Starting phenix.real_space_refine on Sat Feb 17 23:36:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onb_12994/02_2024/7onb_12994_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onb_12994/02_2024/7onb_12994.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onb_12994/02_2024/7onb_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_12994/02_2024/7onb_12994_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onb_12994/02_2024/7onb_12994_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onb_12994/02_2024/7onb_12994.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onb_12994/02_2024/7onb_12994.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onb_12994/02_2024/7onb_12994_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onb_12994/02_2024/7onb_12994_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 Residue "A TYR 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 914": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: {'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: {'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: {'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: {'RNA': 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: {'RNA': 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: {'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: 11.41, per 1000 atoms: 0.57 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: 8.79 Conformation dependent library (CDL) restraints added in 3.5 seconds 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... 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: 10.50 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: 9.14 Time building geometry restraints manager: 9.32 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 1.575 1.448 0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C22 SJT D1401 " pdb=" C23 SJT D1401 " ideal model delta sigma weight residual 1.597 1.522 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C3 SJT D1401 " pdb=" O1 SJT D1401 " ideal model delta sigma weight residual 1.396 1.470 -0.074 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C10 SJT D1401 " pdb=" O3 SJT D1401 " ideal model delta sigma weight residual 1.503 1.435 0.068 2.00e-02 2.50e+03 1.14e+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 68.17 117.85 -49.68 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 85.88 117.92 -32.04 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 112.22 133.89 -21.67 3.00e+00 1.11e-01 5.22e+01 ... (remaining 28232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 12231 35.78 - 71.57: 221 71.57 - 107.35: 25 107.35 - 143.13: 5 143.13 - 178.91: 3 Dihedral angle restraints: 12485 sinusoidal: 5043 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 12482 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 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: 7.470 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: 0.040 Extract box with map and model: 23.790 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 67.120 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 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= 0.360 Angle : 1.011 49.685 28237 Z= 0.503 Chirality : 0.062 0.624 3246 Planarity : 0.007 0.099 3531 Dihedral : 15.085 178.913 7681 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 % 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 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 732 HIS 0.016 0.001 HIS C1007 PHE 0.022 0.002 PHE C1126 TYR 0.023 0.002 TYR C 587 ARG 0.012 0.001 ARG C 625 *********************** 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 : 2.407 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: 0.7966 (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: 0.7857 (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: 0.6977 (p0) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.3644 time to fit residues: 184.2823 Evaluate side-chains 186 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.394 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.9990 chunk 233 optimal weight: 40.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** C 950 GLN C1145 ASN C1209 ASN D 50 ASN N 442 ASN N 451 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20628 Z= 0.259 Angle : 0.645 21.238 28237 Z= 0.318 Chirality : 0.044 0.204 3246 Planarity : 0.005 0.070 3531 Dihedral : 12.871 179.410 3472 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.95 % Allowed : 8.65 % Favored : 89.41 % 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: -0.47 (0.17), residues: 2534 helix: 0.47 (0.17), residues: 933 sheet: -0.45 (0.24), residues: 471 loop : -0.81 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C1216 HIS 0.008 0.001 HIS A 293 PHE 0.016 0.002 PHE C1126 TYR 0.023 0.002 TYR C 805 ARG 0.007 0.001 ARG C1185 *********************** 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 222 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 186 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8897 (pt) REVERT: A 832 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.6218 (mmp80) REVERT: A 1063 ASN cc_start: 0.7697 (t0) cc_final: 0.6557 (p0) REVERT: C 498 MET cc_start: 0.7899 (tpt) cc_final: 0.7384 (tpt) REVERT: C 679 ILE cc_start: 0.8819 (pt) cc_final: 0.8351 (mp) REVERT: C 822 ARG cc_start: 0.7784 (tmt-80) cc_final: 0.7373 (ptm160) REVERT: C 823 MET cc_start: 0.7324 (ppp) cc_final: 0.7033 (ppp) REVERT: C 910 MET cc_start: 0.8392 (mmt) cc_final: 0.8141 (mmt) REVERT: C 932 ILE cc_start: 0.8013 (mt) cc_final: 0.7760 (mm) REVERT: C 1056 MET cc_start: 0.8407 (mtp) cc_final: 0.8069 (ptt) REVERT: C 1060 PHE cc_start: 0.7734 (m-10) cc_final: 0.7416 (m-80) REVERT: F 165 ARG cc_start: 0.7803 (ttm110) cc_final: 0.7263 (ttm-80) REVERT: I 592 TYR cc_start: 0.8432 (p90) cc_final: 0.8004 (p90) REVERT: M 48 LYS cc_start: 0.7089 (mttm) cc_final: 0.6764 (ttpt) REVERT: M 54 TYR cc_start: 0.6502 (m-80) cc_final: 0.6084 (m-80) REVERT: M 55 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7886 (tt0) REVERT: M 84 ARG cc_start: 0.6578 (ttm110) cc_final: 0.5875 (mmt180) REVERT: N 387 TRP cc_start: 0.6655 (m100) cc_final: 0.6215 (m100) REVERT: N 391 PRO cc_start: 0.6902 (Cg_exo) cc_final: 0.6583 (Cg_endo) REVERT: N 420 LYS cc_start: 0.8305 (tttp) cc_final: 0.7839 (mmtt) REVERT: N 474 ASP cc_start: 0.7509 (t70) cc_final: 0.6821 (p0) outliers start: 36 outliers final: 21 residues processed: 211 average time/residue: 0.3082 time to fit residues: 102.1430 Evaluate side-chains 171 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 18 ILE 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 803 ASP Chi-restraints excluded: chain A residue 832 ARG Chi-restraints excluded: chain A residue 842 PHE Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 677 CYS Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 752 TYR 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 1274 ILE Chi-restraints excluded: chain D residue 67 SER 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 129 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 194 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 64 optimal weight: 0.1980 chunk 233 optimal weight: 50.0000 chunk 252 optimal weight: 40.0000 chunk 208 optimal weight: 1.9990 chunk 231 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 HIS C 737 GLN C 903 GLN C 941 ASN D 50 ASN N 423 GLN N 433 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3614 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= 0.252 Angle : 0.621 20.455 28237 Z= 0.305 Chirality : 0.044 0.216 3246 Planarity : 0.005 0.059 3531 Dihedral : 12.843 175.891 3472 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.68 % Allowed : 12.11 % Favored : 86.22 % 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: -0.31 (0.17), residues: 2534 helix: 0.66 (0.17), residues: 931 sheet: -0.56 (0.24), residues: 476 loop : -0.67 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 172 HIS 0.005 0.001 HIS B 46 PHE 0.021 0.002 PHE C 900 TYR 0.028 0.002 TYR D 36 ARG 0.008 0.001 ARG F 173 *********************** 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 190 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 2.842 Fit side-chains revert: symmetry clash REVERT: A 1063 ASN cc_start: 0.7837 (t0) cc_final: 0.6764 (p0) REVERT: C 822 ARG cc_start: 0.7665 (tmt-80) cc_final: 0.7393 (ptm160) REVERT: C 823 MET cc_start: 0.7326 (ppp) cc_final: 0.7027 (ppp) REVERT: C 1104 GLN cc_start: 0.4920 (OUTLIER) cc_final: 0.4486 (tt0) REVERT: F 165 ARG cc_start: 0.7858 (ttm110) cc_final: 0.7543 (ttm110) REVERT: I 476 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7702 (mm-30) REVERT: M 48 LYS cc_start: 0.7043 (mttm) cc_final: 0.6717 (ttmt) REVERT: M 54 TYR cc_start: 0.6658 (m-80) cc_final: 0.6237 (m-80) REVERT: M 84 ARG cc_start: 0.6662 (ttm110) cc_final: 0.5888 (mmt180) REVERT: N 404 ILE cc_start: 0.7649 (mm) cc_final: 0.7439 (mm) REVERT: N 420 LYS cc_start: 0.8353 (tttp) cc_final: 0.7967 (mmtt) outliers start: 31 outliers final: 12 residues processed: 179 average time/residue: 0.3221 time to fit residues: 91.3777 Evaluate side-chains 149 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain C residue 677 CYS Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 1104 GLN Chi-restraints excluded: chain D residue 66 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 231 optimal weight: 20.0000 chunk 175 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 222 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** C1209 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20628 Z= 0.235 Angle : 0.571 18.046 28237 Z= 0.280 Chirality : 0.042 0.178 3246 Planarity : 0.004 0.057 3531 Dihedral : 12.762 177.670 3472 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.95 % Allowed : 13.30 % 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 (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: -0.22 (0.17), residues: 2534 helix: 0.88 (0.18), residues: 927 sheet: -0.76 (0.24), residues: 483 loop : -0.63 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 395 HIS 0.005 0.001 HIS A 293 PHE 0.017 0.001 PHE C1126 TYR 0.015 0.001 TYR C 830 ARG 0.004 0.000 ARG D 12 *********************** 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 180 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 144 time to evaluate : 2.509 Fit side-chains revert: symmetry clash REVERT: A 18 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8998 (pt) REVERT: A 1063 ASN cc_start: 0.7916 (t0) cc_final: 0.6823 (p0) REVERT: C 770 MET cc_start: 0.7977 (mmm) cc_final: 0.7716 (mmm) REVERT: C 822 ARG cc_start: 0.7695 (tmt-80) cc_final: 0.7450 (ptm160) REVERT: C 823 MET cc_start: 0.7339 (ppp) cc_final: 0.6967 (ppp) REVERT: F 165 ARG cc_start: 0.7533 (ttm110) cc_final: 0.7321 (ttm110) REVERT: I 476 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7785 (mt-10) REVERT: M 48 LYS cc_start: 0.7037 (mttm) cc_final: 0.6718 (ttmt) REVERT: M 54 TYR cc_start: 0.6527 (m-80) cc_final: 0.5998 (m-80) REVERT: M 84 ARG cc_start: 0.6858 (ttm110) cc_final: 0.5974 (mmt180) REVERT: N 404 ILE cc_start: 0.7879 (mm) cc_final: 0.7677 (mm) REVERT: N 420 LYS cc_start: 0.8398 (tttp) cc_final: 0.8020 (mmtt) outliers start: 36 outliers final: 20 residues processed: 171 average time/residue: 0.3047 time to fit residues: 83.3412 Evaluate side-chains 150 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain C residue 677 CYS Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1184 HIS Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1209 ASN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain I residue 462 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 517 ILE Chi-restraints excluded: chain M residue 60 LEU 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: 0.3980 chunk 3 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 211 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 222 optimal weight: 0.5980 chunk 62 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 C1209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 20628 Z= 0.164 Angle : 0.542 18.101 28237 Z= 0.263 Chirality : 0.041 0.176 3246 Planarity : 0.004 0.041 3531 Dihedral : 12.725 177.896 3472 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.68 % Allowed : 14.27 % 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 (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: -0.07 (0.17), residues: 2534 helix: 0.98 (0.18), residues: 934 sheet: -0.60 (0.24), residues: 468 loop : -0.58 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 471 HIS 0.007 0.001 HIS C 572 PHE 0.017 0.001 PHE C1126 TYR 0.013 0.001 TYR C 830 ARG 0.005 0.000 ARG A 832 *********************** 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 167 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 2.385 Fit side-chains revert: symmetry clash REVERT: A 1063 ASN cc_start: 0.7861 (t0) cc_final: 0.6837 (p0) REVERT: C 822 ARG cc_start: 0.7679 (tmt-80) cc_final: 0.7385 (tmt170) REVERT: C 823 MET cc_start: 0.7368 (ppp) cc_final: 0.7003 (ppp) REVERT: D 88 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7419 (mt) REVERT: I 476 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7747 (mt-10) REVERT: M 48 LYS cc_start: 0.7043 (mttm) cc_final: 0.6720 (ttmt) REVERT: M 54 TYR cc_start: 0.6421 (m-80) cc_final: 0.5936 (m-80) REVERT: M 84 ARG cc_start: 0.6805 (ttm110) cc_final: 0.5948 (mmt180) REVERT: N 420 LYS cc_start: 0.8430 (tttp) cc_final: 0.8062 (mmtt) REVERT: N 428 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8136 (mm-30) outliers start: 31 outliers final: 21 residues processed: 161 average time/residue: 0.2982 time to fit residues: 77.5386 Evaluate side-chains 152 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1207 SER 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 462 VAL 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 480 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 83 optimal weight: 0.0030 chunk 223 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 145 optimal weight: 0.6980 chunk 61 optimal weight: 50.0000 chunk 248 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 130 optimal weight: 0.0060 overall best weight: 1.1208 ------------------------------------------------------------------------------- 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 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 HIS C 931 GLN C1209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 20628 Z= 0.238 Angle : 0.575 18.224 28237 Z= 0.280 Chirality : 0.042 0.182 3246 Planarity : 0.004 0.039 3531 Dihedral : 12.758 178.595 3472 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.73 % Allowed : 14.70 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.17), residues: 2534 helix: 0.99 (0.18), residues: 926 sheet: -0.73 (0.24), residues: 465 loop : -0.60 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 395 HIS 0.007 0.001 HIS C 572 PHE 0.017 0.001 PHE C1126 TYR 0.015 0.001 TYR A 424 ARG 0.007 0.000 ARG I 502 *********************** 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 167 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 2.438 Fit side-chains revert: symmetry clash REVERT: A 819 MET cc_start: 0.7964 (mtp) cc_final: 0.7667 (mtp) REVERT: A 1063 ASN cc_start: 0.7978 (t0) cc_final: 0.6877 (p0) REVERT: C 822 ARG cc_start: 0.7681 (tmt-80) cc_final: 0.7401 (tmt170) REVERT: C 823 MET cc_start: 0.7409 (ppp) cc_final: 0.7084 (ppp) REVERT: D 88 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7620 (mt) REVERT: I 476 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7857 (mt-10) REVERT: M 48 LYS cc_start: 0.7051 (mttm) cc_final: 0.6728 (ttmt) REVERT: M 54 TYR cc_start: 0.6598 (m-80) cc_final: 0.6133 (m-80) REVERT: M 84 ARG cc_start: 0.6870 (ttm110) cc_final: 0.6014 (mmt180) REVERT: N 420 LYS cc_start: 0.8487 (tttp) cc_final: 0.8142 (mmtt) outliers start: 32 outliers final: 24 residues processed: 160 average time/residue: 0.2997 time to fit residues: 77.5588 Evaluate side-chains 157 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 803 ASP 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 C residue 502 LEU Chi-restraints excluded: chain C residue 539 LEU 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 1184 HIS Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1209 ASN 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 I residue 593 GLU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain N residue 468 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 239 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 209 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 247 optimal weight: 0.0370 chunk 155 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- 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 C1209 ASN I 458 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 20628 Z= 0.253 Angle : 0.576 18.168 28237 Z= 0.281 Chirality : 0.042 0.182 3246 Planarity : 0.004 0.040 3531 Dihedral : 12.773 176.717 3472 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.05 % Allowed : 14.70 % Favored : 83.24 % 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: -0.12 (0.17), residues: 2534 helix: 1.00 (0.18), residues: 925 sheet: -0.73 (0.24), residues: 473 loop : -0.60 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 395 HIS 0.008 0.001 HIS C1210 PHE 0.017 0.001 PHE C1126 TYR 0.015 0.001 TYR A 970 ARG 0.005 0.000 ARG A 832 *********************** 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 174 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 2.758 Fit side-chains revert: symmetry clash REVERT: A 1063 ASN cc_start: 0.8012 (t0) cc_final: 0.6910 (p0) REVERT: C 770 MET cc_start: 0.7992 (mmm) cc_final: 0.7511 (mmm) REVERT: C 822 ARG cc_start: 0.7639 (tmt-80) cc_final: 0.7358 (ptm160) REVERT: C 823 MET cc_start: 0.7484 (ppp) cc_final: 0.7142 (ppp) REVERT: C 971 MET cc_start: 0.7624 (mpp) cc_final: 0.7382 (mtt) REVERT: I 458 ASN cc_start: 0.7041 (OUTLIER) cc_final: 0.6820 (p0) REVERT: I 476 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7936 (mt-10) REVERT: M 48 LYS cc_start: 0.6987 (mttm) cc_final: 0.6670 (ttmt) REVERT: M 54 TYR cc_start: 0.6615 (m-80) cc_final: 0.6155 (m-80) REVERT: M 84 ARG cc_start: 0.6827 (ttm110) cc_final: 0.5997 (mmt180) REVERT: N 420 LYS cc_start: 0.8467 (tttp) cc_final: 0.8113 (mmtt) outliers start: 38 outliers final: 26 residues processed: 168 average time/residue: 0.3048 time to fit residues: 83.9933 Evaluate side-chains 155 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 677 CYS Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1184 HIS Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1222 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain I residue 458 ASN Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 517 ILE Chi-restraints excluded: chain I residue 593 GLU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain N residue 438 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 chunk 48 optimal weight: 40.0000 chunk 47 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 ASN I 458 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 20628 Z= 0.417 Angle : 0.678 18.367 28237 Z= 0.336 Chirality : 0.046 0.201 3246 Planarity : 0.005 0.047 3531 Dihedral : 12.898 174.814 3472 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.27 % Allowed : 14.70 % Favored : 83.03 % 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: -0.49 (0.17), residues: 2534 helix: 0.61 (0.17), residues: 933 sheet: -0.93 (0.23), residues: 488 loop : -0.73 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 732 HIS 0.009 0.002 HIS A 293 PHE 0.022 0.002 PHE C1155 TYR 0.023 0.002 TYR I 592 ARG 0.014 0.001 ARG I 459 *********************** 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 171 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 129 time to evaluate : 2.228 Fit side-chains revert: symmetry clash REVERT: A 819 MET cc_start: 0.8464 (mtp) cc_final: 0.8214 (mtt) REVERT: A 834 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7900 (mt) REVERT: A 1063 ASN cc_start: 0.8130 (t0) cc_final: 0.6971 (p0) REVERT: C 770 MET cc_start: 0.8046 (mmm) cc_final: 0.7730 (mmm) REVERT: C 822 ARG cc_start: 0.7676 (tmt-80) cc_final: 0.7371 (tmt170) REVERT: C 823 MET cc_start: 0.7374 (ppp) cc_final: 0.7170 (ppp) REVERT: C 971 MET cc_start: 0.7801 (mpp) cc_final: 0.7578 (mpp) REVERT: I 477 MET cc_start: 0.8059 (mmm) cc_final: 0.7836 (tpt) REVERT: M 48 LYS cc_start: 0.6910 (mttm) cc_final: 0.6622 (ttmt) REVERT: M 54 TYR cc_start: 0.6658 (m-80) cc_final: 0.6163 (m-80) REVERT: M 84 ARG cc_start: 0.6915 (ttm110) cc_final: 0.6050 (mmt180) REVERT: N 420 LYS cc_start: 0.8367 (tttp) cc_final: 0.8057 (mmtt) outliers start: 42 outliers final: 30 residues processed: 162 average time/residue: 0.2901 time to fit residues: 75.8579 Evaluate side-chains 152 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 834 LEU 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 C residue 502 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 677 CYS Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1184 HIS Chi-restraints excluded: chain C residue 1209 ASN 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 I residue 517 ILE Chi-restraints excluded: chain I residue 593 GLU Chi-restraints excluded: chain M residue 60 LEU 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 225 optimal weight: 0.1980 chunk 237 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 chunk 230 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 208 optimal weight: 1.9990 chunk 218 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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** C1104 GLN C1209 ASN I 458 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 20628 Z= 0.274 Angle : 0.602 18.116 28237 Z= 0.294 Chirality : 0.043 0.191 3246 Planarity : 0.004 0.043 3531 Dihedral : 12.844 175.878 3472 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.84 % Allowed : 15.62 % Favored : 82.54 % 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: -0.37 (0.17), residues: 2534 helix: 0.75 (0.17), residues: 931 sheet: -0.87 (0.24), residues: 488 loop : -0.70 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 471 HIS 0.005 0.001 HIS A 293 PHE 0.020 0.001 PHE C1126 TYR 0.015 0.002 TYR A 970 ARG 0.006 0.000 ARG A 832 *********************** 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 163 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 2.354 Fit side-chains revert: symmetry clash REVERT: A 1063 ASN cc_start: 0.8091 (t0) cc_final: 0.6996 (p0) REVERT: C 770 MET cc_start: 0.7976 (mmm) cc_final: 0.7669 (mmm) REVERT: C 822 ARG cc_start: 0.7688 (tmt-80) cc_final: 0.7369 (tmt170) REVERT: C 823 MET cc_start: 0.7356 (ppp) cc_final: 0.7135 (ppp) REVERT: C 971 MET cc_start: 0.7853 (mpp) cc_final: 0.7604 (mpp) REVERT: M 48 LYS cc_start: 0.6893 (mttm) cc_final: 0.6631 (ttmt) REVERT: M 54 TYR cc_start: 0.6632 (m-80) cc_final: 0.6200 (m-80) REVERT: M 84 ARG cc_start: 0.6866 (ttm110) cc_final: 0.6028 (mmt180) REVERT: N 420 LYS cc_start: 0.8464 (tttp) cc_final: 0.8115 (mmtt) outliers start: 34 outliers final: 31 residues processed: 152 average time/residue: 0.3138 time to fit residues: 77.4649 Evaluate side-chains 153 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 830 ASP 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 C residue 502 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 962 MET Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1184 HIS Chi-restraints excluded: chain C residue 1209 ASN Chi-restraints excluded: chain C residue 1222 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain I residue 458 ASN Chi-restraints excluded: chain I residue 461 THR Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 517 ILE Chi-restraints excluded: chain I residue 587 HIS Chi-restraints excluded: chain I residue 593 GLU Chi-restraints excluded: chain M residue 60 LEU 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 244 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 256 optimal weight: 30.0000 chunk 235 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 125 optimal weight: 0.4980 chunk 161 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** ** C1209 ASN ** 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: 0.7584 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 20628 Z= 0.260 Angle : 0.603 18.201 28237 Z= 0.294 Chirality : 0.043 0.190 3246 Planarity : 0.004 0.044 3531 Dihedral : 12.826 175.982 3472 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.89 % Allowed : 15.62 % Favored : 82.49 % 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: -0.33 (0.17), residues: 2534 helix: 0.80 (0.17), residues: 931 sheet: -0.86 (0.24), residues: 488 loop : -0.70 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 471 HIS 0.008 0.001 HIS C1210 PHE 0.019 0.001 PHE C1126 TYR 0.016 0.001 TYR A 970 ARG 0.006 0.000 ARG A 832 ********************** 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 162 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 2.428 Fit side-chains revert: symmetry clash REVERT: A 834 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7939 (mt) REVERT: A 1063 ASN cc_start: 0.8088 (t0) cc_final: 0.7006 (p0) REVERT: C 495 ARG cc_start: 0.8428 (ttm-80) cc_final: 0.7792 (ptm160) REVERT: C 770 MET cc_start: 0.7971 (mmm) cc_final: 0.7677 (mmm) REVERT: C 822 ARG cc_start: 0.7685 (tmt-80) cc_final: 0.7372 (tmt170) REVERT: C 823 MET cc_start: 0.7356 (ppp) cc_final: 0.7131 (ppp) REVERT: C 971 MET cc_start: 0.7823 (mpp) cc_final: 0.7569 (mpp) REVERT: M 48 LYS cc_start: 0.6871 (mttm) cc_final: 0.6635 (ttmt) REVERT: M 54 TYR cc_start: 0.6644 (m-80) cc_final: 0.6211 (m-80) REVERT: M 84 ARG cc_start: 0.6865 (ttm110) cc_final: 0.6027 (mmt180) REVERT: N 420 LYS cc_start: 0.8462 (tttp) cc_final: 0.8111 (mmtt) outliers start: 35 outliers final: 32 residues processed: 152 average time/residue: 0.3193 time to fit residues: 77.9741 Evaluate side-chains 157 residues out of total 2209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 124 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 834 LEU 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 B residue 48 ASP Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 677 CYS Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 962 MET Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1004 ILE 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 461 THR Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 517 ILE Chi-restraints excluded: chain I residue 587 HIS Chi-restraints excluded: chain I residue 593 GLU Chi-restraints excluded: chain M residue 60 LEU 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: 10.0000 chunk 187 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 50.0000 chunk 204 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 209 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 179 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** 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 = 0.3990 r_free = 0.3990 target = 0.096398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.070374 restraints weight = 58178.157| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.56 r_work: 0.3303 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20628 Z= 0.175 Angle : 0.566 18.080 28237 Z= 0.274 Chirality : 0.041 0.189 3246 Planarity : 0.004 0.044 3531 Dihedral : 12.715 177.534 3472 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.41 % Allowed : 16.00 % Favored : 82.59 % 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: 1.02 (0.18), residues: 929 sheet: -0.68 (0.24), residues: 476 loop : -0.66 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 471 HIS 0.003 0.001 HIS N 425 PHE 0.017 0.001 PHE C1126 TYR 0.013 0.001 TYR A 970 ARG 0.005 0.000 ARG A 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4528.77 seconds wall clock time: 83 minutes 33.53 seconds (5013.53 seconds total)