Starting phenix.real_space_refine (version: dev) on Wed Apr 6 11:03:07 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onb_12994/04_2022/7onb_12994_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onb_12994/04_2022/7onb_12994.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onb_12994/04_2022/7onb_12994_ligands.cif 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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onb_12994/04_2022/7onb_12994_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onb_12994/04_2022/7onb_12994_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onb_12994/04_2022/7onb_12994.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onb_12994/04_2022/7onb_12994.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onb_12994/04_2022/7onb_12994_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onb_12994/04_2022/7onb_12994_updated.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/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: {'PTRANS': 58, 'TRANS': 1129, 'PCIS': 2} 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: {'GLN:plan1': 13, 'ARG:plan': 18, 'TYR:plan': 8, 'ASN:plan1': 11, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 10, 'GLU:plan': 24, 'ASP:plan': 15} 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: {'PTRANS': 32, 'TRANS': 781, 'PCIS': 2} 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: {'RNA': 14} Modifications used: {'rna3p_pyr': 5, 'rna2p_pur': 1, 'rna3p_pur': 6, 'rna2p_pyr': 2} Link IDs: {'rna3p': 11, 'rna2p': 2} Chain: "H" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 668 Classifications: {'RNA': 32} Modifications used: {'rna3p_pyr': 18, 'rna2p_pur': 2, 'rna3p_pur': 10, 'rna2p_pyr': 2} Link IDs: {'rna3p': 27, 'rna2p': 4} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 6, 'HIS: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: 12.05, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.50 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral 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... running ksdssp... Secondary structure from input PDB file: 85 helices and 24 sheets defined 37.7% alpha, 17.3% beta 12 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 7.92 Creating SS restraints... Processing helix chain 'A' and resid 190 through 193 No H-bonds generated for 'chain 'A' and resid 190 through 193' Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 809 through 827 removed outlier: 3.706A pdb=" N GLU A 825 " --> pdb=" O GLU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 844 Processing helix chain 'A' and resid 849 through 852 No H-bonds generated for 'chain 'A' and resid 849 through 852' Processing helix chain 'A' and resid 931 through 934 No H-bonds generated for 'chain 'A' and resid 931 through 934' Processing helix chain 'A' and resid 1135 through 1150 removed outlier: 3.667A pdb=" N SER A1150 " --> pdb=" O MET A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1164 Processing helix chain 'A' and resid 1176 through 1181 removed outlier: 3.809A pdb=" N GLN A1181 " --> pdb=" O ASP A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1194 Processing helix chain 'A' and resid 1201 through 1213 removed outlier: 3.564A pdb=" N ARG A1212 " --> pdb=" O LEU A1208 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 45 Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 61 through 72 Processing helix chain 'C' and resid 489 through 506 Processing helix chain 'C' and resid 511 through 521 Processing helix chain 'C' and resid 523 through 526 No H-bonds generated for 'chain 'C' and resid 523 through 526' Processing helix chain 'C' and resid 528 through 539 Proline residue: C 537 - end of helix Processing helix chain 'C' and resid 546 through 562 removed outlier: 3.533A pdb=" N LYS C 562 " --> pdb=" O ARG C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 583 Proline residue: C 569 - end of helix removed outlier: 5.149A pdb=" N HIS C 572 " --> pdb=" O PRO C 569 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU C 579 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Proline residue: C 580 - end of helix removed outlier: 3.554A pdb=" N ILE C 583 " --> pdb=" O PRO C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 604 Processing helix chain 'C' and resid 606 through 616 Proline residue: C 615 - end of helix Processing helix chain 'C' and resid 622 through 639 Processing helix chain 'C' and resid 641 through 652 Proline residue: C 646 - end of helix Processing helix chain 'C' and resid 658 through 695 removed outlier: 7.542A pdb=" N CYS C 677 " --> pdb=" O ILE C 673 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ALA C 678 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE C 679 " --> pdb=" O MET C 675 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU C 680 " --> pdb=" O GLY C 676 " (cutoff:3.500A) Proline residue: C 681 - end of helix removed outlier: 4.893A pdb=" N ARG C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SER C 685 " --> pdb=" O PRO C 681 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N HIS C 692 " --> pdb=" O GLU C 688 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLY C 693 " --> pdb=" O ILE C 689 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU C 694 " --> pdb=" O ILE C 690 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL C 695 " --> pdb=" O GLU C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 716 Processing helix chain 'C' and resid 722 through 736 removed outlier: 5.079A pdb=" N SER C 726 " --> pdb=" O SER C 723 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LYS C 729 " --> pdb=" O SER C 726 " (cutoff:3.500A) Proline residue: C 730 - end of helix removed outlier: 4.088A pdb=" N ILE C 735 " --> pdb=" O TRP C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 756 Proline residue: C 755 - end of helix Processing helix chain 'C' and resid 759 through 778 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) removed outlier: 4.555A pdb=" N GLN C 778 " --> pdb=" O ILE C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 796 Processing helix chain 'C' and resid 803 through 809 Processing helix chain 'C' and resid 811 through 818 Processing helix chain 'C' and resid 823 through 825 No H-bonds generated for 'chain 'C' and resid 823 through 825' Processing helix chain 'C' and resid 827 through 844 Processing helix chain 'C' and resid 846 through 852 removed outlier: 4.349A pdb=" N ARG C 852 " --> pdb=" O GLU C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 858 Processing helix chain 'C' and resid 862 through 879 Processing helix chain 'C' and resid 886 through 901 Processing helix chain 'C' and resid 908 through 941 removed outlier: 6.525A pdb=" N LYS C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ARG C 924 " --> pdb=" O ALA C 920 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL C 925 " --> pdb=" O LEU C 921 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LYS C 926 " --> pdb=" O GLY C 922 " (cutoff:3.500A) Proline residue: C 927 - end of helix Proline residue: C 930 - end of helix Processing helix chain 'C' and resid 945 through 964 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 968 through 981 Processing helix chain 'C' and resid 987 through 1004 Processing helix chain 'C' and resid 1013 through 1025 Proline residue: C1018 - end of helix Proline residue: C1022 - end of helix removed outlier: 4.924A pdb=" N LYS C1025 " --> pdb=" O THR C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1045 Processing helix chain 'C' and resid 1047 through 1049 No H-bonds generated for 'chain 'C' and resid 1047 through 1049' Processing helix chain 'C' and resid 1052 through 1067 removed outlier: 4.545A pdb=" N GLU C1064 " --> pdb=" O PHE C1060 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU C1065 " --> pdb=" O GLU C1061 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU C1066 " --> pdb=" O LEU C1062 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LYS C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) Processing helix chain 'C' and resid 1071 through 1087 Processing helix chain 'C' and resid 1090 through 1104 Processing helix chain 'C' and resid 1107 through 1122 removed outlier: 3.537A pdb=" N THR C1122 " --> pdb=" O VAL C1119 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1127 No H-bonds generated for 'chain 'C' and resid 1125 through 1127' Processing helix chain 'C' and resid 1129 through 1137 removed outlier: 3.935A pdb=" N ARG C1137 " --> pdb=" O MET C1133 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1164 removed outlier: 6.785A pdb=" N GLU C1160 " --> pdb=" O GLU C1156 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N MET C1161 " --> pdb=" O TYR C1157 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLY C1162 " --> pdb=" O ILE C1158 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS C1163 " --> pdb=" O GLY C1159 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASP C1164 " --> pdb=" O GLU C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1177 Proline residue: C1171 - end of helix Processing helix chain 'C' and resid 1182 through 1198 Processing helix chain 'C' and resid 1205 through 1220 removed outlier: 3.631A pdb=" N TYR C1214 " --> pdb=" O HIS C1210 " (cutoff:3.500A) Proline residue: C1217 - end of helix removed outlier: 5.414A pdb=" N PHE C1220 " --> pdb=" O TRP C1216 " (cutoff:3.500A) Processing helix chain 'C' and resid 1224 through 1241 Processing helix chain 'C' and resid 1243 through 1250 Processing helix chain 'C' and resid 1253 through 1255 No H-bonds generated for 'chain 'C' and resid 1253 through 1255' Processing helix chain 'C' and resid 1259 through 1275 Processing helix chain 'C' and resid 1279 through 1282 Processing helix chain 'C' and resid 1299 through 1301 No H-bonds generated for 'chain 'C' and resid 1299 through 1301' Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'F' and resid 165 through 179 Processing helix chain 'I' and resid 462 through 468 Processing helix chain 'I' and resid 478 through 481 Processing helix chain 'I' and resid 485 through 492 Processing helix chain 'I' and resid 502 through 504 No H-bonds generated for 'chain 'I' and resid 502 through 504' Processing helix chain 'I' and resid 526 through 531 removed outlier: 4.016A pdb=" N THR I 531 " --> pdb=" O PHE I 527 " (cutoff:3.500A) Processing helix chain 'I' and resid 568 through 576 Processing helix chain 'I' and resid 611 through 616 Processing helix chain 'I' and resid 631 through 638 Processing helix chain 'M' and resid 66 through 73 Processing helix chain 'M' and resid 76 through 86 Processing helix chain 'N' and resid 394 through 400 Processing helix chain 'N' and resid 419 through 427 removed outlier: 4.172A pdb=" N PHE N 426 " --> pdb=" O PHE N 422 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ALA N 427 " --> pdb=" O GLN N 423 " (cutoff:3.500A) Processing helix chain 'N' and resid 429 through 437 Processing helix chain 'N' and resid 444 through 446 No H-bonds generated for 'chain 'N' and resid 444 through 446' Processing helix chain 'N' and resid 452 through 469 Processing helix chain 'K' and resid 26 through 32 Processing helix chain 'K' and resid 64 through 76 removed outlier: 3.573A pdb=" N ASN K 75 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N MET K 76 " --> pdb=" O LYS K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 81 No H-bonds generated for 'chain 'K' and resid 79 through 81' Processing sheet with id= A, first strand: chain 'A' and resid 1173 through 1175 removed outlier: 6.969A pdb=" N LEU A 3 " --> pdb=" O ILE A1174 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A1126 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A1103 " --> pdb=" O THR A1120 " (cutoff:3.500A) Processing sheet with id= B, 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: 6.501A pdb=" N ARG A 42 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N THR A 52 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 62 through 68 removed outlier: 6.698A pdb=" N GLY A 81 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 65 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA A 67 " --> pdb=" O TYR A 77 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR A 77 " --> pdb=" O ALA A 67 " (cutoff:3.500A) 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= D, first strand: chain 'A' and resid 120 through 123 Processing sheet with id= E, first strand: chain 'A' and resid 166 through 173 removed outlier: 6.687A pdb=" N LEU A 185 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 170 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA A 183 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLY A 172 " --> pdb=" O MET A 181 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N MET A 181 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A 212 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ARG A 222 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP A 214 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL A 220 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 267 through 270 removed outlier: 3.927A pdb=" N TYR A 255 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 234 " --> pdb=" O CYS A 251 " (cutoff:3.500A) Processing sheet with id= G, 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: 3.587A pdb=" N ASP A 331 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS A 312 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR A 329 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR A 314 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU A 327 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU A 316 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE A 325 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 336 through 341 removed outlier: 7.295A pdb=" N ALA A 350 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N MET A 339 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N PHE A 348 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL A 341 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE A 346 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLN A 360 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU A 397 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 774 through 780 removed outlier: 3.894A pdb=" N PHE A 409 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 515 through 519 Processing sheet with id= K, first strand: chain 'A' and resid 546 through 549 Processing sheet with id= L, first strand: chain 'A' and resid 629 through 631 removed outlier: 4.207A pdb=" N THR A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 687 through 690 removed outlier: 5.265A pdb=" N VAL A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing sheet with id= N, 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= O, first strand: chain 'A' and resid 741 through 745 removed outlier: 3.672A pdb=" N THR A 761 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 448 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA A 766 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU A 446 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 785 through 790 removed outlier: 6.994A pdb=" N ILE A 800 " --> pdb=" O ARG A 786 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE A 788 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE A 798 " --> pdb=" O PHE A 788 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE A 790 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN A 796 " --> pdb=" O ILE A 790 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASN A 870 " --> pdb=" O THR A 876 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR A 876 " --> pdb=" O ASN A 870 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 886 through 894 removed outlier: 6.557A pdb=" N GLY A 908 " --> pdb=" O PHE A 889 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL A 891 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 906 " --> pdb=" O VAL A 891 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL A 893 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR A 904 " --> pdb=" O VAL A 893 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS A 941 " --> pdb=" O THR A 927 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 949 through 955 removed outlier: 6.547A pdb=" N GLY A 962 " --> pdb=" O ALA A 950 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE A 952 " --> pdb=" O LEU A 960 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 960 " --> pdb=" O ILE A 952 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG A 958 " --> pdb=" O PRO A 954 " (cutoff:3.500A) 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= S, first strand: chain 'A' and resid 990 through 996 removed outlier: 6.539A pdb=" N SER A1003 " --> pdb=" O SER A 991 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE A 993 " --> pdb=" O ILE A1001 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A1001 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR A 995 " --> pdb=" O ARG A 999 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ARG A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N PHE A1009 " --> pdb=" O ASP A1027 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A1027 " --> pdb=" O PHE A1009 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A1025 " --> pdb=" O TRP A1011 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ARG A1013 " --> pdb=" O ILE A1023 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE A1023 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LYS A1015 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU A1021 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLN A1087 " --> 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= T, first strand: chain 'D' and resid 15 through 19 removed outlier: 4.839A pdb=" N ILE D 45 " --> pdb=" O GLY D 16 " (cutoff:3.500A) Processing sheet with id= U, 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= V, first strand: chain 'M' and resid 46 through 48 Processing sheet with id= W, first strand: chain 'N' and resid 405 through 408 Processing sheet with id= X, first strand: chain 'K' and resid 85 through 87 806 hydrogen bonds defined for protein. 2235 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: 9.39 Time building geometry restraints manager: 9.68 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=" N SJT D1401 " pdb=" C SJT D1401 " ideal model delta sigma weight residual 1.481 1.343 0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C16 SJT D1401 " pdb=" C18 SJT D1401 " ideal model delta sigma weight residual 1.572 1.448 0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C3 SJT D1401 " pdb=" O1 SJT D1401 " ideal model delta sigma weight residual 1.397 1.470 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C22 SJT D1401 " pdb=" C23 SJT D1401 " ideal model delta sigma weight residual 1.592 1.522 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C SJT D1401 " pdb=" C1 SJT D1401 " ideal model delta sigma weight residual 1.548 1.481 0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 20623 not shown) Histogram of bond angle deviations from ideal: 97.92 - 105.49: 657 105.49 - 113.05: 11046 113.05 - 120.61: 8903 120.61 - 128.18: 7435 128.18 - 135.74: 196 Bond angle restraints: 28237 Sorted by residual: angle pdb=" C17 SJT D1401 " pdb=" C16 SJT D1401 " pdb=" C18 SJT D1401 " ideal model delta sigma weight residual 68.19 117.85 -49.66 3.00e+00 1.11e-01 2.74e+02 angle pdb=" C15 SJT D1401 " pdb=" C16 SJT D1401 " pdb=" C18 SJT D1401 " ideal model delta sigma weight residual 85.86 117.92 -32.06 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C15 SJT D1401 " pdb=" C16 SJT D1401 " pdb=" C17 SJT D1401 " ideal model delta sigma weight residual 152.69 124.20 28.49 3.00e+00 1.11e-01 9.02e+01 angle pdb=" C1 SJT D1401 " pdb=" C2 SJT D1401 " pdb=" C3 SJT D1401 " ideal model delta sigma weight residual 152.65 126.82 25.83 3.00e+00 1.11e-01 7.41e+01 angle pdb=" C SJT D1401 " pdb=" C1 SJT D1401 " pdb=" C2 SJT D1401 " ideal model delta sigma weight residual 112.20 133.89 -21.69 3.00e+00 1.11e-01 5.23e+01 ... (remaining 28232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 12137 35.78 - 71.57: 160 71.57 - 107.35: 15 107.35 - 143.13: 4 143.13 - 178.91: 3 Dihedral angle restraints: 12319 sinusoidal: 4877 harmonic: 7442 Sorted by residual: dihedral pdb=" O4' U G 131 " pdb=" C1' U G 131 " pdb=" N1 U G 131 " pdb=" C2 U G 131 " ideal model delta sinusoidal sigma weight residual -128.00 50.91 -178.91 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C G 137 " pdb=" C1' C G 137 " pdb=" N1 C G 137 " pdb=" C2 C G 137 " ideal model delta sinusoidal sigma weight residual -160.00 -37.87 -122.13 1 1.50e+01 4.44e-03 6.54e+01 dihedral pdb=" O4' U H 34 " pdb=" C1' U H 34 " pdb=" N1 U H 34 " pdb=" C2 U H 34 " ideal model delta sinusoidal sigma weight residual -160.00 -46.01 -113.99 1 1.50e+01 4.44e-03 6.00e+01 ... (remaining 12316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 3098 0.125 - 0.249: 133 0.249 - 0.374: 10 0.374 - 0.499: 4 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=" CB VAL C 727 " pdb=" CA VAL C 727 " pdb=" CG1 VAL C 727 " pdb=" CG2 VAL C 727 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.85e+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: 5019 2.80 - 3.32: 18181 3.32 - 3.85: 35515 3.85 - 4.37: 39676 4.37 - 4.90: 66928 Nonbonded interactions: 165319 Sorted by model distance: nonbonded pdb=" OH TYR A 329 " pdb=" OG1 THR A 332 " model vdw 2.273 2.440 nonbonded pdb=" OE2 GLU A 136 " pdb=" OH TYR A 189 " model vdw 2.286 2.440 nonbonded pdb=" O VAL C 701 " pdb=" OG SER C 705 " model vdw 2.296 2.440 nonbonded pdb=" OD1 ASN C1213 " pdb=" OH TYR C1249 " model vdw 2.304 2.440 nonbonded pdb=" O2' U H 39 " pdb=" O LEU M 62 " model vdw 2.304 2.440 ... (remaining 165314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 26.720 Check model and map are aligned: 0.290 Convert atoms to be neutral: 0.180 Process input model: 65.700 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.430 ------------------------------------------------------------------------------- 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 0.138 20628 Z= 0.356 Angle : 1.011 49.665 28237 Z= 0.503 Chirality : 0.062 0.624 3246 Planarity : 0.007 0.099 3531 Dihedral : 13.897 178.913 7515 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (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 *********************** 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 fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 2.432 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 outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.3600 time to fit residues: 183.7179 Evaluate side-chains 174 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.297 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 233 optimal weight: 40.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1061 ASN ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1145 ASN C1209 ASN D 50 ASN N 451 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.086 20628 Z= 0.276 Angle : 0.638 21.314 28237 Z= 0.319 Chirality : 0.044 0.190 3246 Planarity : 0.005 0.093 3531 Dihedral : 9.583 179.701 3306 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.16), residues: 2534 helix: 0.45 (0.17), residues: 935 sheet: -0.42 (0.24), residues: 469 loop : -0.86 (0.18), residues: 1130 *********************** 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 210 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 179 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 19 residues processed: 200 average time/residue: 0.3040 time to fit residues: 97.5914 Evaluate side-chains 159 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 2.601 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2233 time to fit residues: 10.6991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 129 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 194 optimal weight: 0.9980 chunk 158 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 233 optimal weight: 50.0000 chunk 252 optimal weight: 40.0000 chunk 208 optimal weight: 0.4980 chunk 231 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 HIS C 737 GLN C 941 ASN ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN N 433 HIS N 442 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.130 20628 Z= 0.345 Angle : 0.676 19.677 28237 Z= 0.339 Chirality : 0.046 0.225 3246 Planarity : 0.006 0.099 3531 Dihedral : 9.742 174.895 3306 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2534 helix: 0.43 (0.17), residues: 927 sheet: -0.76 (0.24), residues: 474 loop : -0.77 (0.18), residues: 1133 *********************** 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 188 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 151 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 14 residues processed: 175 average time/residue: 0.2896 time to fit residues: 83.2154 Evaluate side-chains 141 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 2.426 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1806 time to fit residues: 7.9955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 231 optimal weight: 20.0000 chunk 175 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 248 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 222 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 HIS ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1104 GLN F 176 GLN I 458 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 20628 Z= 0.245 Angle : 0.582 18.185 28237 Z= 0.287 Chirality : 0.043 0.192 3246 Planarity : 0.004 0.071 3531 Dihedral : 9.648 177.121 3306 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2534 helix: 0.75 (0.17), residues: 925 sheet: -0.79 (0.25), residues: 466 loop : -0.70 (0.18), residues: 1143 *********************** 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 161 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 155 average time/residue: 0.2889 time to fit residues: 73.9837 Evaluate side-chains 129 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 2.403 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1833 time to fit residues: 5.8770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 206 optimal weight: 4.9990 chunk 141 optimal weight: 0.0870 chunk 3 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 222 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 HIS ** C 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 458 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.092 20628 Z= 0.273 Angle : 0.598 18.130 28237 Z= 0.293 Chirality : 0.043 0.204 3246 Planarity : 0.004 0.059 3531 Dihedral : 9.706 175.984 3306 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.17), residues: 2534 helix: 0.79 (0.17), residues: 930 sheet: -0.82 (0.24), residues: 466 loop : -0.63 (0.18), residues: 1138 *********************** 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 169 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 138 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 162 average time/residue: 0.2924 time to fit residues: 78.3711 Evaluate side-chains 142 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 2.397 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1910 time to fit residues: 8.4750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 83 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 145 optimal weight: 0.9980 chunk 61 optimal weight: 50.0000 chunk 248 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 HIS ** C 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 903 GLN C 950 GLN I 458 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.097 20628 Z= 0.325 Angle : 0.626 18.025 28237 Z= 0.307 Chirality : 0.044 0.205 3246 Planarity : 0.004 0.054 3531 Dihedral : 9.857 175.171 3306 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.17), residues: 2534 helix: 0.75 (0.17), residues: 917 sheet: -0.95 (0.24), residues: 476 loop : -0.74 (0.18), residues: 1141 *********************** 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 149 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 146 average time/residue: 0.2993 time to fit residues: 72.8013 Evaluate side-chains 129 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 2.526 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2324 time to fit residues: 5.9329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 239 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 181 optimal weight: 3.9990 chunk 140 optimal weight: 0.0870 chunk 209 optimal weight: 0.4980 chunk 138 optimal weight: 5.9990 chunk 247 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 151 optimal weight: 0.0970 chunk 114 optimal weight: 2.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 20628 Z= 0.156 Angle : 0.560 18.100 28237 Z= 0.272 Chirality : 0.041 0.189 3246 Planarity : 0.004 0.050 3531 Dihedral : 9.703 177.111 3306 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2534 helix: 0.97 (0.17), residues: 924 sheet: -0.76 (0.24), residues: 463 loop : -0.60 (0.19), residues: 1147 *********************** 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 140 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 138 average time/residue: 0.3101 time to fit residues: 70.7975 Evaluate side-chains 122 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 2.391 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1869 time to fit residues: 3.2843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 48 optimal weight: 40.0000 chunk 47 optimal weight: 20.0000 chunk 157 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 458 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.095 20628 Z= 0.371 Angle : 0.639 18.046 28237 Z= 0.312 Chirality : 0.044 0.210 3246 Planarity : 0.004 0.050 3531 Dihedral : 9.826 178.593 3306 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2534 helix: 0.77 (0.17), residues: 930 sheet: -0.91 (0.24), residues: 475 loop : -0.77 (0.18), residues: 1129 *********************** 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 136 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 2.487 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 131 average time/residue: 0.3093 time to fit residues: 66.8109 Evaluate side-chains 127 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 2.493 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2160 time to fit residues: 6.9750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 225 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 230 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 181 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 208 optimal weight: 0.0970 chunk 218 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 442 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 20628 Z= 0.209 Angle : 0.585 18.071 28237 Z= 0.282 Chirality : 0.042 0.196 3246 Planarity : 0.004 0.049 3531 Dihedral : 9.774 178.935 3306 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.17), residues: 2534 helix: 0.89 (0.17), residues: 926 sheet: -0.78 (0.25), residues: 455 loop : -0.71 (0.18), residues: 1153 *********************** 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 132 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 131 average time/residue: 0.3137 time to fit residues: 67.0224 Evaluate side-chains 124 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 2.388 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2014 time to fit residues: 4.6617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 244 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 115 optimal weight: 0.0870 chunk 169 optimal weight: 6.9990 chunk 256 optimal weight: 40.0000 chunk 235 optimal weight: 30.0000 chunk 203 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 467 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 20628 Z= 0.186 Angle : 0.579 18.049 28237 Z= 0.277 Chirality : 0.042 0.214 3246 Planarity : 0.004 0.049 3531 Dihedral : 9.700 179.783 3306 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2534 helix: 1.03 (0.18), residues: 925 sheet: -0.72 (0.24), residues: 468 loop : -0.66 (0.18), residues: 1141 ********************** 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 133 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 2.275 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 132 average time/residue: 0.3094 time to fit residues: 67.2492 Evaluate side-chains 126 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 2.379 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2340 time to fit residues: 4.5449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 187 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 204 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 209 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 37 optimal weight: 0.0670 chunk 179 optimal weight: 7.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.096402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.070807 restraints weight = 57553.551| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.50 r_work: 0.3410 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work: 0.3390 rms_B_bonded: 2.32 restraints_weight: 0.1250 r_work: 0.3379 rms_B_bonded: 2.39 restraints_weight: 0.0625 r_work: 0.3367 rms_B_bonded: 2.49 restraints_weight: 0.0312 r_work: 0.3355 rms_B_bonded: 2.63 restraints_weight: 0.0156 r_work: 0.3341 rms_B_bonded: 2.80 restraints_weight: 0.0078 r_work: 0.3327 rms_B_bonded: 3.00 restraints_weight: 0.0039 r_work: 0.3312 rms_B_bonded: 3.24 restraints_weight: 0.0020 r_work: 0.3295 rms_B_bonded: 3.53 restraints_weight: 0.0010 r_work: 0.3277 rms_B_bonded: 3.87 restraints_weight: 0.0005 r_work: 0.3257 rms_B_bonded: 4.25 restraints_weight: 0.0002 r_work: 0.3236 rms_B_bonded: 4.70 restraints_weight: 0.0001 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 20628 Z= 0.169 Angle : 0.561 18.035 28237 Z= 0.269 Chirality : 0.041 0.188 3246 Planarity : 0.004 0.058 3531 Dihedral : 9.653 178.785 3306 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2534 helix: 1.09 (0.18), residues: 929 sheet: -0.69 (0.25), residues: 458 loop : -0.60 (0.18), residues: 1147 =============================================================================== Job complete usr+sys time: 3623.99 seconds wall clock time: 67 minutes 25.92 seconds (4045.92 seconds total)