: A 1230 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7016 (mmtt) REVERT: A 1277 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.6106 (ptp90) REVERT: A 1300 PHE cc_start: 0.8182 (m-10) cc_final: 0.7119 (t80) REVERT: A 1416 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: A 1422 LYS cc_start: 0.7595 (tttm) cc_final: 0.7073 (mtmp) REVERT: A 1450 TYR cc_start: 0.7440 (t80) cc_final: 0.7216 (t80) REVERT: B 22 SER cc_start: 0.7903 (t) cc_final: 0.7603 (m) outliers start: 38 outliers final: 20 residues processed: 183 average time/residue: 1.0339 time to fit residues: 207.2377 Evaluate side-chains 181 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1277 ARG Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 17 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11374 Z= 0.224 Angle : 0.604 11.264 15462 Z= 0.308 Chirality : 0.043 0.299 1775 Planarity : 0.003 0.040 1908 Dihedral : 6.533 59.031 1657 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.93 % Allowed : 17.36 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.12 (0.24), residues: 1372 helix: 0.82 (0.18), residues: 879 sheet: -3.84 (0.63), residues: 22 loop : -1.58 (0.31), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 PHE 0.023 0.001 PHE A1279 TYR 0.018 0.002 TYR A 381 ARG 0.006 0.000 ARG A1325 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 154 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6322 (mpp) REVERT: A 198 ARG cc_start: 0.6753 (mmm160) cc_final: 0.6136 (mmt90) REVERT: A 236 ARG cc_start: 0.8375 (ptm160) cc_final: 0.7984 (ttt180) REVERT: A 628 ASN cc_start: 0.8565 (t0) cc_final: 0.8229 (t0) REVERT: A 631 MET cc_start: 0.7996 (mtp) cc_final: 0.7538 (mtt) REVERT: A 636 LYS cc_start: 0.7811 (tmmt) cc_final: 0.7166 (mppt) REVERT: A 665 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6841 (mpp) REVERT: A 708 ASP cc_start: 0.8153 (p0) cc_final: 0.7832 (m-30) REVERT: A 999 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7821 (tpp) REVERT: A 1042 MET cc_start: 0.9120 (mmp) cc_final: 0.8809 (mmm) REVERT: A 1078 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8675 (mttm) REVERT: A 1083 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: A 1147 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7506 (mtpp) REVERT: A 1230 LYS cc_start: 0.7839 (mmmt) cc_final: 0.6966 (mmtt) REVERT: A 1300 PHE cc_start: 0.8299 (m-10) cc_final: 0.7292 (t80) REVERT: A 1325 ARG cc_start: 0.7499 (ttp80) cc_final: 0.7291 (ttp80) REVERT: A 1416 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7622 (tt0) REVERT: A 1473 LYS cc_start: 0.6875 (mtmm) cc_final: 0.6517 (pttt) REVERT: B 22 SER cc_start: 0.7873 (t) cc_final: 0.7602 (m) outliers start: 45 outliers final: 23 residues processed: 181 average time/residue: 1.0528 time to fit residues: 208.3807 Evaluate side-chains 183 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 941 CYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1227 HIS Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1277 ARG Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 17 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.0980 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11374 Z= 0.202 Angle : 0.601 11.133 15462 Z= 0.306 Chirality : 0.043 0.328 1775 Planarity : 0.004 0.073 1908 Dihedral : 6.542 59.609 1657 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.14 % Allowed : 18.24 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.01 (0.24), residues: 1372 helix: 0.89 (0.18), residues: 882 sheet: -3.80 (0.64), residues: 22 loop : -1.51 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 PHE 0.021 0.001 PHE A1279 TYR 0.018 0.001 TYR A 381 ARG 0.005 0.000 ARG A1325 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6292 (mpp) REVERT: A 198 ARG cc_start: 0.6741 (mmm160) cc_final: 0.6102 (mmt90) REVERT: A 236 ARG cc_start: 0.8371 (ptm160) cc_final: 0.7994 (ttt180) REVERT: A 628 ASN cc_start: 0.8592 (t0) cc_final: 0.8245 (t0) REVERT: A 631 MET cc_start: 0.8001 (mtp) cc_final: 0.7529 (mtt) REVERT: A 636 LYS cc_start: 0.7806 (tmmt) cc_final: 0.7150 (mtpt) REVERT: A 661 GLN cc_start: 0.8320 (mm-40) cc_final: 0.7922 (mm-40) REVERT: A 665 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6768 (mpp) REVERT: A 708 ASP cc_start: 0.8124 (p0) cc_final: 0.7860 (m-30) REVERT: A 926 ASP cc_start: 0.7084 (m-30) cc_final: 0.6726 (m-30) REVERT: A 999 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7813 (tpp) REVERT: A 1042 MET cc_start: 0.9112 (mmp) cc_final: 0.8808 (mmm) REVERT: A 1078 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8664 (mttm) REVERT: A 1083 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: A 1147 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7848 (tttm) REVERT: A 1174 TYR cc_start: 0.6766 (m-80) cc_final: 0.6556 (m-80) REVERT: A 1230 LYS cc_start: 0.7762 (mmmt) cc_final: 0.6924 (mmtt) REVERT: A 1300 PHE cc_start: 0.8282 (m-10) cc_final: 0.7267 (t80) REVERT: A 1416 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: A 1473 LYS cc_start: 0.7008 (mtmm) cc_final: 0.6686 (pttt) outliers start: 36 outliers final: 23 residues processed: 178 average time/residue: 1.0593 time to fit residues: 205.7728 Evaluate side-chains 182 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 941 CYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1227 HIS Chi-restraints excluded: chain A residue 1277 ARG Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 17 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11374 Z= 0.190 Angle : 0.591 10.925 15462 Z= 0.300 Chirality : 0.043 0.301 1775 Planarity : 0.003 0.067 1908 Dihedral : 6.507 59.926 1657 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.23 % Allowed : 18.50 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.12 (0.24), residues: 1372 helix: 0.99 (0.18), residues: 882 sheet: -3.69 (0.67), residues: 22 loop : -1.46 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 PHE 0.022 0.001 PHE A1279 TYR 0.018 0.001 TYR A 381 ARG 0.004 0.000 ARG A1325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 158 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7621 (mtt) cc_final: 0.7247 (mtp) REVERT: A 159 MET cc_start: 0.6600 (OUTLIER) cc_final: 0.6268 (mpp) REVERT: A 198 ARG cc_start: 0.6676 (mmm160) cc_final: 0.5972 (mmt90) REVERT: A 236 ARG cc_start: 0.8368 (ptm160) cc_final: 0.7914 (ttt180) REVERT: A 628 ASN cc_start: 0.8584 (t0) cc_final: 0.8234 (t0) REVERT: A 631 MET cc_start: 0.8000 (mtp) cc_final: 0.7519 (mtt) REVERT: A 636 LYS cc_start: 0.7799 (tmmt) cc_final: 0.7150 (mtpt) REVERT: A 661 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7922 (mm-40) REVERT: A 665 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6762 (mpp) REVERT: A 708 ASP cc_start: 0.8080 (p0) cc_final: 0.7854 (m-30) REVERT: A 999 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7793 (tpp) REVERT: A 1042 MET cc_start: 0.9108 (mmp) cc_final: 0.8804 (mmm) REVERT: A 1078 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8660 (mttm) REVERT: A 1083 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: A 1147 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7862 (tttm) REVERT: A 1174 TYR cc_start: 0.6895 (m-80) cc_final: 0.6665 (m-80) REVERT: A 1230 LYS cc_start: 0.7773 (mmmt) cc_final: 0.6924 (mmtt) REVERT: A 1300 PHE cc_start: 0.8221 (m-10) cc_final: 0.7133 (t80) REVERT: A 1416 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: A 1473 LYS cc_start: 0.6841 (mtmm) cc_final: 0.6535 (pttt) outliers start: 37 outliers final: 25 residues processed: 179 average time/residue: 1.0694 time to fit residues: 208.9246 Evaluate side-chains 185 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 941 CYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1147 LYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1227 HIS Chi-restraints excluded: chain A residue 1277 ARG Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1416 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 17 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 95 optimal weight: 0.0570 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS A 839 GLN A1133 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.155476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.113114 restraints weight = 13415.254| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.70 r_work: 0.2992 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11374 Z= 0.170 Angle : 0.580 10.134 15462 Z= 0.295 Chirality : 0.042 0.294 1775 Planarity : 0.003 0.066 1908 Dihedral : 6.472 59.764 1657 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.14 % Allowed : 18.67 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.24 (0.24), residues: 1372 helix: 1.10 (0.18), residues: 881 sheet: -3.61 (0.68), residues: 22 loop : -1.46 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 624 HIS 0.003 0.001 HIS A1191 PHE 0.020 0.001 PHE A1279 TYR 0.018 0.001 TYR A 381 ARG 0.005 0.000 ARG A 846 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4316.43 seconds wall clock time: 76 minutes 15.51 seconds (4575.51 seconds total)