Starting phenix.real_space_refine on Sat Mar 16 15:09:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y50_10688/03_2024/6y50_10688.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y50_10688/03_2024/6y50_10688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y50_10688/03_2024/6y50_10688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y50_10688/03_2024/6y50_10688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y50_10688/03_2024/6y50_10688.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y50_10688/03_2024/6y50_10688.pdb" } resolution = 4.1 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 50 5.49 5 S 14 5.16 5 C 9000 2.51 5 N 2854 2.21 5 O 2995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "v ARG 128": "NH1" <-> "NH2" Residue "v ARG 815": "NH1" <-> "NH2" Residue "v ARG 1013": "NH1" <-> "NH2" Residue "u ARG 1238": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14916 Number of models: 1 Model: "" Number of chains: 10 Chain: "9" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 537 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 378 Unresolved non-hydrogen angles: 489 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 250 Chain: "y" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 554 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 3, 'TRANS': 89} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 60 Chain: "x" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 540 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "8" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 552 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain breaks: 1 Unresolved non-hydrogen bonds: 372 Unresolved non-hydrogen angles: 472 Unresolved non-hydrogen dihedrals: 320 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 221 Chain: "v" Number of atoms: 6500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 6500 Classifications: {'peptide': 1177} Incomplete info: {'truncation_to_alanine': 832} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1116} Chain breaks: 5 Unresolved non-hydrogen bonds: 2810 Unresolved non-hydrogen angles: 3595 Unresolved non-hydrogen dihedrals: 2225 Unresolved non-hydrogen chiralities: 309 Planarities with less than four sites: {'GLN:plan1': 40, 'ASP:plan': 62, 'TYR:plan': 22, 'ASN:plan1': 51, 'TRP:plan': 4, 'HIS:plan': 21, 'PHE:plan': 32, 'GLU:plan': 82, 'ARG:plan': 49} Unresolved non-hydrogen planarities: 1559 Chain: "u" Number of atoms: 4500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 4500 Classifications: {'peptide': 842} Incomplete info: {'truncation_to_alanine': 634} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 36, 'TRANS': 803} Unresolved non-hydrogen bonds: 2276 Unresolved non-hydrogen angles: 2898 Unresolved non-hydrogen dihedrals: 1833 Unresolved non-hydrogen chiralities: 255 Planarities with less than four sites: {'GLN:plan1': 27, 'HIS:plan': 17, 'TYR:plan': 26, 'ASN:plan1': 27, 'TRP:plan': 5, 'ASP:plan': 44, 'PHE:plan': 16, 'GLU:plan': 56, 'ARG:plan': 44} Unresolved non-hydrogen planarities: 1173 Chain: "2" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1056 Classifications: {'RNA': 50} Modifications used: {'rna3p_pur': 23, 'rna3p_pyr': 27} Link IDs: {'rna3p': 49} Chain breaks: 1 Chain: "q" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 470 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 169 Chain: "p" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 204 Classifications: {'peptide': 51} Incomplete info: {'backbone_only': 48} Link IDs: {'CIS': 1, 'TRANS': 49} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 122 Chain: "y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 576 SG CYS y 11 42.389 73.477 69.033 1.00 36.92 S ATOM 799 SG CYS y 49 42.782 70.304 71.877 1.00 44.17 S Time building chain proxies: 9.44, per 1000 atoms: 0.63 Number of scatterers: 14916 At special positions: 0 Unit cell: (133.4, 134.56, 134.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 14 16.00 P 50 15.00 O 2995 8.00 N 2854 7.00 C 9000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.19 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN y 203 " pdb="ZN ZN y 203 " - pdb=" SG CYS y 49 " pdb="ZN ZN y 203 " - pdb=" SG CYS y 11 " 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4664 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 28 sheets defined 39.3% alpha, 14.7% beta 10 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 4.98 Creating SS restraints... Processing helix chain '9' and resid 393 through 401 Processing helix chain '9' and resid 418 through 425 removed outlier: 3.762A pdb=" N ARG 9 424 " --> pdb=" O LYS 9 420 " (cutoff:3.500A) Processing helix chain '9' and resid 428 through 439 Processing helix chain '9' and resid 452 through 462 Processing helix chain '9' and resid 490 through 498 removed outlier: 3.792A pdb=" N GLN 9 498 " --> pdb=" O ASP 9 494 " (cutoff:3.500A) Processing helix chain 'y' and resid 46 through 50 removed outlier: 3.890A pdb=" N ASN y 50 " --> pdb=" O ASP y 47 " (cutoff:3.500A) Processing helix chain 'y' and resid 51 through 55 Processing helix chain 'y' and resid 73 through 77 Processing helix chain 'x' and resid 27 through 40 removed outlier: 3.553A pdb=" N ASN x 34 " --> pdb=" O GLU x 30 " (cutoff:3.500A) Processing helix chain 'x' and resid 40 through 45 Processing helix chain 'x' and resid 47 through 52 Processing helix chain 'x' and resid 52 through 57 removed outlier: 3.527A pdb=" N ALA x 56 " --> pdb=" O TYR x 52 " (cutoff:3.500A) Processing helix chain 'x' and resid 60 through 72 Processing helix chain '8' and resid 463 through 468 Processing helix chain '8' and resid 471 through 475 removed outlier: 4.023A pdb=" N VAL 8 474 " --> pdb=" O ARG 8 471 " (cutoff:3.500A) Processing helix chain '8' and resid 477 through 482 removed outlier: 3.639A pdb=" N THR 8 481 " --> pdb=" O HIS 8 478 " (cutoff:3.500A) Processing helix chain '8' and resid 484 through 493 Processing helix chain '8' and resid 525 through 530 removed outlier: 3.511A pdb=" N LYS 8 529 " --> pdb=" O PRO 8 525 " (cutoff:3.500A) Processing helix chain '8' and resid 571 through 576 Processing helix chain 'v' and resid 198 through 202 removed outlier: 3.864A pdb=" N ALA v 201 " --> pdb=" O GLY v 198 " (cutoff:3.500A) Processing helix chain 'v' and resid 559 through 561 No H-bonds generated for 'chain 'v' and resid 559 through 561' Processing helix chain 'v' and resid 808 through 824 Processing helix chain 'v' and resid 835 through 845 Processing helix chain 'v' and resid 848 through 853 Processing helix chain 'v' and resid 930 through 934 removed outlier: 3.808A pdb=" N ASN v 933 " --> pdb=" O LEU v 930 " (cutoff:3.500A) Processing helix chain 'v' and resid 1134 through 1152 removed outlier: 3.976A pdb=" N SER v1150 " --> pdb=" O MET v1146 " (cutoff:3.500A) Processing helix chain 'v' and resid 1175 through 1180 Processing helix chain 'v' and resid 1186 through 1197 Processing helix chain 'v' and resid 1200 through 1216 removed outlier: 3.870A pdb=" N ILE v1211 " --> pdb=" O LYS v1207 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG v1212 " --> pdb=" O LEU v1208 " (cutoff:3.500A) Processing helix chain 'u' and resid 468 through 472 removed outlier: 3.543A pdb=" N ILE u 472 " --> pdb=" O PRO u 469 " (cutoff:3.500A) Processing helix chain 'u' and resid 492 through 506 removed outlier: 3.682A pdb=" N LYS u 496 " --> pdb=" O GLN u 492 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS u 499 " --> pdb=" O ARG u 495 " (cutoff:3.500A) Processing helix chain 'u' and resid 508 through 521 removed outlier: 3.819A pdb=" N ALA u 515 " --> pdb=" O MET u 511 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU u 516 " --> pdb=" O ARG u 512 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP u 521 " --> pdb=" O ARG u 517 " (cutoff:3.500A) Processing helix chain 'u' and resid 522 through 526 removed outlier: 3.541A pdb=" N PHE u 526 " --> pdb=" O ALA u 523 " (cutoff:3.500A) Processing helix chain 'u' and resid 527 through 541 Proline residue: u 537 - end of helix Processing helix chain 'u' and resid 545 through 563 Processing helix chain 'u' and resid 564 through 569 Proline residue: u 569 - end of helix Processing helix chain 'u' and resid 570 through 583 removed outlier: 3.618A pdb=" N VAL u 576 " --> pdb=" O HIS u 572 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU u 579 " --> pdb=" O LEU u 575 " (cutoff:3.500A) Proline residue: u 580 - end of helix Processing helix chain 'u' and resid 586 through 604 removed outlier: 3.527A pdb=" N ALA u 604 " --> pdb=" O LEU u 600 " (cutoff:3.500A) Processing helix chain 'u' and resid 605 through 614 Processing helix chain 'u' and resid 615 through 619 removed outlier: 3.796A pdb=" N ASP u 618 " --> pdb=" O PRO u 615 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN u 619 " --> pdb=" O ASP u 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 615 through 619' Processing helix chain 'u' and resid 621 through 639 Processing helix chain 'u' and resid 640 through 653 Proline residue: u 646 - end of helix Processing helix chain 'u' and resid 657 through 676 removed outlier: 3.607A pdb=" N ARG u 661 " --> pdb=" O SER u 657 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE u 665 " --> pdb=" O ARG u 661 " (cutoff:3.500A) Processing helix chain 'u' and resid 677 through 680 removed outlier: 3.954A pdb=" N LEU u 680 " --> pdb=" O CYS u 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 677 through 680' Processing helix chain 'u' and resid 681 through 691 removed outlier: 4.631A pdb=" N SER u 685 " --> pdb=" O PRO u 681 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE u 689 " --> pdb=" O SER u 685 " (cutoff:3.500A) Processing helix chain 'u' and resid 692 through 694 No H-bonds generated for 'chain 'u' and resid 692 through 694' Processing helix chain 'u' and resid 698 through 716 Processing helix chain 'u' and resid 722 through 726 Processing helix chain 'u' and resid 727 through 734 Processing helix chain 'u' and resid 735 through 737 No H-bonds generated for 'chain 'u' and resid 735 through 737' Processing helix chain 'u' and resid 740 through 757 removed outlier: 3.641A pdb=" N TYR u 752 " --> pdb=" O LYS u 748 " (cutoff:3.500A) Proline residue: u 755 - end of helix Processing helix chain 'u' and resid 759 through 774 removed outlier: 4.262A pdb=" N ASN u 763 " --> pdb=" O ALA u 759 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR u 764 " --> pdb=" O GLU u 760 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU u 771 " --> pdb=" O ARG u 767 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE u 772 " --> pdb=" O GLU u 768 " (cutoff:3.500A) Processing helix chain 'u' and resid 781 through 798 removed outlier: 3.634A pdb=" N LYS u 785 " --> pdb=" O ASP u 781 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE u 787 " --> pdb=" O GLU u 783 " (cutoff:3.500A) Processing helix chain 'u' and resid 802 through 810 Processing helix chain 'u' and resid 810 through 818 Processing helix chain 'u' and resid 820 through 824 removed outlier: 4.387A pdb=" N MET u 823 " --> pdb=" O GLN u 820 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA u 824 " --> pdb=" O HIS u 821 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 820 through 824' Processing helix chain 'u' and resid 826 through 845 removed outlier: 4.036A pdb=" N ASN u 842 " --> pdb=" O VAL u 838 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS u 843 " --> pdb=" O GLU u 839 " (cutoff:3.500A) Processing helix chain 'u' and resid 845 through 851 removed outlier: 3.709A pdb=" N ILE u 849 " --> pdb=" O GLY u 845 " (cutoff:3.500A) Processing helix chain 'u' and resid 861 through 880 removed outlier: 3.724A pdb=" N MET u 867 " --> pdb=" O GLN u 863 " (cutoff:3.500A) Processing helix chain 'u' and resid 885 through 902 Processing helix chain 'u' and resid 907 through 922 removed outlier: 4.029A pdb=" N LEU u 911 " --> pdb=" O ASP u 907 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY u 915 " --> pdb=" O LEU u 911 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR u 916 " --> pdb=" O ASN u 912 " (cutoff:3.500A) Processing helix chain 'u' and resid 923 through 926 Processing helix chain 'u' and resid 928 through 941 removed outlier: 3.758A pdb=" N ILE u 932 " --> pdb=" O TYR u 928 " (cutoff:3.500A) Processing helix chain 'u' and resid 944 through 958 Processing helix chain 'u' and resid 958 through 963 removed outlier: 3.599A pdb=" N MET u 962 " --> pdb=" O THR u 958 " (cutoff:3.500A) Processing helix chain 'u' and resid 969 through 979 removed outlier: 4.471A pdb=" N HIS u 973 " --> pdb=" O LYS u 969 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL u 977 " --> pdb=" O HIS u 973 " (cutoff:3.500A) Processing helix chain 'u' and resid 986 through 1004 Processing helix chain 'u' and resid 1012 through 1025 Proline residue: u1018 - end of helix Proline residue: u1022 - end of helix removed outlier: 3.896A pdb=" N LYS u1025 " --> pdb=" O THR u1021 " (cutoff:3.500A) Processing helix chain 'u' and resid 1028 through 1043 removed outlier: 3.531A pdb=" N ASP u1037 " --> pdb=" O GLU u1033 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA u1043 " --> pdb=" O VAL u1039 " (cutoff:3.500A) Processing helix chain 'u' and resid 1051 through 1063 Processing helix chain 'u' and resid 1064 through 1066 No H-bonds generated for 'chain 'u' and resid 1064 through 1066' Processing helix chain 'u' and resid 1070 through 1089 removed outlier: 4.195A pdb=" N TYR u1083 " --> pdb=" O ASN u1079 " (cutoff:3.500A) Processing helix chain 'u' and resid 1089 through 1103 removed outlier: 4.381A pdb=" N LYS u1102 " --> pdb=" O LEU u1098 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL u1103 " --> pdb=" O ASN u1099 " (cutoff:3.500A) Processing helix chain 'u' and resid 1108 through 1123 removed outlier: 4.137A pdb=" N THR u1112 " --> pdb=" O ASN u1108 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR u1113 " --> pdb=" O ARG u1109 " (cutoff:3.500A) Processing helix chain 'u' and resid 1124 through 1127 Processing helix chain 'u' and resid 1128 through 1134 removed outlier: 3.612A pdb=" N ASN u1134 " --> pdb=" O PRO u1130 " (cutoff:3.500A) Processing helix chain 'u' and resid 1135 through 1137 No H-bonds generated for 'chain 'u' and resid 1135 through 1137' Processing helix chain 'u' and resid 1140 through 1158 removed outlier: 3.519A pdb=" N GLN u1144 " --> pdb=" O GLU u1140 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY u1146 " --> pdb=" O ASN u1142 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE u1153 " --> pdb=" O LYS u1149 " (cutoff:3.500A) Processing helix chain 'u' and resid 1159 through 1162 removed outlier: 3.897A pdb=" N GLY u1162 " --> pdb=" O GLY u1159 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 1159 through 1162' Processing helix chain 'u' and resid 1169 through 1178 removed outlier: 3.648A pdb=" N ALA u1176 " --> pdb=" O LEU u1172 " (cutoff:3.500A) Processing helix chain 'u' and resid 1185 through 1197 Processing helix chain 'u' and resid 1204 through 1216 removed outlier: 3.896A pdb=" N TYR u1214 " --> pdb=" O HIS u1210 " (cutoff:3.500A) Processing helix chain 'u' and resid 1217 through 1220 removed outlier: 3.770A pdb=" N PHE u1220 " --> pdb=" O PRO u1217 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 1217 through 1220' Processing helix chain 'u' and resid 1223 through 1242 removed outlier: 4.430A pdb=" N GLN u1228 " --> pdb=" O PRO u1224 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA u1229 " --> pdb=" O HIS u1225 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL u1230 " --> pdb=" O VAL u1226 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA u1233 " --> pdb=" O ALA u1229 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL u1239 " --> pdb=" O GLU u1235 " (cutoff:3.500A) Processing helix chain 'u' and resid 1242 through 1251 removed outlier: 3.656A pdb=" N MET u1246 " --> pdb=" O GLY u1242 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN u1248 " --> pdb=" O CYS u1244 " (cutoff:3.500A) Processing helix chain 'u' and resid 1261 through 1275 removed outlier: 3.812A pdb=" N LYS u1267 " --> pdb=" O ASP u1263 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY u1275 " --> pdb=" O SER u1271 " (cutoff:3.500A) Processing helix chain 'u' and resid 1280 through 1284 removed outlier: 3.934A pdb=" N TYR u1284 " --> pdb=" O ILE u1281 " (cutoff:3.500A) Processing helix chain 'u' and resid 1297 through 1301 Processing helix chain 'q' and resid 145 through 155 removed outlier: 3.562A pdb=" N PHE q 149 " --> pdb=" O THR q 145 " (cutoff:3.500A) Processing helix chain 'q' and resid 190 through 201 removed outlier: 3.753A pdb=" N VAL q 194 " --> pdb=" O LYS q 190 " (cutoff:3.500A) Processing helix chain 'p' and resid 148 through 179 Processing helix chain 'p' and resid 189 through 194 removed outlier: 3.850A pdb=" N LYS p 193 " --> pdb=" O ILE p 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '9' and resid 406 through 408 Processing sheet with id=AA2, first strand: chain 'y' and resid 18 through 19 removed outlier: 4.387A pdb=" N ALA y 18 " --> pdb=" O ILE y 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'y' and resid 39 through 42 removed outlier: 3.935A pdb=" N THR y 41 " --> pdb=" O TYR y 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'v' and resid 1104 through 1107 Processing sheet with id=AA5, first strand: chain 'v' and resid 18 through 20 removed outlier: 3.861A pdb=" N LEU v 54 " --> pdb=" O LEU v 40 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG v 42 " --> pdb=" O THR v 52 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR v 52 " --> pdb=" O ARG v 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'v' and resid 65 through 66 removed outlier: 3.785A pdb=" N MET v 66 " --> pdb=" O VAL v 79 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL v 79 " --> pdb=" O MET v 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'v' and resid 120 through 122 Processing sheet with id=AA8, first strand: chain 'v' and resid 144 through 146 Processing sheet with id=AA9, first strand: chain 'v' and resid 165 through 173 removed outlier: 6.328A pdb=" N LEU v 185 " --> pdb=" O TYR v 168 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL v 170 " --> pdb=" O ALA v 183 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA v 183 " --> pdb=" O VAL v 170 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLY v 172 " --> pdb=" O MET v 181 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N MET v 181 " --> pdb=" O GLY v 172 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU v 208 " --> pdb=" O SER v 225 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER v 225 " --> pdb=" O LEU v 208 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE v 210 " --> pdb=" O LYS v 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'v' and resid 237 through 238 removed outlier: 3.618A pdb=" N TYR v 255 " --> pdb=" O SER v 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'v' and resid 302 through 304 Processing sheet with id=AB3, first strand: chain 'v' and resid 316 through 317 Processing sheet with id=AB4, first strand: chain 'v' and resid 336 through 342 removed outlier: 3.703A pdb=" N ALA v 338 " --> pdb=" O ALA v 350 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE v 346 " --> pdb=" O LEU v 342 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N HIS v 356 " --> pdb=" O GLU v 400 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU v 400 " --> pdb=" O HIS v 356 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU v 358 " --> pdb=" O VAL v 398 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'v' and resid 407 through 413 Processing sheet with id=AB6, first strand: chain 'v' and resid 442 through 443 removed outlier: 5.302A pdb=" N SER v 724 " --> pdb=" O GLU v 710 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLU v 710 " --> pdb=" O SER v 724 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'v' and resid 448 through 450 removed outlier: 3.637A pdb=" N THR v 761 " --> pdb=" O SER v 758 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'v' and resid 458 through 463 Processing sheet with id=AB9, first strand: chain 'v' and resid 507 through 509 Processing sheet with id=AC1, first strand: chain 'v' and resid 546 through 548 Processing sheet with id=AC2, first strand: chain 'v' and resid 589 through 592 removed outlier: 6.885A pdb=" N VAL v 614 " --> pdb=" O MET v 630 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N MET v 630 " --> pdb=" O VAL v 614 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE v 616 " --> pdb=" O LEU v 628 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLN v 626 " --> pdb=" O SER v 618 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'v' and resid 637 through 643 removed outlier: 5.491A pdb=" N VAL v 673 " --> pdb=" O LEU v 669 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'v' and resid 784 through 787 removed outlier: 6.571A pdb=" N ILE v 800 " --> pdb=" O ARG v 786 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'v' and resid 891 through 894 removed outlier: 6.729A pdb=" N GLY v 923 " --> pdb=" O PRO v 944 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL v 925 " --> pdb=" O LYS v 942 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS v 942 " --> pdb=" O VAL v 925 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR v 927 " --> pdb=" O LEU v 940 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'v' and resid 959 through 963 removed outlier: 7.065A pdb=" N ASP v 971 " --> pdb=" O ARG v 979 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG v 979 " --> pdb=" O ASP v 971 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'v' and resid 999 through 1003 Processing sheet with id=AC8, first strand: chain 'v' and resid 1025 through 1026 removed outlier: 3.938A pdb=" N ASP v1026 " --> pdb=" O GLN v1087 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'v' and resid 1036 through 1037 removed outlier: 6.393A pdb=" N ARG v1057 " --> pdb=" O VAL v1091 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL v1091 " --> pdb=" O ARG v1057 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'q' and resid 183 through 187 820 hydrogen bonds defined for protein. 2274 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 6.71 Time building geometry restraints manager: 6.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5071 1.34 - 1.45: 1748 1.45 - 1.57: 8294 1.57 - 1.69: 97 1.69 - 1.81: 24 Bond restraints: 15234 Sorted by residual: bond pdb=" O3' C 2 45 " pdb=" P U 2 46 " ideal model delta sigma weight residual 1.607 1.469 0.138 1.50e-02 4.44e+03 8.50e+01 bond pdb=" N VAL v 444 " pdb=" CA VAL v 444 " ideal model delta sigma weight residual 1.456 1.501 -0.045 1.15e-02 7.56e+03 1.56e+01 bond pdb=" N TYR 9 416 " pdb=" CA TYR 9 416 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.14e-02 7.69e+03 8.89e+00 bond pdb=" N ILE 9 452 " pdb=" CA ILE 9 452 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.01e+00 bond pdb=" N ILE p 182 " pdb=" CA ILE p 182 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.84e+00 ... (remaining 15229 not shown) Histogram of bond angle deviations from ideal: 97.07 - 104.45: 523 104.45 - 111.83: 7438 111.83 - 119.21: 4468 119.21 - 126.58: 8625 126.58 - 133.96: 277 Bond angle restraints: 21331 Sorted by residual: angle pdb=" O3' A 2 24 " pdb=" P G 2 25 " pdb=" O5' G 2 25 " ideal model delta sigma weight residual 104.00 114.57 -10.57 1.50e+00 4.44e-01 4.97e+01 angle pdb=" C SER v 445 " pdb=" N GLU v 446 " pdb=" CA GLU v 446 " ideal model delta sigma weight residual 121.89 114.97 6.92 1.74e+00 3.30e-01 1.58e+01 angle pdb=" N ASP p 147 " pdb=" CA ASP p 147 " pdb=" C ASP p 147 " ideal model delta sigma weight residual 114.31 109.27 5.04 1.29e+00 6.01e-01 1.53e+01 angle pdb=" C3' C 2 45 " pdb=" O3' C 2 45 " pdb=" P U 2 46 " ideal model delta sigma weight residual 120.20 125.68 -5.48 1.50e+00 4.44e-01 1.33e+01 angle pdb=" O3' A 2 24 " pdb=" P G 2 25 " pdb=" OP1 G 2 25 " ideal model delta sigma weight residual 108.00 97.07 10.93 3.00e+00 1.11e-01 1.33e+01 ... (remaining 21326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.12: 8815 31.12 - 62.24: 96 62.24 - 93.36: 34 93.36 - 124.48: 0 124.48 - 155.60: 1 Dihedral angle restraints: 8946 sinusoidal: 1725 harmonic: 7221 Sorted by residual: dihedral pdb=" O4' U 2 47 " pdb=" C1' U 2 47 " pdb=" N1 U 2 47 " pdb=" C2 U 2 47 " ideal model delta sinusoidal sigma weight residual 200.00 44.40 155.60 1 1.50e+01 4.44e-03 8.15e+01 dihedral pdb=" CA PRO x 78 " pdb=" C PRO x 78 " pdb=" N PRO x 79 " pdb=" CA PRO x 79 " ideal model delta harmonic sigma weight residual 180.00 151.91 28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA GLU u1048 " pdb=" C GLU u1048 " pdb=" N TYR u1049 " pdb=" CA TYR u1049 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 8943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1867 0.038 - 0.075: 541 0.075 - 0.113: 215 0.113 - 0.151: 31 0.151 - 0.188: 1 Chirality restraints: 2655 Sorted by residual: chirality pdb=" CA ILE 9 452 " pdb=" N ILE 9 452 " pdb=" C ILE 9 452 " pdb=" CB ILE 9 452 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CA ILE v 132 " pdb=" N ILE v 132 " pdb=" C ILE v 132 " pdb=" CB ILE v 132 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA VAL v 865 " pdb=" N VAL v 865 " pdb=" C VAL v 865 " pdb=" CB VAL v 865 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 2652 not shown) Planarity restraints: 2844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU v 443 " 0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C GLU v 443 " -0.068 2.00e-02 2.50e+03 pdb=" O GLU v 443 " 0.026 2.00e-02 2.50e+03 pdb=" N VAL v 444 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP v 195 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO v 196 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO v 196 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO v 196 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR 9 415 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C THR 9 415 " 0.037 2.00e-02 2.50e+03 pdb=" O THR 9 415 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR 9 416 " -0.012 2.00e-02 2.50e+03 ... (remaining 2841 not shown) Histogram of nonbonded interaction distances: 0.76 - 1.59: 4 1.59 - 2.42: 33 2.42 - 3.24: 15063 3.24 - 4.07: 33028 4.07 - 4.90: 56445 Warning: very small nonbonded interaction distances. Nonbonded interactions: 104573 Sorted by model distance: nonbonded pdb=" CB CYS y 33 " pdb="ZN ZN y 201 " model vdw 0.761 2.630 nonbonded pdb=" C ASP v1067 " pdb=" CB SER v1086 " model vdw 0.895 3.670 nonbonded pdb=" O ASP v1067 " pdb=" CB SER v1086 " model vdw 1.019 3.440 nonbonded pdb=" CA CYS y 33 " pdb="ZN ZN y 201 " model vdw 1.503 2.660 nonbonded pdb=" CB PRO u 780 " pdb=" O ILE p 189 " model vdw 1.740 3.440 ... (remaining 104568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.680 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 51.440 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 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 : 0.003 0.138 15234 Z= 0.184 Angle : 0.522 10.931 21331 Z= 0.318 Chirality : 0.041 0.188 2655 Planarity : 0.004 0.057 2844 Dihedral : 11.032 155.600 4282 Min Nonbonded Distance : 0.761 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.90 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.08 % 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: -3.48 (0.15), residues: 2509 helix: -0.82 (0.16), residues: 822 sheet: -2.88 (0.20), residues: 476 loop : -3.18 (0.16), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP x 29 HIS 0.009 0.001 HIS u1210 PHE 0.012 0.001 PHE v 182 TYR 0.013 0.001 TYR u1249 ARG 0.003 0.000 ARG u1238 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: u 1192 VAL cc_start: 0.8114 (t) cc_final: 0.7706 (t) REVERT: u 1237 LEU cc_start: 0.8949 (mt) cc_final: 0.8718 (mt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2411 time to fit residues: 60.6322 Evaluate side-chains 112 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 7.9990 chunk 193 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 121 optimal weight: 0.0270 chunk 148 optimal weight: 20.0000 chunk 231 optimal weight: 0.0970 overall best weight: 4.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** y 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 34 ASN x 46 HIS v1160 HIS ** u1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u1248 GLN ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15234 Z= 0.358 Angle : 0.620 6.679 21331 Z= 0.340 Chirality : 0.046 0.162 2655 Planarity : 0.005 0.058 2844 Dihedral : 11.937 155.878 3342 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.20 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.08 % Twisted Proline : 0.85 % Twisted General : 0.04 % 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: -2.61 (0.17), residues: 2509 helix: 0.20 (0.19), residues: 821 sheet: -2.64 (0.21), residues: 482 loop : -2.78 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP u1216 HIS 0.011 0.002 HIS u1210 PHE 0.032 0.002 PHE v 120 TYR 0.019 0.002 TYR v1095 ARG 0.006 0.001 ARG x 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.721 Fit side-chains revert: symmetry clash REVERT: x 65 ARG cc_start: 0.8165 (ptp-110) cc_final: 0.7892 (mtm110) REVERT: u 1231 MET cc_start: 0.8274 (tpp) cc_final: 0.7803 (ttp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2320 time to fit residues: 45.4849 Evaluate side-chains 102 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 192 optimal weight: 40.0000 chunk 157 optimal weight: 30.0000 chunk 63 optimal weight: 10.0000 chunk 231 optimal weight: 0.0970 chunk 250 optimal weight: 0.0030 chunk 206 optimal weight: 0.5980 chunk 230 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 186 optimal weight: 6.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: y 50 ASN x 34 ASN v1096 HIS ** u1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u1210 HIS u1248 GLN u1252 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15234 Z= 0.130 Angle : 0.482 6.563 21331 Z= 0.250 Chirality : 0.043 0.200 2655 Planarity : 0.004 0.060 2844 Dihedral : 11.650 156.951 3342 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.02 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.08 % 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: -1.86 (0.18), residues: 2509 helix: 0.93 (0.19), residues: 837 sheet: -2.15 (0.23), residues: 457 loop : -2.50 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP x 29 HIS 0.007 0.001 HIS u1210 PHE 0.014 0.001 PHE v 120 TYR 0.012 0.001 TYR u1265 ARG 0.007 0.001 ARG y 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.692 Fit side-chains REVERT: x 65 ARG cc_start: 0.7941 (ptp-110) cc_final: 0.7731 (mtm110) REVERT: u 1216 TRP cc_start: 0.7279 (t-100) cc_final: 0.7040 (t-100) REVERT: u 1231 MET cc_start: 0.8183 (tpp) cc_final: 0.7932 (ttm) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2293 time to fit residues: 47.3908 Evaluate side-chains 103 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 6.9990 chunk 174 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 232 optimal weight: 0.6980 chunk 246 optimal weight: 50.0000 chunk 121 optimal weight: 5.9990 chunk 220 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** y 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 34 ASN ** x 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 119 GLN ** u1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u1194 HIS u1213 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15234 Z= 0.326 Angle : 0.608 9.738 21331 Z= 0.329 Chirality : 0.046 0.152 2655 Planarity : 0.005 0.057 2844 Dihedral : 11.998 151.551 3342 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.55 % Favored : 87.33 % Rotamer: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.08 (0.18), residues: 2509 helix: 0.71 (0.19), residues: 839 sheet: -2.18 (0.23), residues: 449 loop : -2.65 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP u1216 HIS 0.008 0.002 HIS u1210 PHE 0.020 0.002 PHE v 120 TYR 0.025 0.002 TYR u1273 ARG 0.008 0.001 ARG u1245 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.664 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2108 time to fit residues: 39.0688 Evaluate side-chains 96 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 5.9990 chunk 139 optimal weight: 0.0980 chunk 3 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 210 optimal weight: 30.0000 chunk 170 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 221 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** y 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15234 Z= 0.328 Angle : 0.611 7.620 21331 Z= 0.333 Chirality : 0.046 0.226 2655 Planarity : 0.005 0.053 2844 Dihedral : 12.194 148.809 3342 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.16 % Favored : 88.72 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.14 (0.17), residues: 2509 helix: 0.67 (0.19), residues: 833 sheet: -2.19 (0.23), residues: 449 loop : -2.70 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP u1216 HIS 0.010 0.002 HIS x 23 PHE 0.026 0.002 PHE v1182 TYR 0.030 0.002 TYR v1166 ARG 0.008 0.001 ARG x 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.749 Fit side-chains REVERT: u 1216 TRP cc_start: 0.7543 (t-100) cc_final: 0.7188 (t-100) REVERT: u 1266 TRP cc_start: 0.7986 (m100) cc_final: 0.7753 (m100) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2168 time to fit residues: 40.0492 Evaluate side-chains 96 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 50.0000 chunk 221 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 246 optimal weight: 50.0000 chunk 204 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 50.0000 chunk 129 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: y 50 ASN x 35 GLN ** x 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u1194 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15234 Z= 0.280 Angle : 0.581 7.124 21331 Z= 0.314 Chirality : 0.045 0.177 2655 Planarity : 0.005 0.056 2844 Dihedral : 12.164 147.734 3342 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.44 % Favored : 87.45 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.03 (0.18), residues: 2509 helix: 0.81 (0.19), residues: 838 sheet: -2.08 (0.24), residues: 440 loop : -2.69 (0.18), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP u1216 HIS 0.004 0.002 HIS v 231 PHE 0.020 0.002 PHE v1182 TYR 0.020 0.002 TYR v1095 ARG 0.008 0.001 ARG u1245 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.646 Fit side-chains revert: symmetry clash REVERT: v 1024 PHE cc_start: 0.8160 (t80) cc_final: 0.7854 (t80) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1992 time to fit residues: 35.7811 Evaluate side-chains 95 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 20.0000 chunk 27 optimal weight: 0.0970 chunk 140 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 245 optimal weight: 0.0770 chunk 153 optimal weight: 30.0000 chunk 149 optimal weight: 0.5980 chunk 113 optimal weight: 10.0000 overall best weight: 2.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: y 50 ASN x 35 GLN ** u1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15234 Z= 0.209 Angle : 0.538 6.535 21331 Z= 0.287 Chirality : 0.044 0.161 2655 Planarity : 0.005 0.048 2844 Dihedral : 12.030 148.364 3342 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.09 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.08 % Twisted Proline : 0.85 % Twisted General : 0.04 % 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: -1.74 (0.18), residues: 2509 helix: 1.09 (0.19), residues: 840 sheet: -1.85 (0.25), residues: 430 loop : -2.59 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP u1266 HIS 0.006 0.001 HIS x 23 PHE 0.018 0.001 PHE v1182 TYR 0.017 0.002 TYR u1265 ARG 0.006 0.001 ARG u1245 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.547 Fit side-chains revert: symmetry clash REVERT: v 1024 PHE cc_start: 0.8039 (t80) cc_final: 0.7736 (t80) REVERT: u 1216 TRP cc_start: 0.7291 (t-100) cc_final: 0.6880 (t-100) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2243 time to fit residues: 41.2076 Evaluate side-chains 101 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 156 optimal weight: 20.0000 chunk 167 optimal weight: 0.0060 chunk 121 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: y 50 ASN x 23 HIS x 46 HIS u1194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15234 Z= 0.130 Angle : 0.500 6.542 21331 Z= 0.260 Chirality : 0.043 0.147 2655 Planarity : 0.004 0.052 2844 Dihedral : 11.796 151.128 3342 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.33 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.08 % Twisted Proline : 0.85 % Twisted General : 0.04 % 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: -1.30 (0.18), residues: 2509 helix: 1.49 (0.19), residues: 844 sheet: -1.67 (0.25), residues: 429 loop : -2.34 (0.19), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP x 29 HIS 0.008 0.001 HIS u1256 PHE 0.011 0.001 PHE v 182 TYR 0.017 0.001 TYR u1284 ARG 0.006 0.001 ARG y 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: u 1216 TRP cc_start: 0.7116 (t-100) cc_final: 0.6773 (t-100) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2187 time to fit residues: 41.4032 Evaluate side-chains 104 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 214 optimal weight: 0.9980 chunk 229 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 99 optimal weight: 30.0000 chunk 179 optimal weight: 40.0000 chunk 70 optimal weight: 10.0000 chunk 206 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 228 optimal weight: 9.9990 overall best weight: 7.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** y 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 15234 Z= 0.518 Angle : 0.753 12.770 21331 Z= 0.420 Chirality : 0.050 0.179 2655 Planarity : 0.006 0.053 2844 Dihedral : 12.604 143.786 3342 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.15 % Favored : 84.77 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.42 (0.17), residues: 2509 helix: 0.31 (0.18), residues: 843 sheet: -2.09 (0.24), residues: 425 loop : -2.89 (0.18), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP v 862 HIS 0.016 0.002 HIS x 23 PHE 0.041 0.003 PHE v1182 TYR 0.045 0.003 TYR v1095 ARG 0.013 0.001 ARG x 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.788 Fit side-chains REVERT: u 1266 TRP cc_start: 0.8487 (m100) cc_final: 0.8254 (m100) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2086 time to fit residues: 35.1565 Evaluate side-chains 92 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 8.9990 chunk 242 optimal weight: 0.0050 chunk 147 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 168 optimal weight: 20.0000 chunk 254 optimal weight: 0.2980 chunk 233 optimal weight: 0.9980 chunk 202 optimal weight: 40.0000 chunk 21 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: y 50 ASN ** u1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u1218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15234 Z= 0.139 Angle : 0.534 8.628 21331 Z= 0.280 Chirality : 0.044 0.158 2655 Planarity : 0.005 0.050 2844 Dihedral : 12.068 147.943 3342 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.90 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.08 % Twisted Proline : 0.85 % Twisted General : 0.04 % 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: -1.42 (0.18), residues: 2509 helix: 1.34 (0.19), residues: 849 sheet: -1.76 (0.25), residues: 414 loop : -2.39 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP v 862 HIS 0.004 0.001 HIS x 23 PHE 0.015 0.001 PHE v 788 TYR 0.022 0.001 TYR u1200 ARG 0.007 0.001 ARG y 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: u 1216 TRP cc_start: 0.7446 (t-100) cc_final: 0.7111 (t-100) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2164 time to fit residues: 41.4419 Evaluate side-chains 103 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 56 optimal weight: 30.0000 chunk 202 optimal weight: 20.0000 chunk 84 optimal weight: 40.0000 chunk 208 optimal weight: 0.0040 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 overall best weight: 2.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: y 50 ASN x 46 HIS ** u1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u1218 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.094251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.077671 restraints weight = 68332.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.076455 restraints weight = 116000.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.076962 restraints weight = 95508.842| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15234 Z= 0.185 Angle : 0.526 9.272 21331 Z= 0.276 Chirality : 0.044 0.147 2655 Planarity : 0.004 0.048 2844 Dihedral : 11.977 148.516 3342 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.76 % Favored : 90.16 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.08 % Twisted Proline : 0.85 % Twisted General : 0.04 % 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: -1.33 (0.18), residues: 2509 helix: 1.49 (0.19), residues: 839 sheet: -1.69 (0.25), residues: 417 loop : -2.37 (0.19), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP u1266 HIS 0.006 0.001 HIS x 23 PHE 0.017 0.001 PHE v1182 TYR 0.021 0.002 TYR v1095 ARG 0.005 0.001 ARG y 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2278.31 seconds wall clock time: 41 minutes 33.94 seconds (2493.94 seconds total)