Starting phenix.real_space_refine on Sun Sep 13 03:56:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7onb_12994/09_2026/7onb_12994.cif Found real_map, /net/cci-nas-00/data/ceres_data/7onb_12994/09_2026/7onb_12994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7onb_12994/09_2026/7onb_12994.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7onb_12994/09_2026/7onb_12994.cif" model { file = "/net/cci-nas-00/data/ceres_data/7onb_12994/09_2026/7onb_12994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7onb_12994/09_2026/7onb_12994.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7onb_12994/09_2026/7onb_12994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7onb_12994/09_2026/7onb_12994.map" } resolution = 3.1 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= 0.001 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 5 6.06 5 P 46 5.49 5 S 97 5.16 5 C 12589 2.51 5 N 3525 2.21 5 O 3878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 20140 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 8494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 8494 Classifications: {'peptide': 1190} Incomplete info: {'truncation_to_alanine': 261} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1129} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 880 Unresolved non-hydrogen angles: 1134 Unresolved non-hydrogen dihedrals: 702 Unresolved non-hydrogen chiralities: 103 Planarities with less than four sites: {'GLU:plan': 24, 'ASN:plan1': 11, 'TRP:plan': 3, 'ARG:plan': 18, 'HIS:plan': 3, 'ASP:plan': 15, 'PHE:plan': 10, 'TYR:plan': 8, 'GLN:plan1': 13} Unresolved non-hydrogen planarities: 474 Chain: "B" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "C" Number of atoms: 6493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6493 Classifications: {'peptide': 816} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 781} Chain breaks: 1 Chain: "D" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 613 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "G" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 297 Classifications: {'RNAv2': 14} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "H" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 668 Classifications: {'RNAv2': 32} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 18} Link IDs: {'rna2p': 4, 'rna3p': 27} Chain: "I" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1323 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 22, 'TRANS': 158} Chain breaks: 3 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 76 Chain: "M" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 378 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "N" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 804 Classifications: {'peptide': 97} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 340 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 4, 'GLU:plan': 6, 'TRP:plan': 1, 'PHE:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 114 Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 40 Unusual residues: {' ZN': 3, 'SJT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15560 SG CYS D 11 72.147 45.512 62.276 1.00 81.38 S ATOM 15823 SG CYS D 46 73.158 47.668 59.250 1.00 86.33 S ATOM 15846 SG CYS D 49 71.703 44.785 58.540 1.00 98.99 S ATOM 16117 SG CYS D 85 69.496 47.521 60.303 1.00 76.95 S ATOM 15698 SG CYS D 30 55.686 48.508 63.101 1.00 93.84 S ATOM 15719 SG CYS D 33 53.337 47.141 65.798 1.00 90.47 S ATOM 16014 SG CYS D 72 52.944 50.566 64.911 1.00 84.61 S ATOM 16038 SG CYS D 75 56.100 49.712 66.669 1.00 80.84 S ATOM 15647 SG CYS D 23 58.309 39.887 51.618 1.00106.09 S ATOM 15918 SG CYS D 58 60.950 41.719 53.456 1.00109.30 S ATOM 15939 SG CYS D 61 61.629 38.313 52.555 1.00114.85 S ATOM 18711 SG CYS M 56 32.399 19.532 93.393 1.00166.32 S ATOM 18734 SG CYS M 59 35.306 18.104 95.517 1.00166.67 S ATOM 19146 SG CYS N 408 54.299 37.442 120.301 1.00140.04 S ATOM 19169 SG CYS N 411 50.600 36.312 121.107 1.00146.60 S Time building chain proxies: 4.38, per 1000 atoms: 0.22 Number of scatterers: 20140 At special positions: 0 Unit cell: (120.75, 140.7, 136.5, 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 5 29.99 S 97 16.00 P 46 15.00 O 3878 8.00 N 3525 7.00 C 12589 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 884.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 46 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 49 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 11 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 85 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 33 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 30 " pdb=" ZN D1404 " pdb="ZN ZN D1404 " - pdb=" SG CYS D 23 " pdb="ZN ZN D1404 " - pdb=" SG CYS D 58 " pdb="ZN ZN D1404 " - pdb=" SG CYS D 61 " pdb=" ZN M 501 " pdb="ZN ZN M 501 " - pdb=" NE2 HIS M 72 " pdb="ZN ZN M 501 " - pdb=" ND1 HIS M 78 " pdb="ZN ZN M 501 " - pdb=" SG CYS M 59 " pdb="ZN ZN M 501 " - pdb=" SG CYS M 56 " pdb=" ZN N 601 " pdb="ZN ZN N 601 " - pdb=" NE2 HIS N 425 " pdb="ZN ZN N 601 " - pdb=" ND1 HIS N 431 " pdb="ZN ZN N 601 " - pdb=" SG CYS N 408 " pdb="ZN ZN N 601 " - pdb=" SG CYS N 411 " Number of angles added : 14 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4804 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 29 sheets defined 42.9% alpha, 17.9% beta 12 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.710A pdb=" N ASN A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.781A pdb=" N ALA A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 432 Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.790A pdb=" N CYS A 624 " --> pdb=" O PRO A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 828 removed outlier: 3.706A pdb=" N GLU A 825 " --> pdb=" O GLU A 821 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY A 828 " --> pdb=" O VAL A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 845 removed outlier: 3.898A pdb=" N GLU A 845 " --> pdb=" O ALA A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 853 Processing helix chain 'A' and resid 930 through 935 removed outlier: 3.964A pdb=" N GLY A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1151 removed outlier: 3.667A pdb=" N SER A1150 " --> pdb=" O MET A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1164 Processing helix chain 'A' and resid 1176 through 1180 Processing helix chain 'A' and resid 1186 through 1195 Processing helix chain 'A' and resid 1200 through 1214 removed outlier: 3.564A pdb=" N ARG A1212 " --> pdb=" O LEU A1208 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 46 Processing helix chain 'B' and resid 46 through 57 Processing helix chain 'B' and resid 60 through 72 Processing helix chain 'C' and resid 489 through 507 Processing helix chain 'C' and resid 511 through 522 Processing helix chain 'C' and resid 522 through 527 Processing helix chain 'C' and resid 527 through 540 removed outlier: 3.700A pdb=" N LEU C 531 " --> pdb=" O GLY C 527 " (cutoff:3.500A) Proline residue: C 537 - end of helix Processing helix chain 'C' and resid 545 through 563 removed outlier: 3.533A pdb=" N LYS C 562 " --> pdb=" O ARG C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 569 Proline residue: C 569 - end of helix Processing helix chain 'C' and resid 570 through 579 Processing helix chain 'C' and resid 580 through 584 removed outlier: 3.554A pdb=" N ILE C 583 " --> pdb=" O PRO C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 605 Processing helix chain 'C' and resid 605 through 614 Processing helix chain 'C' and resid 615 through 617 No H-bonds generated for 'chain 'C' and resid 615 through 617' Processing helix chain 'C' and resid 621 through 640 removed outlier: 3.597A pdb=" N ARG C 625 " --> pdb=" O ASP C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 653 removed outlier: 3.756A pdb=" N LEU C 644 " --> pdb=" O GLY C 640 " (cutoff:3.500A) Proline residue: C 646 - end of helix removed outlier: 3.815A pdb=" N LYS C 653 " --> pdb=" O LYS C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 676 removed outlier: 3.922A pdb=" N ARG C 661 " --> pdb=" O SER C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 681 Proline residue: C 681 - end of helix Processing helix chain 'C' and resid 682 through 691 Processing helix chain 'C' and resid 692 through 696 Processing helix chain 'C' and resid 698 through 717 Processing helix chain 'C' and resid 721 through 726 removed outlier: 5.079A pdb=" N SER C 726 " --> pdb=" O SER C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 735 removed outlier: 3.674A pdb=" N LEU C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 754 removed outlier: 3.674A pdb=" N LEU C 743 " --> pdb=" O ARG C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 777 removed outlier: 4.665A pdb=" N LEU C 771 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE C 772 " --> pdb=" O GLU C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 797 Processing helix chain 'C' and resid 802 through 810 Processing helix chain 'C' and resid 810 through 819 removed outlier: 3.721A pdb=" N TRP C 819 " --> pdb=" O PHE C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 825 removed outlier: 3.598A pdb=" N LEU C 825 " --> pdb=" O ARG C 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 822 through 825' Processing helix chain 'C' and resid 826 through 845 Processing helix chain 'C' and resid 845 through 851 removed outlier: 3.680A pdb=" N ILE C 849 " --> pdb=" O GLY C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 853 No H-bonds generated for 'chain 'C' and resid 852 through 853' Processing helix chain 'C' and resid 854 through 859 Processing helix chain 'C' and resid 861 through 880 Processing helix chain 'C' and resid 885 through 902 Processing helix chain 'C' and resid 907 through 922 removed outlier: 3.596A pdb=" N LEU C 911 " --> pdb=" O ASP C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 927 removed outlier: 3.517A pdb=" N LYS C 926 " --> pdb=" O LYS C 923 " (cutoff:3.500A) Proline residue: C 927 - end of helix No H-bonds generated for 'chain 'C' and resid 923 through 927' Processing helix chain 'C' and resid 928 through 941 Processing helix chain 'C' and resid 944 through 965 removed outlier: 3.576A pdb=" N ARG C 948 " --> pdb=" O SER C 944 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL C 960 " --> pdb=" O SER C 956 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL C 961 " --> pdb=" O ARG C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 981 Processing helix chain 'C' and resid 986 through 1005 Processing helix chain 'C' and resid 1012 through 1021 Proline residue: C1018 - end of helix Processing helix chain 'C' and resid 1022 through 1026 removed outlier: 3.697A pdb=" N LYS C1025 " --> pdb=" O PRO C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1046 Processing helix chain 'C' and resid 1047 through 1050 Processing helix chain 'C' and resid 1051 through 1063 Processing helix chain 'C' and resid 1064 through 1068 removed outlier: 3.672A pdb=" N LYS C1067 " --> pdb=" O GLU C1064 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C1068 " --> pdb=" O LEU C1065 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1064 through 1068' Processing helix chain 'C' and resid 1070 through 1088 Processing helix chain 'C' and resid 1089 through 1105 removed outlier: 4.553A pdb=" N VAL C1093 " --> pdb=" O GLY C1089 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1107 through 1123 removed outlier: 4.045A pdb=" N CYS C1111 " --> pdb=" O GLN C1107 " (cutoff:3.500A) Processing helix chain 'C' and resid 1124 through 1127 Processing helix chain 'C' and resid 1128 through 1135 Processing helix chain 'C' and resid 1136 through 1138 No H-bonds generated for 'chain 'C' and resid 1136 through 1138' Processing helix chain 'C' and resid 1141 through 1159 Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.920A pdb=" N ASP C1164 " --> pdb=" O MET C1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1178 Proline residue: C1171 - end of helix Processing helix chain 'C' and resid 1181 through 1199 removed outlier: 3.504A pdb=" N ARG C1185 " --> pdb=" O ASP C1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 1204 through 1216 removed outlier: 3.631A pdb=" N TYR C1214 " --> pdb=" O HIS C1210 " (cutoff:3.500A) Processing helix chain 'C' and resid 1217 through 1221 removed outlier: 4.116A pdb=" N PHE C1220 " --> pdb=" O PRO C1217 " (cutoff:3.500A) Processing helix chain 'C' and resid 1223 through 1242 Processing helix chain 'C' and resid 1242 through 1251 removed outlier: 3.665A pdb=" N MET C1246 " --> pdb=" O GLY C1242 " (cutoff:3.500A) Processing helix chain 'C' and resid 1252 through 1256 removed outlier: 4.147A pdb=" N PHE C1255 " --> pdb=" O GLN C1252 " (cutoff:3.500A) Processing helix chain 'C' and resid 1258 through 1276 Processing helix chain 'C' and resid 1278 through 1283 removed outlier: 3.639A pdb=" N ILE C1281 " --> pdb=" O ASP C1278 " (cutoff:3.500A) Processing helix chain 'C' and resid 1298 through 1302 Processing helix chain 'D' and resid 47 through 55 removed outlier: 7.058A pdb=" N GLY D 52 " --> pdb=" O CYS D 49 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N SER D 53 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN D 55 " --> pdb=" O GLY D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 78 Processing helix chain 'F' and resid 164 through 180 Processing helix chain 'I' and resid 461 through 469 Processing helix chain 'I' and resid 477 through 482 removed outlier: 4.153A pdb=" N VAL I 480 " --> pdb=" O MET I 477 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA I 482 " --> pdb=" O ASP I 479 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 493 Processing helix chain 'I' and resid 501 through 505 removed outlier: 3.594A pdb=" N TRP I 504 " --> pdb=" O PRO I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 525 through 530 Processing helix chain 'I' and resid 567 through 577 removed outlier: 3.545A pdb=" N LEU I 571 " --> pdb=" O ASP I 567 " (cutoff:3.500A) Processing helix chain 'I' and resid 610 through 617 Processing helix chain 'I' and resid 631 through 639 removed outlier: 3.962A pdb=" N ALA I 635 " --> pdb=" O PRO I 631 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 74 removed outlier: 3.528A pdb=" N TYR M 69 " --> pdb=" O ASN M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 87 removed outlier: 3.503A pdb=" N GLN M 79 " --> pdb=" O GLY M 75 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA M 87 " --> pdb=" O ALA M 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 393 through 401 removed outlier: 3.639A pdb=" N GLY N 401 " --> pdb=" O TYR N 397 " (cutoff:3.500A) Processing helix chain 'N' and resid 418 through 425 Processing helix chain 'N' and resid 428 through 438 Processing helix chain 'N' and resid 443 through 447 removed outlier: 3.512A pdb=" N PHE N 446 " --> pdb=" O THR N 443 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA N 447 " --> pdb=" O ALA N 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 443 through 447' Processing helix chain 'N' and resid 451 through 470 Processing helix chain 'K' and resid 25 through 33 Processing helix chain 'K' and resid 63 through 74 Processing sheet with id=AA1, first strand: chain 'A' and resid 1101 through 1107 removed outlier: 3.653A pdb=" N SER A1103 " --> pdb=" O THR A1120 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A1126 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.796A pdb=" N PHE A 16 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 38 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR A 55 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A 40 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 68 removed outlier: 4.081A pdb=" N SER A 82 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU A 91 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LYS A 101 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLN A 93 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N PHE A 99 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 123 Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 123 Processing sheet with id=AA6, first strand: chain 'A' and resid 166 through 173 removed outlier: 5.637A pdb=" N VAL A 167 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N MET A 187 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N HIS A 169 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N MET A 181 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 208 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER A 225 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE A 210 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 219 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 232 through 237 removed outlier: 3.802A pdb=" N PHE A 234 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR A 255 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 273 through 274 removed outlier: 6.828A pdb=" N ARG A 273 " --> pdb=" O PHE A 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 289 through 293 removed outlier: 3.841A pdb=" N CYS A 289 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE A 310 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 336 through 341 removed outlier: 3.550A pdb=" N ALA A 338 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N HIS A 356 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU A 400 " --> pdb=" O HIS A 356 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 358 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 407 through 413 removed outlier: 3.894A pdb=" N PHE A 409 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 735 removed outlier: 7.419A pdb=" N LEU A 442 " --> pdb=" O SER A 735 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 764 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL A 449 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU A 762 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 761 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 486 through 487 Processing sheet with id=AB5, first strand: chain 'A' and resid 515 through 519 removed outlier: 3.697A pdb=" N ILE A 524 " --> pdb=" O TRP A 536 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 546 through 549 Processing sheet with id=AB7, first strand: chain 'A' and resid 587 through 592 removed outlier: 4.207A pdb=" N THR A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 637 through 643 removed outlier: 5.265A pdb=" N VAL A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 700 through 706 removed outlier: 3.808A pdb=" N MET A 715 " --> pdb=" O LYS A 700 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N GLU A 710 " --> pdb=" O SER A 724 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N SER A 724 " --> pdb=" O GLU A 710 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A 712 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 732 " --> pdb=" O LEU A 721 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 785 through 790 removed outlier: 6.207A pdb=" N THR A 802 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A 787 " --> pdb=" O ILE A 800 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 886 through 894 removed outlier: 5.370A pdb=" N ALA A 888 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA A 910 " --> pdb=" O ALA A 888 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS A 941 " --> pdb=" O THR A 927 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 953 through 955 removed outlier: 6.537A pdb=" N ASP A 971 " --> pdb=" O ARG A 979 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ARG A 979 " --> pdb=" O ASP A 971 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 990 through 996 removed outlier: 3.597A pdb=" N GLY A 992 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE A1009 " --> pdb=" O ASP A1026 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP A1026 " --> pdb=" O PHE A1009 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TRP A1011 " --> pdb=" O PHE A1024 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN A1020 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 10.435A pdb=" N GLN A1087 " --> pdb=" O ILE A1022 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE A1024 " --> pdb=" O GLN A1087 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ALA A1089 " --> pdb=" O PHE A1024 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP A1026 " --> pdb=" O ALA A1089 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL A1091 " --> pdb=" O ASP A1026 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A1055 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN A1094 " --> pdb=" O ILE A1053 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE A1053 " --> pdb=" O ASN A1094 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 18 through 19 removed outlier: 4.250A pdb=" N ALA D 18 " --> pdb=" O ILE D 45 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 21 through 22 Processing sheet with id=AC7, first strand: chain 'D' and resid 39 through 42 removed outlier: 6.406A pdb=" N TYR D 71 " --> pdb=" O CYS D 40 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 46 through 48 Processing sheet with id=AC9, first strand: chain 'N' and resid 405 through 408 Processing sheet with id=AD1, first strand: chain 'K' and resid 39 through 43 Processing sheet with id=AD2, first strand: chain 'K' and resid 78 through 79 960 hydrogen bonds defined for protein. 2676 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 4.25 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3345 1.32 - 1.44: 5459 1.44 - 1.56: 11587 1.56 - 1.69: 90 1.69 - 1.81: 147 Bond restraints: 20628 Sorted by residual: bond pdb=" CB GLU C 873 " pdb=" CG GLU C 873 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.34e+00 bond pdb=" C ILE C 641 " pdb=" N PRO C 642 " ideal model delta sigma weight residual 1.335 1.367 -0.032 1.28e-02 6.10e+03 6.24e+00 bond pdb=" C ARG C 614 " pdb=" N PRO C 615 " ideal model delta sigma weight residual 1.335 1.362 -0.028 1.19e-02 7.06e+03 5.42e+00 bond pdb=" C LYS C 729 " pdb=" N PRO C 730 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.22e+00 bond pdb=" CB VAL C 989 " pdb=" CG1 VAL C 989 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.12e+00 ... (remaining 20623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 27992 3.89 - 7.78: 213 7.78 - 11.67: 27 11.67 - 15.55: 4 15.55 - 19.44: 1 Bond angle restraints: 28237 Sorted by residual: angle pdb=" C3' U G 131 " pdb=" O3' U G 131 " pdb=" P G G 132 " ideal model delta sigma weight residual 119.70 127.70 -8.00 1.20e+00 6.94e-01 4.45e+01 angle pdb=" CA LEU C 539 " pdb=" CB LEU C 539 " pdb=" CG LEU C 539 " ideal model delta sigma weight residual 116.30 135.74 -19.44 3.50e+00 8.16e-02 3.09e+01 angle pdb=" CA VAL C 936 " pdb=" CB VAL C 936 " pdb=" CG2 VAL C 936 " ideal model delta sigma weight residual 110.40 118.51 -8.11 1.70e+00 3.46e-01 2.28e+01 angle pdb=" N GLU C 579 " pdb=" CA GLU C 579 " pdb=" C GLU C 579 " ideal model delta sigma weight residual 109.81 119.55 -9.74 2.21e+00 2.05e-01 1.94e+01 angle pdb=" C LEU C 563 " pdb=" N ASP C 564 " pdb=" CA ASP C 564 " ideal model delta sigma weight residual 121.54 113.19 8.35 1.91e+00 2.74e-01 1.91e+01 ... (remaining 28232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.40: 12099 34.40 - 68.80: 249 68.80 - 103.21: 22 103.21 - 137.61: 0 137.61 - 172.01: 2 Dihedral angle restraints: 12372 sinusoidal: 4930 harmonic: 7442 Sorted by residual: dihedral pdb=" C4' A H 35 " pdb=" C3' A H 35 " pdb=" C2' A H 35 " pdb=" C1' A H 35 " ideal model delta sinusoidal sigma weight residual 36.34 -37.28 73.63 1 3.10e+00 1.04e-01 7.17e+02 dihedral pdb=" C4' U G 142 " pdb=" C3' U G 142 " pdb=" C2' U G 142 " pdb=" C1' U G 142 " ideal model delta sinusoidal sigma weight residual 36.34 -35.83 72.18 1 3.10e+00 1.04e-01 6.93e+02 dihedral pdb=" C4' A H 48 " pdb=" C3' A H 48 " pdb=" C2' A H 48 " pdb=" C1' A H 48 " ideal model delta sinusoidal sigma weight residual 36.34 -35.83 72.18 1 3.10e+00 1.04e-01 6.93e+02 ... (remaining 12369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 3044 0.125 - 0.249: 174 0.249 - 0.374: 20 0.374 - 0.499: 7 0.499 - 0.624: 1 Chirality restraints: 3246 Sorted by residual: chirality pdb=" CB VAL C 936 " pdb=" CA VAL C 936 " pdb=" CG1 VAL C 936 " pdb=" CG2 VAL C 936 " both_signs ideal model delta sigma weight residual False -2.63 -2.01 -0.62 2.00e-01 2.50e+01 9.72e+00 chirality pdb=" CB VAL C 925 " pdb=" CA VAL C 925 " pdb=" CG1 VAL C 925 " pdb=" CG2 VAL C 925 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.47 2.00e-01 2.50e+01 5.53e+00 chirality pdb=" P U H 34 " pdb=" OP1 U H 34 " pdb=" OP2 U H 34 " pdb=" O5' U H 34 " both_signs ideal model delta sigma weight residual True 2.17 -2.64 -0.47 2.00e-01 2.50e+01 5.50e+00 ... (remaining 3243 not shown) Planarity restraints: 3531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS C1225 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C HIS C1225 " -0.066 2.00e-02 2.50e+03 pdb=" O HIS C1225 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL C1226 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C1089 " 0.052 5.00e-02 4.00e+02 7.77e-02 9.67e+00 pdb=" N PRO C1090 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO C1090 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C1090 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 574 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.03e+00 pdb=" C ILE C 574 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE C 574 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU C 575 " -0.017 2.00e-02 2.50e+03 ... (remaining 3528 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4987 2.80 - 3.32: 18085 3.32 - 3.85: 35363 3.85 - 4.37: 39407 4.37 - 4.90: 66893 Nonbonded interactions: 164735 Sorted by model distance: nonbonded pdb=" OH TYR A 329 " pdb=" OG1 THR A 332 " model vdw 2.273 3.040 nonbonded pdb=" OE2 GLU A 136 " pdb=" OH TYR A 189 " model vdw 2.286 3.040 nonbonded pdb=" O VAL C 701 " pdb=" OG SER C 705 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASN C1213 " pdb=" OH TYR C1249 " model vdw 2.304 3.040 nonbonded pdb=" O2' U H 39 " pdb=" O LEU M 62 " model vdw 2.304 3.040 ... (remaining 164730 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.470 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.730 Find NCS groups from input model: 0.090 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 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 : 0.005 0.076 20648 Z= 0.234 Angle : 0.932 19.442 28251 Z= 0.483 Chirality : 0.070 0.624 3246 Planarity : 0.007 0.099 3531 Dihedral : 14.242 172.012 7568 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % 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: -1.28 (0.16), residues: 2534 helix: -0.44 (0.16), residues: 936 sheet: -0.67 (0.23), residues: 491 loop : -1.16 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 625 TYR 0.023 0.002 TYR C 587 PHE 0.022 0.002 PHE C1126 TRP 0.032 0.002 TRP C 732 HIS 0.016 0.001 HIS C1007 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.23 (20628) covalent geometry : angle 0.92231 / 0.48 (28237) hydrogen bonds : bond 0.13616 / 8.94 ( 979) hydrogen bonds : angle 6.29121 / 4.31 ( 2726) metal coordination : bond 0.01203 / 0.75 ( 19) metal coordination : angle 6.13559 / 3.21 ( 14) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 823 MET cc_start: 0.8282 (ppp) cc_final: 0.7687 (ppp) REVERT: A 931 VAL cc_start: 0.6766 (m) cc_final: 0.5606 (t) REVERT: A 1063 ASN cc_start: 0.7276 (t0) cc_final: 0.6300 (p0) REVERT: C 747 LEU cc_start: 0.7980 (pp) cc_final: 0.7392 (mt) REVERT: C 822 ARG cc_start: 0.7782 (tmt-80) cc_final: 0.7358 (ptm160) REVERT: C 910 MET cc_start: 0.8179 (mmt) cc_final: 0.7967 (mmt) REVERT: C 932 ILE cc_start: 0.7825 (mt) cc_final: 0.7592 (mm) REVERT: C 993 ILE cc_start: 0.8935 (mt) cc_final: 0.8641 (mm) REVERT: C 1056 MET cc_start: 0.8472 (mtp) cc_final: 0.8206 (ptp) REVERT: C 1060 PHE cc_start: 0.7856 (m-10) cc_final: 0.7547 (m-10) REVERT: F 165 ARG cc_start: 0.7544 (ttm110) cc_final: 0.7169 (ttm110) REVERT: I 476 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7153 (mm-30) REVERT: I 517 ILE cc_start: 0.7941 (mm) cc_final: 0.7459 (mm) REVERT: I 569 GLN cc_start: 0.8546 (tp-100) cc_final: 0.7624 (tp-100) REVERT: M 48 LYS cc_start: 0.7075 (mttm) cc_final: 0.6655 (ttpt) REVERT: M 54 TYR cc_start: 0.6253 (m-80) cc_final: 0.5925 (m-80) REVERT: M 62 LEU cc_start: 0.8086 (mm) cc_final: 0.7857 (mm) REVERT: M 84 ARG cc_start: 0.6520 (ttm110) cc_final: 0.5898 (mmt180) REVERT: N 387 TRP cc_start: 0.6258 (m100) cc_final: 0.5814 (m100) REVERT: N 391 PRO cc_start: 0.6834 (Cg_exo) cc_final: 0.6552 (Cg_endo) REVERT: N 404 ILE cc_start: 0.7336 (mm) cc_final: 0.7093 (mm) REVERT: N 420 LYS cc_start: 0.8329 (tttp) cc_final: 0.7831 (mmtt) REVERT: N 474 ASP cc_start: 0.7468 (t70) cc_final: 0.6978 (p0) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1666 time to fit residues: 85.1379 Evaluate side-chains 186 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 804 HIS ** C1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 ASN D 50 ASN N 423 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.100504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.074523 restraints weight = 58318.310| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.64 r_work: 0.3410 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20648 Z= 0.161 Angle : 0.729 15.222 28251 Z= 0.340 Chirality : 0.056 0.738 3246 Planarity : 0.005 0.058 3531 Dihedral : 9.219 158.517 3359 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.51 % Allowed : 8.27 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % 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: -0.50 (0.16), residues: 2534 helix: 0.51 (0.17), residues: 942 sheet: -0.49 (0.24), residues: 488 loop : -0.89 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1185 TYR 0.020 0.001 TYR C 830 PHE 0.019 0.002 PHE C1126 TRP 0.016 0.001 TRP C1216 HIS 0.006 0.001 HIS A 804 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (20628) covalent geometry : angle 0.72581 / 0.34 (28237) hydrogen bonds : bond 0.04180 / 2.69 ( 979) hydrogen bonds : angle 4.99859 / 3.44 ( 2726) metal coordination : bond 0.00750 / 0.36 ( 19) metal coordination : angle 3.31500 / 1.77 ( 14) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 832 ARG cc_start: 0.5711 (OUTLIER) cc_final: 0.5511 (mmp80) REVERT: A 1063 ASN cc_start: 0.7718 (t0) cc_final: 0.6612 (p0) REVERT: C 822 ARG cc_start: 0.7848 (tmt-80) cc_final: 0.7495 (ptm160) REVERT: C 902 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7273 (mp0) REVERT: C 910 MET cc_start: 0.8302 (mmt) cc_final: 0.8034 (mmt) REVERT: C 932 ILE cc_start: 0.7999 (mt) cc_final: 0.7699 (mm) REVERT: D 54 TYR cc_start: 0.7187 (m-80) cc_final: 0.6937 (m-80) REVERT: F 165 ARG cc_start: 0.7709 (ttm110) cc_final: 0.7179 (ttm-80) REVERT: I 476 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7522 (mm-30) REVERT: I 569 GLN cc_start: 0.8203 (tp-100) cc_final: 0.7992 (tp-100) REVERT: I 578 TRP cc_start: 0.8506 (m100) cc_final: 0.7572 (m-90) REVERT: M 47 MET cc_start: 0.7519 (ptm) cc_final: 0.7284 (ptm) REVERT: M 48 LYS cc_start: 0.7158 (mttm) cc_final: 0.6731 (ttpt) REVERT: M 54 TYR cc_start: 0.6369 (m-80) cc_final: 0.6040 (m-80) REVERT: M 84 ARG cc_start: 0.6415 (ttm110) cc_final: 0.5780 (mmt180) REVERT: N 387 TRP cc_start: 0.7055 (m100) cc_final: 0.6762 (m100) REVERT: N 391 PRO cc_start: 0.6637 (Cg_exo) cc_final: 0.6389 (Cg_endo) REVERT: N 420 LYS cc_start: 0.8583 (tttp) cc_final: 0.8052 (mmtt) outliers start: 28 outliers final: 15 residues processed: 214 average time/residue: 0.1460 time to fit residues: 49.6688 Evaluate side-chains 176 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 832 ARG Chi-restraints excluded: chain A residue 842 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain C residue 677 CYS Chi-restraints excluded: chain C residue 752 TYR Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1274 ILE Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 480 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 93 optimal weight: 0.7980 chunk 150 optimal weight: 0.6980 chunk 178 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 163 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 254 optimal weight: 50.0000 chunk 235 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 572 HIS C1145 ASN C1209 ASN D 50 ASN N 442 ASN N 448 ASN N 451 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.100477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.074897 restraints weight = 58071.558| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.60 r_work: 0.3402 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20648 Z= 0.132 Angle : 0.633 13.027 28251 Z= 0.302 Chirality : 0.051 0.750 3246 Planarity : 0.004 0.058 3531 Dihedral : 9.154 170.495 3359 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.68 % Allowed : 10.76 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % 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: -0.19 (0.17), residues: 2534 helix: 0.81 (0.17), residues: 947 sheet: -0.43 (0.24), residues: 476 loop : -0.71 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 767 TYR 0.021 0.001 TYR D 36 PHE 0.018 0.001 PHE C1126 TRP 0.009 0.001 TRP N 471 HIS 0.004 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (20628) covalent geometry : angle 0.62902 / 0.30 (28237) hydrogen bonds : bond 0.03566 / 2.32 ( 979) hydrogen bonds : angle 4.63547 / 3.19 ( 2726) metal coordination : bond 0.00418 / 0.26 ( 19) metal coordination : angle 3.19795 / 1.88 ( 14) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 ASN cc_start: 0.8006 (m-40) cc_final: 0.6692 (p0) REVERT: A 823 MET cc_start: 0.8456 (ppp) cc_final: 0.7601 (ppp) REVERT: A 832 ARG cc_start: 0.5895 (OUTLIER) cc_final: 0.5593 (mmp80) REVERT: A 1063 ASN cc_start: 0.7752 (t0) cc_final: 0.6675 (p0) REVERT: C 731 LEU cc_start: 0.7463 (mp) cc_final: 0.7181 (mp) REVERT: C 822 ARG cc_start: 0.7782 (tmt-80) cc_final: 0.7443 (ptm160) REVERT: C 823 MET cc_start: 0.7470 (ppp) cc_final: 0.7206 (ppp) REVERT: C 932 ILE cc_start: 0.8027 (mt) cc_final: 0.7792 (mm) REVERT: C 1056 MET cc_start: 0.8220 (ptt) cc_final: 0.7593 (ptm) REVERT: C 1060 PHE cc_start: 0.7357 (m-10) cc_final: 0.7105 (m-10) REVERT: D 54 TYR cc_start: 0.7175 (m-80) cc_final: 0.6667 (m-80) REVERT: I 484 ASP cc_start: 0.8476 (t70) cc_final: 0.7939 (t70) REVERT: I 578 TRP cc_start: 0.8527 (m100) cc_final: 0.7593 (m-90) REVERT: I 592 TYR cc_start: 0.8783 (p90) cc_final: 0.8535 (p90) REVERT: M 47 MET cc_start: 0.7423 (ptm) cc_final: 0.7198 (ptm) REVERT: M 48 LYS cc_start: 0.7163 (mttm) cc_final: 0.6688 (ttpt) REVERT: M 54 TYR cc_start: 0.6185 (m-80) cc_final: 0.5859 (m-80) REVERT: M 55 GLU cc_start: 0.7969 (tt0) cc_final: 0.7616 (tt0) REVERT: M 84 ARG cc_start: 0.6433 (ttm110) cc_final: 0.5784 (mmt180) REVERT: N 387 TRP cc_start: 0.7152 (m100) cc_final: 0.6724 (m100) REVERT: N 391 PRO cc_start: 0.6753 (Cg_exo) cc_final: 0.6486 (Cg_endo) REVERT: N 420 LYS cc_start: 0.8598 (tttp) cc_final: 0.8084 (mmtt) REVERT: N 461 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8269 (ttmt) outliers start: 31 outliers final: 15 residues processed: 194 average time/residue: 0.1511 time to fit residues: 46.4043 Evaluate side-chains 172 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 832 ARG Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1209 ASN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 461 LYS Chi-restraints excluded: chain N residue 480 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 192 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 120 optimal weight: 0.0050 chunk 251 optimal weight: 50.0000 chunk 53 optimal weight: 0.3980 chunk 140 optimal weight: 0.9990 chunk 254 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 GLN C 737 GLN C 950 GLN N 433 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.097534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.071490 restraints weight = 58105.638| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.57 r_work: 0.3337 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 20648 Z= 0.186 Angle : 0.649 10.418 28251 Z= 0.314 Chirality : 0.051 0.892 3246 Planarity : 0.004 0.062 3531 Dihedral : 9.045 177.602 3359 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.78 % Allowed : 11.95 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % 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: -0.12 (0.17), residues: 2534 helix: 0.93 (0.17), residues: 924 sheet: -0.59 (0.24), residues: 476 loop : -0.59 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 165 TYR 0.016 0.002 TYR C 765 PHE 0.019 0.002 PHE C1126 TRP 0.013 0.001 TRP C1216 HIS 0.007 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (20628) covalent geometry : angle 0.64457 / 0.31 (28237) hydrogen bonds : bond 0.03732 / 2.41 ( 979) hydrogen bonds : angle 4.71729 / 3.23 ( 2726) metal coordination : bond 0.01233 / 0.49 ( 19) metal coordination : angle 3.55422 / 1.88 ( 14) Misc. bond : bond 0.00051 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 ASN cc_start: 0.8530 (m-40) cc_final: 0.7293 (p0) REVERT: A 832 ARG cc_start: 0.6192 (OUTLIER) cc_final: 0.5935 (mmp80) REVERT: A 1063 ASN cc_start: 0.8181 (t0) cc_final: 0.6934 (p0) REVERT: C 511 MET cc_start: 0.7332 (ptm) cc_final: 0.6741 (ppp) REVERT: C 822 ARG cc_start: 0.7764 (tmt-80) cc_final: 0.7512 (ptm160) REVERT: C 823 MET cc_start: 0.7666 (ppp) cc_final: 0.7212 (ppp) REVERT: C 902 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: D 54 TYR cc_start: 0.7314 (m-80) cc_final: 0.6960 (m-80) REVERT: I 476 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7940 (mt-10) REVERT: I 484 ASP cc_start: 0.8682 (t70) cc_final: 0.8141 (t70) REVERT: I 578 TRP cc_start: 0.8487 (m100) cc_final: 0.8180 (m-10) REVERT: I 598 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7187 (mt-10) REVERT: M 47 MET cc_start: 0.7437 (ptm) cc_final: 0.7234 (ptm) REVERT: M 48 LYS cc_start: 0.7087 (mttm) cc_final: 0.6609 (ttpt) REVERT: M 54 TYR cc_start: 0.6416 (m-80) cc_final: 0.6082 (m-80) REVERT: M 84 ARG cc_start: 0.6601 (ttm110) cc_final: 0.5780 (mmt180) REVERT: N 420 LYS cc_start: 0.8751 (tttp) cc_final: 0.8305 (mmtt) REVERT: N 428 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8450 (mm-30) REVERT: N 451 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8076 (mt0) outliers start: 33 outliers final: 22 residues processed: 186 average time/residue: 0.1510 time to fit residues: 44.5718 Evaluate side-chains 160 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 832 ARG Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain I residue 517 ILE Chi-restraints excluded: chain N residue 399 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 93 optimal weight: 0.6980 chunk 228 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 161 optimal weight: 0.0870 chunk 150 optimal weight: 3.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 903 GLN I 569 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.098310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.072205 restraints weight = 58107.083| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.59 r_work: 0.3353 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20648 Z= 0.125 Angle : 0.600 11.560 28251 Z= 0.283 Chirality : 0.050 1.034 3246 Planarity : 0.004 0.045 3531 Dihedral : 8.935 173.904 3359 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.73 % Allowed : 12.97 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % 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: 0.02 (0.17), residues: 2534 helix: 1.14 (0.17), residues: 925 sheet: -0.65 (0.24), residues: 478 loop : -0.53 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 165 TYR 0.013 0.001 TYR I 592 PHE 0.017 0.001 PHE C1126 TRP 0.012 0.001 TRP A1032 HIS 0.003 0.001 HIS C1184 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (20628) covalent geometry : angle 0.59643 / 0.28 (28237) hydrogen bonds : bond 0.03326 / 2.19 ( 979) hydrogen bonds : angle 4.55918 / 3.12 ( 2726) metal coordination : bond 0.00762 / 0.31 ( 19) metal coordination : angle 2.84578 / 1.52 ( 14) Misc. bond : bond 0.00049 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1063 ASN cc_start: 0.8163 (t0) cc_final: 0.6972 (p0) REVERT: C 511 MET cc_start: 0.7013 (ptm) cc_final: 0.6694 (ppp) REVERT: C 822 ARG cc_start: 0.7719 (tmt-80) cc_final: 0.7502 (ptm160) REVERT: C 823 MET cc_start: 0.7764 (ppp) cc_final: 0.7216 (ppp) REVERT: C 1178 MET cc_start: 0.8969 (ptt) cc_final: 0.8641 (ptp) REVERT: D 54 TYR cc_start: 0.7204 (m-80) cc_final: 0.6890 (m-80) REVERT: D 88 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7591 (mt) REVERT: I 476 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7955 (mt-10) REVERT: I 484 ASP cc_start: 0.8695 (t70) cc_final: 0.8486 (t70) REVERT: M 48 LYS cc_start: 0.7139 (mttm) cc_final: 0.6643 (ttmt) REVERT: M 54 TYR cc_start: 0.6277 (m-80) cc_final: 0.5832 (m-80) REVERT: M 84 ARG cc_start: 0.6594 (ttm110) cc_final: 0.5772 (mmt180) REVERT: N 420 LYS cc_start: 0.8735 (tttp) cc_final: 0.8299 (mmtt) REVERT: N 428 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8401 (mm-30) outliers start: 32 outliers final: 21 residues processed: 172 average time/residue: 0.1355 time to fit residues: 37.5218 Evaluate side-chains 157 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 677 CYS Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1184 HIS Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 468 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 40 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 235 optimal weight: 0.0270 chunk 158 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 73 optimal weight: 30.0000 chunk 10 optimal weight: 0.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN C 931 GLN ** I 467 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 = 0.4018 r_free = 0.4018 target = 0.097521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.071545 restraints weight = 57162.566| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.52 r_work: 0.3336 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 20648 Z= 0.144 Angle : 0.608 12.044 28251 Z= 0.288 Chirality : 0.050 1.072 3246 Planarity : 0.004 0.041 3531 Dihedral : 8.831 170.555 3359 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.68 % Allowed : 13.68 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % 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: 0.13 (0.17), residues: 2534 helix: 1.22 (0.17), residues: 929 sheet: -0.51 (0.24), residues: 474 loop : -0.51 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 594 TYR 0.013 0.001 TYR A 424 PHE 0.018 0.001 PHE C1126 TRP 0.010 0.001 TRP C1216 HIS 0.005 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (20628) covalent geometry : angle 0.60386 / 0.29 (28237) hydrogen bonds : bond 0.03377 / 2.21 ( 979) hydrogen bonds : angle 4.59165 / 3.15 ( 2726) metal coordination : bond 0.00960 / 0.38 ( 19) metal coordination : angle 3.20761 / 1.73 ( 14) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 1063 ASN cc_start: 0.8209 (t0) cc_final: 0.7034 (p0) REVERT: C 511 MET cc_start: 0.7242 (ptm) cc_final: 0.6830 (ppp) REVERT: C 587 TYR cc_start: 0.7937 (t80) cc_final: 0.7688 (t80) REVERT: C 770 MET cc_start: 0.8096 (mmm) cc_final: 0.7634 (mmm) REVERT: C 822 ARG cc_start: 0.7596 (tmt-80) cc_final: 0.7396 (ptm160) REVERT: C 823 MET cc_start: 0.7847 (ppp) cc_final: 0.7185 (ppp) REVERT: C 902 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: C 1178 MET cc_start: 0.8891 (ptt) cc_final: 0.8668 (ptp) REVERT: D 54 TYR cc_start: 0.7031 (m-80) cc_final: 0.6771 (m-80) REVERT: D 88 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7691 (mt) REVERT: I 476 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7964 (mt-10) REVERT: M 47 MET cc_start: 0.7588 (ptm) cc_final: 0.7347 (ptm) REVERT: M 48 LYS cc_start: 0.7067 (mttm) cc_final: 0.6712 (ttmt) REVERT: M 54 TYR cc_start: 0.6392 (m-80) cc_final: 0.5979 (m-80) REVERT: M 84 ARG cc_start: 0.6584 (ttm110) cc_final: 0.5749 (mmt180) REVERT: N 420 LYS cc_start: 0.8719 (tttp) cc_final: 0.8293 (mmtt) outliers start: 31 outliers final: 24 residues processed: 169 average time/residue: 0.1405 time to fit residues: 38.7552 Evaluate side-chains 158 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 677 CYS Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1184 HIS Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 517 ILE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain N residue 399 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 59 optimal weight: 0.0070 chunk 160 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 80 optimal weight: 0.0870 chunk 172 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 HIS C 931 GLN I 467 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.098204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.072341 restraints weight = 57515.484| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.55 r_work: 0.3356 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 20648 Z= 0.108 Angle : 0.580 12.215 28251 Z= 0.273 Chirality : 0.049 1.074 3246 Planarity : 0.004 0.041 3531 Dihedral : 8.791 169.247 3359 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.73 % Allowed : 13.51 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % 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: 0.25 (0.17), residues: 2534 helix: 1.36 (0.18), residues: 929 sheet: -0.49 (0.24), residues: 477 loop : -0.47 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 502 TYR 0.012 0.001 TYR C 830 PHE 0.017 0.001 PHE C1126 TRP 0.009 0.001 TRP I 578 HIS 0.003 0.001 HIS M 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (20628) covalent geometry : angle 0.57760 / 0.27 (28237) hydrogen bonds : bond 0.03147 / 2.06 ( 979) hydrogen bonds : angle 4.47838 / 3.07 ( 2726) metal coordination : bond 0.00661 / 0.26 ( 19) metal coordination : angle 2.52844 / 1.36 ( 14) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1063 ASN cc_start: 0.8201 (t0) cc_final: 0.7078 (p0) REVERT: C 511 MET cc_start: 0.7167 (ptm) cc_final: 0.6830 (ppp) REVERT: C 587 TYR cc_start: 0.7984 (t80) cc_final: 0.7759 (t80) REVERT: C 770 MET cc_start: 0.8242 (mmm) cc_final: 0.7830 (mmm) REVERT: C 776 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7760 (tt0) REVERT: C 822 ARG cc_start: 0.7636 (tmt-80) cc_final: 0.7316 (ptm160) REVERT: C 823 MET cc_start: 0.7802 (ppp) cc_final: 0.7062 (ppp) REVERT: C 902 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: C 971 MET cc_start: 0.7454 (mtt) cc_final: 0.7064 (mtt) REVERT: C 1178 MET cc_start: 0.8763 (ptt) cc_final: 0.8490 (ptp) REVERT: D 54 TYR cc_start: 0.6932 (m-80) cc_final: 0.6678 (m-80) REVERT: D 88 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7669 (mt) REVERT: I 476 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7818 (mt-10) REVERT: M 47 MET cc_start: 0.7449 (ptm) cc_final: 0.7085 (ptm) REVERT: M 48 LYS cc_start: 0.7039 (mttm) cc_final: 0.6688 (ttmt) REVERT: M 54 TYR cc_start: 0.6328 (m-80) cc_final: 0.5944 (m-80) REVERT: M 84 ARG cc_start: 0.6592 (ttm110) cc_final: 0.5764 (mmt180) REVERT: N 420 LYS cc_start: 0.8798 (tttp) cc_final: 0.8340 (mmtt) outliers start: 32 outliers final: 21 residues processed: 164 average time/residue: 0.1373 time to fit residues: 36.6958 Evaluate side-chains 156 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 964 THR Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1184 HIS Chi-restraints excluded: chain C residue 1222 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 517 ILE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain N residue 399 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 160 optimal weight: 4.9990 chunk 250 optimal weight: 0.4980 chunk 112 optimal weight: 0.0000 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 83 optimal weight: 0.2980 chunk 162 optimal weight: 0.8980 chunk 201 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 ASN C 931 GLN I 467 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.098334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.072481 restraints weight = 57406.366| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.56 r_work: 0.3361 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 20648 Z= 0.109 Angle : 0.579 12.220 28251 Z= 0.272 Chirality : 0.049 1.035 3246 Planarity : 0.004 0.041 3531 Dihedral : 8.728 168.287 3359 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.68 % Allowed : 13.89 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % 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: 0.32 (0.17), residues: 2534 helix: 1.40 (0.18), residues: 936 sheet: -0.39 (0.24), residues: 483 loop : -0.45 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 832 TYR 0.012 0.001 TYR C 830 PHE 0.017 0.001 PHE C1126 TRP 0.008 0.001 TRP N 471 HIS 0.003 0.001 HIS C1184 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (20628) covalent geometry : angle 0.57618 / 0.27 (28237) hydrogen bonds : bond 0.03115 / 2.04 ( 979) hydrogen bonds : angle 4.41434 / 3.03 ( 2726) metal coordination : bond 0.00534 / 0.23 ( 19) metal coordination : angle 2.41701 / 1.31 ( 14) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1063 ASN cc_start: 0.8169 (t0) cc_final: 0.7088 (p0) REVERT: C 511 MET cc_start: 0.7184 (ptm) cc_final: 0.6845 (ppp) REVERT: C 770 MET cc_start: 0.8223 (mmm) cc_final: 0.7865 (mmm) REVERT: C 776 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7816 (tt0) REVERT: C 822 ARG cc_start: 0.7600 (tmt-80) cc_final: 0.7350 (ptm160) REVERT: C 823 MET cc_start: 0.7832 (ppp) cc_final: 0.7046 (ppp) REVERT: C 938 TRP cc_start: 0.8720 (t-100) cc_final: 0.8423 (m-10) REVERT: C 1060 PHE cc_start: 0.7714 (m-10) cc_final: 0.7372 (m-10) REVERT: C 1178 MET cc_start: 0.8656 (ptt) cc_final: 0.8364 (ptp) REVERT: D 54 TYR cc_start: 0.6521 (m-80) cc_final: 0.6230 (m-80) REVERT: D 88 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7751 (mt) REVERT: I 476 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7817 (mt-10) REVERT: M 47 MET cc_start: 0.7484 (ptm) cc_final: 0.7178 (ptm) REVERT: M 48 LYS cc_start: 0.7051 (mttm) cc_final: 0.6686 (ttmt) REVERT: M 54 TYR cc_start: 0.6316 (m-80) cc_final: 0.5960 (m-80) REVERT: M 84 ARG cc_start: 0.6531 (ttm110) cc_final: 0.5722 (mmt180) REVERT: N 420 LYS cc_start: 0.8854 (tttp) cc_final: 0.8355 (mmtt) outliers start: 31 outliers final: 25 residues processed: 164 average time/residue: 0.1378 time to fit residues: 36.6408 Evaluate side-chains 156 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 964 THR Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1184 HIS Chi-restraints excluded: chain C residue 1222 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 517 ILE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 425 HIS Chi-restraints excluded: chain N residue 468 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 53 optimal weight: 30.0000 chunk 145 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 185 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 171 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 HIS C 941 ASN ** C1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 467 GLN N 448 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.095166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.069078 restraints weight = 57529.646| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.51 r_work: 0.3277 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 20648 Z= 0.233 Angle : 0.684 12.061 28251 Z= 0.326 Chirality : 0.051 0.927 3246 Planarity : 0.004 0.043 3531 Dihedral : 8.894 171.618 3359 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.51 % Allowed : 14.43 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % 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: 0.01 (0.17), residues: 2534 helix: 1.14 (0.17), residues: 928 sheet: -0.66 (0.23), residues: 506 loop : -0.54 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1079 TYR 0.025 0.002 TYR I 592 PHE 0.023 0.002 PHE C1126 TRP 0.011 0.002 TRP N 395 HIS 0.006 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 (20628) covalent geometry : angle 0.67602 / 0.33 (28237) hydrogen bonds : bond 0.03825 / 2.50 ( 979) hydrogen bonds : angle 4.75666 / 3.28 ( 2726) metal coordination : bond 0.01293 / 0.56 ( 19) metal coordination : angle 4.59627 / 2.53 ( 14) Misc. bond : bond 0.00084 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 1063 ASN cc_start: 0.8376 (t0) cc_final: 0.7107 (p0) REVERT: C 511 MET cc_start: 0.7357 (ptm) cc_final: 0.6932 (ppp) REVERT: C 770 MET cc_start: 0.8274 (mmm) cc_final: 0.7877 (mmm) REVERT: C 823 MET cc_start: 0.8001 (ppp) cc_final: 0.7300 (ppp) REVERT: C 1178 MET cc_start: 0.8659 (ptt) cc_final: 0.8413 (ptp) REVERT: D 88 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7940 (mt) REVERT: I 476 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8051 (mt-10) REVERT: M 47 MET cc_start: 0.7500 (ptm) cc_final: 0.7187 (ptm) REVERT: M 48 LYS cc_start: 0.7048 (mttm) cc_final: 0.6598 (ttmt) REVERT: M 54 TYR cc_start: 0.6601 (m-80) cc_final: 0.6117 (m-80) REVERT: M 84 ARG cc_start: 0.6614 (ttm110) cc_final: 0.5802 (mmt180) REVERT: N 420 LYS cc_start: 0.8798 (tttp) cc_final: 0.8435 (mmtt) outliers start: 28 outliers final: 20 residues processed: 153 average time/residue: 0.1406 time to fit residues: 35.1404 Evaluate side-chains 147 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 964 THR Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1184 HIS Chi-restraints excluded: chain C residue 1222 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain N residue 399 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 195 optimal weight: 0.8980 chunk 253 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 176 optimal weight: 0.5980 chunk 150 optimal weight: 3.9990 chunk 151 optimal weight: 0.0980 chunk 233 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 49 optimal weight: 30.0000 chunk 199 optimal weight: 0.6980 chunk 164 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 467 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.096406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.070493 restraints weight = 57674.711| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.50 r_work: 0.3310 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 20648 Z= 0.153 Angle : 0.622 12.119 28251 Z= 0.295 Chirality : 0.049 0.889 3246 Planarity : 0.004 0.044 3531 Dihedral : 8.840 169.919 3359 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.14 % Allowed : 14.81 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % 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: 0.13 (0.17), residues: 2534 helix: 1.27 (0.18), residues: 928 sheet: -0.55 (0.24), residues: 494 loop : -0.54 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 832 TYR 0.014 0.001 TYR I 592 PHE 0.019 0.001 PHE C1126 TRP 0.009 0.001 TRP C 819 HIS 0.008 0.001 HIS N 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (20628) covalent geometry : angle 0.61760 / 0.29 (28237) hydrogen bonds : bond 0.03442 / 2.23 ( 979) hydrogen bonds : angle 4.63251 / 3.19 ( 2726) metal coordination : bond 0.00646 / 0.31 ( 19) metal coordination : angle 3.42134 / 1.82 ( 14) Misc. bond : bond 0.00044 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 1063 ASN cc_start: 0.8276 (t0) cc_final: 0.7153 (p0) REVERT: C 511 MET cc_start: 0.7254 (ptm) cc_final: 0.6937 (ppp) REVERT: C 770 MET cc_start: 0.8337 (mmm) cc_final: 0.7955 (mmm) REVERT: C 1178 MET cc_start: 0.8662 (ptt) cc_final: 0.8421 (ptp) REVERT: I 476 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7934 (mt-10) REVERT: M 47 MET cc_start: 0.7432 (ptm) cc_final: 0.7154 (ptm) REVERT: M 48 LYS cc_start: 0.7027 (mttm) cc_final: 0.6576 (ttmt) REVERT: M 54 TYR cc_start: 0.6365 (m-80) cc_final: 0.5939 (m-80) REVERT: M 84 ARG cc_start: 0.6532 (ttm110) cc_final: 0.5765 (mmt180) REVERT: N 420 LYS cc_start: 0.8760 (tttp) cc_final: 0.8316 (mmtt) outliers start: 21 outliers final: 17 residues processed: 150 average time/residue: 0.1326 time to fit residues: 32.9869 Evaluate side-chains 146 residues out of total 2209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 964 THR Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1184 HIS Chi-restraints excluded: chain C residue 1222 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 461 LYS Chi-restraints excluded: chain N residue 468 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 203 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 112 optimal weight: 0.0470 chunk 208 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 58 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 overall best weight: 1.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.095830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.069896 restraints weight = 57864.492| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.53 r_work: 0.3296 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 20648 Z= 0.178 Angle : 0.638 11.725 28251 Z= 0.303 Chirality : 0.049 0.789 3246 Planarity : 0.004 0.042 3531 Dihedral : 8.851 169.784 3359 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.14 % Allowed : 14.92 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % 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: 0.13 (0.17), residues: 2534 helix: 1.28 (0.18), residues: 922 sheet: -0.56 (0.24), residues: 499 loop : -0.53 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 832 TYR 0.017 0.002 TYR I 592 PHE 0.020 0.002 PHE C1126 TRP 0.010 0.001 TRP C 819 HIS 0.010 0.001 HIS N 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (20628) covalent geometry : angle 0.63297 / 0.30 (28237) hydrogen bonds : bond 0.03571 / 2.33 ( 979) hydrogen bonds : angle 4.68140 / 3.23 ( 2726) metal coordination : bond 0.00841 / 0.38 ( 19) metal coordination : angle 3.78612 / 2.04 ( 14) Misc. bond : bond 0.00068 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6930.99 seconds wall clock time: 119 minutes 9.59 seconds (7149.59 seconds total)