Starting phenix.real_space_refine on Sat Sep 12 10:17:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6y50_10688/09_2026/6y50_10688.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y50_10688/09_2026/6y50_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6y50_10688/09_2026/6y50_10688.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6y50_10688/09_2026/6y50_10688.cif" model { file = "/net/cci-nas-00/data/ceres_data/6y50_10688/09_2026/6y50_10688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y50_10688/09_2026/6y50_10688.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y50_10688/09_2026/6y50_10688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y50_10688/09_2026/6y50_10688.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'TYR:plan': 7, 'TRP:plan': 4, 'HIS:plan': 5, 'ASN:plan1': 8, 'GLU:plan': 9, 'ARG:plan': 6, 'PHE:plan': 3, 'GLN:plan1': 5, 'ASP:plan': 4} 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: {'ASP:plan': 8, 'GLN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1} 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: {'ASN:plan1': 2, 'ARG:plan': 7, 'PHE:plan': 7, 'GLU:plan': 7, 'GLN:plan1': 5, 'ASP:plan': 8, 'HIS:plan': 4, 'TRP:plan': 2, 'TYR:plan': 4} 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: {'ARG:plan': 49, 'ASN:plan1': 51, 'GLN:plan1': 40, 'GLU:plan': 82, 'ASP:plan': 62, 'HIS:plan': 21, 'TYR:plan': 22, 'PHE:plan': 32, 'TRP:plan': 4} 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: {'ASN:plan1': 27, 'PHE:plan': 16, 'ASP:plan': 44, 'GLN:plan1': 27, 'TYR:plan': 26, 'GLU:plan': 56, 'ARG:plan': 44, 'HIS:plan': 17, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 1173 Chain: "2" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1056 Classifications: {'RNAv2': 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: {'GLU:plan': 10, 'ASP:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 4, 'TYR:plan': 4, 'PHE:plan': 4, 'GLN:plan1': 4, 'HIS:plan': 1} 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: {'ASP:plan': 2, 'ASN:plan1': 3, 'PHE:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 12, 'ARG:plan': 5, 'TRP:plan': 1} 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: 3.30, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 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: 1.24 Conformation dependent library (CDL) restraints added in 823.1 milliseconds 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: 1.86 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: 3.13 Time building geometry restraints manager: 1.59 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 1.20e-02 6.94e+03 1.33e+02 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: 0.00 - 2.19: 21000 2.19 - 4.37: 313 4.37 - 6.56: 15 6.56 - 8.74: 1 8.74 - 10.93: 2 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 1.90e+00 2.77e-01 3.09e+01 angle pdb=" C3' C 2 45 " pdb=" O3' C 2 45 " pdb=" P U 2 46 " ideal model delta sigma weight residual 119.70 125.68 -5.98 1.20e+00 6.94e-01 2.48e+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=" 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 - 15.06: 8608 15.06 - 30.12: 98 30.12 - 45.18: 48 45.18 - 60.24: 19 60.24 - 75.29: 5 Dihedral angle restraints: 8778 sinusoidal: 1557 harmonic: 7221 Sorted by residual: 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 dihedral pdb=" O5' A 2 56 " pdb=" C5' A 2 56 " pdb=" C4' A 2 56 " pdb=" C3' A 2 56 " ideal model delta sinusoidal sigma weight residual 60.00 35.96 24.04 3 6.40e+00 2.44e-02 1.80e+01 ... (remaining 8775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2165 0.055 - 0.109: 391 0.109 - 0.164: 48 0.164 - 0.219: 2 0.219 - 0.273: 49 Chirality restraints: 2655 Sorted by residual: chirality pdb=" P C 2 28 " pdb=" OP1 C 2 28 " pdb=" OP2 C 2 28 " pdb=" O5' C 2 28 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" P A 2 48 " pdb=" OP1 A 2 48 " pdb=" OP2 A 2 48 " pdb=" O5' A 2 48 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" P U 2 39 " pdb=" OP1 U 2 39 " pdb=" OP2 U 2 39 " pdb=" O5' U 2 39 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 2.550 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.660 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.699 15236 Z= 0.276 Angle : 0.560 10.931 21331 Z= 0.324 Chirality : 0.053 0.273 2655 Planarity : 0.004 0.057 2844 Dihedral : 7.828 75.295 4114 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG u1238 TYR 0.013 0.001 TYR u1249 PHE 0.012 0.001 PHE v 182 TRP 0.015 0.001 TRP x 29 HIS 0.009 0.001 HIS u1210 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.19 (15234) covalent geometry : angle 0.55987 / 0.32 (21331) hydrogen bonds : bond 0.15391 / 11.39 ( 845) hydrogen bonds : angle 6.41777 / 4.47 ( 2320) metal coordination : bond 0.51140 / 26.75 ( 2) *********************** 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 to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.392 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: 0.1048 time to fit residues: 26.7995 Evaluate side-chains 112 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 247 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... y 50 ASN x 34 ASN x 46 HIS v1096 HIS u1186 GLN u1210 HIS u1252 GLN u1256 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.099004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.081531 restraints weight = 68419.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.080749 restraints weight = 95616.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.081220 restraints weight = 78605.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.081235 restraints weight = 60441.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.081309 restraints weight = 55458.619| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15236 Z= 0.102 Angle : 0.516 6.667 21331 Z= 0.257 Chirality : 0.045 0.218 2655 Planarity : 0.004 0.051 2844 Dihedral : 7.376 68.334 3174 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.38 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.08 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.17), residues: 2509 helix: 0.39 (0.18), residues: 848 sheet: -2.45 (0.21), residues: 480 loop : -2.70 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG y 82 TYR 0.012 0.001 TYR v 424 PHE 0.022 0.001 PHE v 120 TRP 0.012 0.001 TRP v 862 HIS 0.010 0.001 HIS u1210 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 (15234) covalent geometry : angle 0.51600 / 0.26 (21331) hydrogen bonds : bond 0.02789 / 2.03 ( 845) hydrogen bonds : angle 4.85889 / 3.43 ( 2320) metal coordination : bond 0.00922 / 0.48 ( 2) *********************** 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 140 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: u 1231 MET cc_start: 0.7979 (tpp) cc_final: 0.7753 (ttp) REVERT: u 1295 TYR cc_start: 0.8199 (m-80) cc_final: 0.7953 (m-10) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1027 time to fit residues: 22.4223 Evaluate side-chains 108 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 178 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 167 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 chunk 191 optimal weight: 40.0000 chunk 206 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 61 optimal weight: 0.2980 chunk 60 optimal weight: 8.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** y 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 34 ASN ** x 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 119 GLN v1160 HIS u1213 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.094614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.077021 restraints weight = 69028.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.075627 restraints weight = 98223.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.076052 restraints weight = 87547.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.076145 restraints weight = 62910.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.076229 restraints weight = 56235.071| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 15236 Z= 0.240 Angle : 0.637 6.641 21331 Z= 0.333 Chirality : 0.049 0.321 2655 Planarity : 0.005 0.058 2844 Dihedral : 7.831 71.105 3174 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.56 % Favored : 89.32 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.08 % Twisted Proline : 0.85 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.17), residues: 2509 helix: 0.57 (0.19), residues: 837 sheet: -2.37 (0.22), residues: 468 loop : -2.63 (0.19), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG x 37 TYR 0.024 0.003 TYR u1273 PHE 0.021 0.002 PHE v 120 TRP 0.020 0.003 TRP u1216 HIS 0.008 0.002 HIS u1210 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.24 (15234) covalent geometry : angle 0.63740 / 0.33 (21331) hydrogen bonds : bond 0.03625 / 2.65 ( 845) hydrogen bonds : angle 5.41794 / 3.83 ( 2320) metal coordination : bond 0.00518 / 0.25 ( 2) *********************** 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 118 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.444 Fit side-chains REVERT: u 1195 MET cc_start: 0.8667 (ttt) cc_final: 0.8323 (ttt) REVERT: u 1231 MET cc_start: 0.8542 (tpp) cc_final: 0.7770 (ttm) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0916 time to fit residues: 17.6750 Evaluate side-chains 95 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 155 optimal weight: 3.9990 chunk 97 optimal weight: 30.0000 chunk 238 optimal weight: 20.0000 chunk 109 optimal weight: 40.0000 chunk 7 optimal weight: 20.0000 chunk 232 optimal weight: 0.0570 chunk 154 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 248 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... y 50 ASN v 231 HIS u1194 HIS u1252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.096684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.079625 restraints weight = 68160.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.078381 restraints weight = 116236.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.078878 restraints weight = 93670.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.078964 restraints weight = 65916.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.079044 restraints weight = 60948.722| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15236 Z= 0.107 Angle : 0.528 6.601 21331 Z= 0.264 Chirality : 0.046 0.214 2655 Planarity : 0.004 0.057 2844 Dihedral : 7.429 71.796 3174 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.94 % Favored : 93.94 % 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 : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.18), residues: 2509 helix: 1.05 (0.19), residues: 844 sheet: -1.97 (0.23), residues: 465 loop : -2.42 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG u1245 TYR 0.018 0.001 TYR u1273 PHE 0.014 0.001 PHE v 120 TRP 0.015 0.001 TRP u1216 HIS 0.003 0.001 HIS v 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 (15234) covalent geometry : angle 0.52753 / 0.26 (21331) hydrogen bonds : bond 0.02510 / 1.86 ( 845) hydrogen bonds : angle 4.66746 / 3.28 ( 2320) metal coordination : bond 0.00040 / 0.02 ( 2) *********************** 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 124 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.612 Fit side-chains REVERT: x 65 ARG cc_start: 0.8365 (ptp-110) cc_final: 0.7754 (mtm110) REVERT: u 1195 MET cc_start: 0.8892 (ttt) cc_final: 0.8564 (ttt) REVERT: u 1231 MET cc_start: 0.8513 (tpp) cc_final: 0.7833 (ttm) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.0902 time to fit residues: 18.2206 Evaluate side-chains 101 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 200 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 233 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 181 optimal weight: 0.0370 chunk 1 optimal weight: 50.0000 chunk 45 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 5 optimal weight: 0.4980 overall best weight: 2.7064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... y 50 ASN x 23 HIS x 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.095197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.079490 restraints weight = 68492.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.078761 restraints weight = 98214.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.079041 restraints weight = 96863.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.078813 restraints weight = 65153.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.078944 restraints weight = 64052.868| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15236 Z= 0.158 Angle : 0.561 6.609 21331 Z= 0.285 Chirality : 0.047 0.214 2655 Planarity : 0.004 0.051 2844 Dihedral : 7.518 74.377 3174 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.00 % Favored : 89.88 % 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 : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.18), residues: 2509 helix: 1.13 (0.19), residues: 842 sheet: -1.93 (0.23), residues: 459 loop : -2.41 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG x 37 TYR 0.015 0.002 TYR v1095 PHE 0.015 0.001 PHE v1024 TRP 0.012 0.002 TRP x 29 HIS 0.007 0.001 HIS x 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (15234) covalent geometry : angle 0.56133 / 0.28 (21331) hydrogen bonds : bond 0.02769 / 2.04 ( 845) hydrogen bonds : angle 4.77780 / 3.36 ( 2320) metal coordination : bond 0.00279 / 0.14 ( 2) *********************** 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 115 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.535 Fit side-chains REVERT: x 65 ARG cc_start: 0.8292 (ptp-110) cc_final: 0.8069 (mtm110) REVERT: v 1024 PHE cc_start: 0.8136 (t80) cc_final: 0.7876 (t80) REVERT: u 1195 MET cc_start: 0.8902 (ttt) cc_final: 0.8595 (ttt) REVERT: u 1216 TRP cc_start: 0.7916 (t-100) cc_final: 0.7474 (t-100) REVERT: u 1231 MET cc_start: 0.8568 (tpp) cc_final: 0.7843 (ttm) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0869 time to fit residues: 16.7337 Evaluate side-chains 99 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 221 optimal weight: 4.9990 chunk 67 optimal weight: 30.0000 chunk 59 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 245 optimal weight: 20.0000 chunk 11 optimal weight: 30.0000 chunk 161 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** y 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 46 HIS u1194 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.092809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.076605 restraints weight = 69065.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.075676 restraints weight = 100271.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.076070 restraints weight = 99283.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.075921 restraints weight = 70853.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.076164 restraints weight = 63328.509| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15236 Z= 0.267 Angle : 0.685 6.636 21331 Z= 0.357 Chirality : 0.050 0.266 2655 Planarity : 0.005 0.060 2844 Dihedral : 8.203 82.222 3174 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.76 % Favored : 88.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.17), residues: 2509 helix: 0.64 (0.19), residues: 845 sheet: -2.11 (0.23), residues: 445 loop : -2.67 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG x 37 TYR 0.044 0.003 TYR u1265 PHE 0.027 0.002 PHE v1182 TRP 0.018 0.003 TRP u1216 HIS 0.011 0.002 HIS x 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.27 (15234) covalent geometry : angle 0.68525 / 0.36 (21331) hydrogen bonds : bond 0.03676 / 2.68 ( 845) hydrogen bonds : angle 5.64772 / 3.98 ( 2320) metal coordination : bond 0.00533 / 0.28 ( 2) *********************** 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 104 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: u 1195 MET cc_start: 0.8678 (ttt) cc_final: 0.8237 (ttt) REVERT: u 1216 TRP cc_start: 0.8179 (t-100) cc_final: 0.7899 (t-100) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0834 time to fit residues: 15.3245 Evaluate side-chains 94 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 45 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 152 optimal weight: 0.0000 chunk 212 optimal weight: 9.9990 chunk 83 optimal weight: 50.0000 chunk 50 optimal weight: 5.9990 chunk 179 optimal weight: 0.0170 chunk 113 optimal weight: 9.9990 chunk 157 optimal weight: 30.0000 chunk 188 optimal weight: 40.0000 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... y 50 ASN ** u1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.094627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.077081 restraints weight = 68026.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.075793 restraints weight = 107975.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.076253 restraints weight = 89038.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.076307 restraints weight = 67162.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.076364 restraints weight = 62947.548| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15236 Z= 0.145 Angle : 0.575 6.597 21331 Z= 0.291 Chirality : 0.047 0.211 2655 Planarity : 0.004 0.048 2844 Dihedral : 7.794 80.967 3174 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.53 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.08 % Twisted Proline : 0.85 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.18), residues: 2509 helix: 1.06 (0.19), residues: 846 sheet: -1.98 (0.24), residues: 441 loop : -2.46 (0.19), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG u1245 TYR 0.026 0.002 TYR u1265 PHE 0.016 0.001 PHE v 182 TRP 0.013 0.002 TRP u1266 HIS 0.007 0.001 HIS x 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (15234) covalent geometry : angle 0.57508 / 0.29 (21331) hydrogen bonds : bond 0.02787 / 2.05 ( 845) hydrogen bonds : angle 4.96291 / 3.48 ( 2320) metal coordination : bond 0.00246 / 0.12 ( 2) *********************** 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 114 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: u 1195 MET cc_start: 0.8642 (ttt) cc_final: 0.8238 (ttt) REVERT: u 1216 TRP cc_start: 0.7905 (t-100) cc_final: 0.7325 (t-100) REVERT: u 1266 TRP cc_start: 0.8415 (m100) cc_final: 0.7628 (t-100) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.0929 time to fit residues: 17.2793 Evaluate side-chains 100 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 206 optimal weight: 7.9990 chunk 240 optimal weight: 10.0000 chunk 179 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 250 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 199 optimal weight: 20.0000 chunk 243 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** y 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 35 GLN ** x 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 46 HIS u1194 HIS u1252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.093207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.076734 restraints weight = 69000.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.075397 restraints weight = 117548.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.075872 restraints weight = 105430.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.075907 restraints weight = 70362.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.075965 restraints weight = 67368.139| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15236 Z= 0.227 Angle : 0.649 9.333 21331 Z= 0.334 Chirality : 0.049 0.235 2655 Planarity : 0.005 0.057 2844 Dihedral : 8.030 80.441 3174 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.08 % Favored : 87.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.18), residues: 2509 helix: 0.82 (0.19), residues: 852 sheet: -1.98 (0.24), residues: 431 loop : -2.64 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG u1245 TYR 0.024 0.002 TYR v1095 PHE 0.024 0.002 PHE v1182 TRP 0.012 0.002 TRP v 862 HIS 0.009 0.002 HIS x 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.23 (15234) covalent geometry : angle 0.64878 / 0.33 (21331) hydrogen bonds : bond 0.03299 / 2.42 ( 845) hydrogen bonds : angle 5.37448 / 3.77 ( 2320) metal coordination : bond 0.00515 / 0.27 ( 2) *********************** 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 107 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: u 1195 MET cc_start: 0.8733 (ttt) cc_final: 0.8273 (ttt) REVERT: u 1216 TRP cc_start: 0.7891 (t-100) cc_final: 0.7276 (t-100) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.0806 time to fit residues: 14.9423 Evaluate side-chains 95 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 94 optimal weight: 0.0070 chunk 193 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 181 optimal weight: 9.9990 chunk 9 optimal weight: 40.0000 chunk 146 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 chunk 90 optimal weight: 50.0000 chunk 234 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 overall best weight: 3.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... y 50 ASN x 35 GLN ** x 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.093587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.077069 restraints weight = 68915.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.075999 restraints weight = 104689.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.076297 restraints weight = 99126.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.076385 restraints weight = 70526.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.076462 restraints weight = 64161.254| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15236 Z= 0.190 Angle : 0.617 8.617 21331 Z= 0.315 Chirality : 0.049 0.220 2655 Planarity : 0.005 0.047 2844 Dihedral : 8.027 79.410 3174 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.08 % Favored : 89.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.18), residues: 2509 helix: 0.91 (0.19), residues: 847 sheet: -2.01 (0.24), residues: 427 loop : -2.59 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG u1245 TYR 0.025 0.002 TYR v1095 PHE 0.021 0.002 PHE v1182 TRP 0.011 0.002 TRP x 31 HIS 0.006 0.002 HIS x 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 (15234) covalent geometry : angle 0.61678 / 0.32 (21331) hydrogen bonds : bond 0.03072 / 2.26 ( 845) hydrogen bonds : angle 5.22417 / 3.66 ( 2320) metal coordination : bond 0.00514 / 0.27 ( 2) *********************** 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 105 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: u 1195 MET cc_start: 0.8829 (ttt) cc_final: 0.8405 (ttt) REVERT: u 1216 TRP cc_start: 0.7948 (t-100) cc_final: 0.7360 (t-100) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.0859 time to fit residues: 15.1547 Evaluate side-chains 96 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 244 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 98 optimal weight: 50.0000 chunk 112 optimal weight: 0.8980 chunk 222 optimal weight: 7.9990 chunk 30 optimal weight: 30.0000 chunk 145 optimal weight: 10.0000 chunk 87 optimal weight: 50.0000 chunk 168 optimal weight: 20.0000 chunk 206 optimal weight: 0.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... y 50 ASN ** x 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 46 HIS u1194 HIS u1218 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.093681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.077407 restraints weight = 68796.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.076214 restraints weight = 104269.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.076534 restraints weight = 101108.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.076593 restraints weight = 69967.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.076669 restraints weight = 66247.420| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15236 Z= 0.172 Angle : 0.602 8.555 21331 Z= 0.305 Chirality : 0.048 0.193 2655 Planarity : 0.005 0.058 2844 Dihedral : 7.902 77.873 3174 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.76 % Favored : 88.16 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.08 % Twisted Proline : 0.85 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.18), residues: 2509 helix: 1.05 (0.19), residues: 848 sheet: -1.84 (0.25), residues: 411 loop : -2.55 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG u1245 TYR 0.023 0.002 TYR v1095 PHE 0.023 0.002 PHE v1182 TRP 0.010 0.002 TRP x 31 HIS 0.006 0.001 HIS x 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (15234) covalent geometry : angle 0.60152 / 0.31 (21331) hydrogen bonds : bond 0.03014 / 2.22 ( 845) hydrogen bonds : angle 5.09436 / 3.57 ( 2320) metal coordination : bond 0.00415 / 0.21 ( 2) ********************** 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 103 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: x 72 MET cc_start: 0.8387 (tpp) cc_final: 0.8179 (mmt) REVERT: u 1195 MET cc_start: 0.8932 (ttt) cc_final: 0.8491 (ttt) REVERT: u 1216 TRP cc_start: 0.8029 (t-100) cc_final: 0.7407 (t-100) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0836 time to fit residues: 14.7019 Evaluate side-chains 98 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 193 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 29 optimal weight: 0.2980 chunk 108 optimal weight: 40.0000 chunk 68 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 241 optimal weight: 0.0470 chunk 97 optimal weight: 50.0000 chunk 61 optimal weight: 0.6980 chunk 138 optimal weight: 0.0050 chunk 83 optimal weight: 50.0000 overall best weight: 0.4092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... y 50 ASN u1186 GLN u1218 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.096694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.079492 restraints weight = 68193.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.078395 restraints weight = 101660.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.078874 restraints weight = 83332.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.078968 restraints weight = 61514.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.079034 restraints weight = 55687.548| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15236 Z= 0.089 Angle : 0.538 6.796 21331 Z= 0.266 Chirality : 0.046 0.182 2655 Planarity : 0.004 0.053 2844 Dihedral : 7.386 74.389 3174 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.50 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.08 % Twisted Proline : 0.85 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.18), residues: 2509 helix: 1.53 (0.19), residues: 855 sheet: -1.73 (0.25), residues: 438 loop : -2.20 (0.19), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG u1245 TYR 0.018 0.001 TYR u1200 PHE 0.010 0.001 PHE v 234 TRP 0.023 0.002 TRP x 29 HIS 0.003 0.001 HIS u1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.09 (15234) covalent geometry : angle 0.53837 / 0.27 (21331) hydrogen bonds : bond 0.02491 / 1.85 ( 845) hydrogen bonds : angle 4.37622 / 3.05 ( 2320) metal coordination : bond 0.00053 / 0.03 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1773.62 seconds wall clock time: 31 minutes 10.86 seconds (1870.86 seconds total)