Starting phenix.real_space_refine on Sat Dec 9 17:32:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roi_4973/12_2023/6roi_4973_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roi_4973/12_2023/6roi_4973.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roi_4973/12_2023/6roi_4973_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roi_4973/12_2023/6roi_4973_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roi_4973/12_2023/6roi_4973_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roi_4973/12_2023/6roi_4973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roi_4973/12_2023/6roi_4973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roi_4973/12_2023/6roi_4973_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roi_4973/12_2023/6roi_4973_updated.pdb" } resolution = 3.7 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= 0.004 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: 8 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 49 5.16 5 Be 1 3.05 5 C 7599 2.51 5 N 1907 2.21 5 O 2213 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ASP 189": "OD1" <-> "OD2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A ASP 530": "OD1" <-> "OD2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 588": "OE1" <-> "OE2" Residue "A ASP 625": "OD1" <-> "OD2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A ASP 643": "OD1" <-> "OD2" Residue "A ASP 654": "OD1" <-> "OD2" Residue "A ASP 664": "OD1" <-> "OD2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "A ARG 704": "NH1" <-> "NH2" Residue "A ASP 724": "OD1" <-> "OD2" Residue "A GLU 729": "OE1" <-> "OE2" Residue "A ARG 730": "NH1" <-> "NH2" Residue "A GLU 740": "OE1" <-> "OE2" Residue "A GLU 752": "OE1" <-> "OE2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A ASP 784": "OD1" <-> "OD2" Residue "A ARG 786": "NH1" <-> "NH2" Residue "A GLU 788": "OE1" <-> "OE2" Residue "A ASP 811": "OD1" <-> "OD2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A ARG 838": "NH1" <-> "NH2" Residue "A ARG 850": "NH1" <-> "NH2" Residue "A GLU 854": "OE1" <-> "OE2" Residue "A GLU 863": "OE1" <-> "OE2" Residue "A ASP 868": "OD1" <-> "OD2" Residue "A ASP 898": "OD1" <-> "OD2" Residue "A ARG 928": "NH1" <-> "NH2" Residue "A ARG 943": "NH1" <-> "NH2" Residue "A ASP 984": "OD1" <-> "OD2" Residue "A PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1071": "NH1" <-> "NH2" Residue "A ASP 1130": "OD1" <-> "OD2" Residue "A TYR 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1219": "NH1" <-> "NH2" Residue "A TYR 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1282": "OE1" <-> "OE2" Residue "A ARG 1298": "NH1" <-> "NH2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C ASP 173": "OD1" <-> "OD2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ASP 257": "OD1" <-> "OD2" Residue "C GLU 258": "OE1" <-> "OE2" Residue "C PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11775 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1108, 8861 Classifications: {'peptide': 1108} Link IDs: {'PTRANS': 30, 'TRANS': 1077} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2754 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 21, 'TRANS': 317} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {' MG': 1, '2Y5': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.67, per 1000 atoms: 0.57 Number of scatterers: 11775 At special positions: 0 Unit cell: (74.313, 99.084, 174.474, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 49 16.00 P 2 15.00 Mg 1 11.99 F 3 9.00 O 2213 8.00 N 1907 7.00 C 7599 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " distance=2.05 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 Links applied BETA1-3 " BMA D 3 " - " BMA D 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG C 503 " - " ASN C 216 " " NAG D 1 " - " ASN C 199 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.14 Conformation dependent library (CDL) restraints added in 2.2 seconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2734 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 11 sheets defined 33.7% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 214 through 222 removed outlier: 4.330A pdb=" N PHE A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.791A pdb=" N LEU A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 270 removed outlier: 3.809A pdb=" N LEU A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 280 removed outlier: 4.696A pdb=" N LEU A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 441 through 444 No H-bonds generated for 'chain 'A' and resid 441 through 444' Processing helix chain 'A' and resid 449 through 460 removed outlier: 4.228A pdb=" N VAL A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.644A pdb=" N VAL A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 492 through 501 removed outlier: 4.051A pdb=" N LEU A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 498 " --> pdb=" O ASP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 513 No H-bonds generated for 'chain 'A' and resid 510 through 513' Processing helix chain 'A' and resid 515 through 527 removed outlier: 3.773A pdb=" N TYR A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 620 through 627 Processing helix chain 'A' and resid 629 through 632 No H-bonds generated for 'chain 'A' and resid 629 through 632' Processing helix chain 'A' and resid 655 through 665 removed outlier: 3.825A pdb=" N GLN A 660 " --> pdb=" O GLY A 656 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP A 664 " --> pdb=" O GLN A 660 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 removed outlier: 5.195A pdb=" N GLU A 729 " --> pdb=" O THR A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 752 removed outlier: 3.664A pdb=" N HIS A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 751 " --> pdb=" O GLU A 747 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 752 " --> pdb=" O ASP A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 778 removed outlier: 3.528A pdb=" N GLU A 770 " --> pdb=" O GLU A 766 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP A 772 " --> pdb=" O GLU A 768 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 795 removed outlier: 4.981A pdb=" N ASP A 791 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 795 " --> pdb=" O ASP A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.836A pdb=" N HIS A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 848 removed outlier: 3.539A pdb=" N ILE A 843 " --> pdb=" O GLN A 839 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN A 844 " --> pdb=" O GLU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 881 removed outlier: 3.619A pdb=" N ASN A 872 " --> pdb=" O ASP A 868 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 876 " --> pdb=" O ASN A 872 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 880 " --> pdb=" O LYS A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 890 No H-bonds generated for 'chain 'A' and resid 887 through 890' Processing helix chain 'A' and resid 899 through 902 No H-bonds generated for 'chain 'A' and resid 899 through 902' Processing helix chain 'A' and resid 911 through 918 Processing helix chain 'A' and resid 933 through 936 No H-bonds generated for 'chain 'A' and resid 933 through 936' Processing helix chain 'A' and resid 938 through 941 No H-bonds generated for 'chain 'A' and resid 938 through 941' Processing helix chain 'A' and resid 959 through 962 No H-bonds generated for 'chain 'A' and resid 959 through 962' Processing helix chain 'A' and resid 978 through 982 removed outlier: 3.798A pdb=" N SER A 982 " --> pdb=" O GLN A 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 978 through 982' Processing helix chain 'A' and resid 990 through 1006 removed outlier: 3.876A pdb=" N LYS A 994 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 995 " --> pdb=" O PHE A 992 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 996 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 997 " --> pdb=" O LYS A 994 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 998 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL A 999 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N HIS A1000 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY A1001 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A1002 " --> pdb=" O VAL A 999 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TRP A1003 " --> pdb=" O HIS A1000 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR A1005 " --> pdb=" O SER A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1011 No H-bonds generated for 'chain 'A' and resid 1008 through 1011' Processing helix chain 'A' and resid 1018 through 1021 No H-bonds generated for 'chain 'A' and resid 1018 through 1021' Processing helix chain 'A' and resid 1043 through 1047 removed outlier: 3.562A pdb=" N SER A1047 " --> pdb=" O SER A1043 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1043 through 1047' Processing helix chain 'A' and resid 1056 through 1063 Processing helix chain 'A' and resid 1070 through 1075 removed outlier: 3.795A pdb=" N GLU A1074 " --> pdb=" O SER A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1085 removed outlier: 3.584A pdb=" N TYR A1080 " --> pdb=" O PRO A1077 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN A1084 " --> pdb=" O LYS A1081 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS A1085 " --> pdb=" O LEU A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1103 removed outlier: 4.623A pdb=" N GLY A1096 " --> pdb=" O TYR A1092 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP A1097 " --> pdb=" O ILE A1093 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN A1100 " --> pdb=" O GLY A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1108 No H-bonds generated for 'chain 'A' and resid 1105 through 1108' Processing helix chain 'A' and resid 1110 through 1114 removed outlier: 3.658A pdb=" N ILE A1113 " --> pdb=" O ILE A1110 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A1114 " --> pdb=" O GLY A1111 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1110 through 1114' Processing helix chain 'A' and resid 1132 through 1153 removed outlier: 3.649A pdb=" N VAL A1136 " --> pdb=" O TRP A1132 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A1146 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A1148 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A1152 " --> pdb=" O GLY A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1164 removed outlier: 3.842A pdb=" N ILE A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A1164 " --> pdb=" O PHE A1160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1159 through 1164' Processing helix chain 'A' and resid 1168 through 1181 removed outlier: 3.663A pdb=" N ILE A1174 " --> pdb=" O LEU A1170 " (cutoff:3.500A) Proline residue: A1177 - end of helix Processing helix chain 'A' and resid 1183 through 1186 Processing helix chain 'A' and resid 1195 through 1200 Processing helix chain 'A' and resid 1203 through 1229 removed outlier: 3.684A pdb=" N LEU A1207 " --> pdb=" O GLY A1203 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL A1211 " --> pdb=" O LEU A1207 " (cutoff:3.500A) Proline residue: A1213 - end of helix removed outlier: 3.699A pdb=" N ALA A1216 " --> pdb=" O LEU A1212 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG A1219 " --> pdb=" O PHE A1215 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A1225 " --> pdb=" O PHE A1221 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET A1229 " --> pdb=" O TYR A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1244 removed outlier: 4.097A pdb=" N ILE A1238 " --> pdb=" O THR A1234 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A1243 " --> pdb=" O GLN A1239 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A1244 " --> pdb=" O GLU A1240 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 49 No H-bonds generated for 'chain 'C' and resid 46 through 49' Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 151 through 154 No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 160 through 163 No H-bonds generated for 'chain 'C' and resid 160 through 163' Processing helix chain 'C' and resid 192 through 195 No H-bonds generated for 'chain 'C' and resid 192 through 195' Processing helix chain 'C' and resid 227 through 230 No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 238 through 240 No H-bonds generated for 'chain 'C' and resid 238 through 240' Processing helix chain 'C' and resid 267 through 273 removed outlier: 3.915A pdb=" N TRP C 272 " --> pdb=" O GLU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 353 removed outlier: 3.670A pdb=" N LEU C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 339 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 184 through 186 Processing sheet with id= B, first strand: chain 'A' and resid 283 through 288 removed outlier: 3.613A pdb=" N SER A 288 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP A 293 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 307 through 310 Processing sheet with id= D, first strand: chain 'A' and resid 345 through 347 removed outlier: 3.671A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 406 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 556 through 558 removed outlier: 6.459A pdb=" N LYS A 830 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL A 924 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA A 923 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN A 857 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL A 896 " --> pdb=" O ASN A 857 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LEU A 859 " --> pdb=" O VAL A 896 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ASP A 898 " --> pdb=" O LEU A 859 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE A 861 " --> pdb=" O ASP A 898 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 580 through 583 removed outlier: 7.321A pdb=" N ALA A 808 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N CYS A 575 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA A 806 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE A 577 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N ILE A 804 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU A 759 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA A 806 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 757 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA A 808 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG A 755 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG A 710 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU A 692 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 637 through 640 Processing sheet with id= H, first strand: chain 'A' and resid 950 through 953 removed outlier: 6.468A pdb=" N VAL A 967 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N GLY A 953 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL A 969 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 985 " --> pdb=" O GLY A 970 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 72 through 75 Processing sheet with id= J, first strand: chain 'C' and resid 110 through 113 Processing sheet with id= K, first strand: chain 'C' and resid 137 through 144 removed outlier: 6.362A pdb=" N TYR C 141 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU C 284 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE C 143 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR C 282 " --> pdb=" O ILE C 143 " (cutoff:3.500A) 237 hydrogen bonds defined for protein. 660 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.26 Time building geometry restraints manager: 5.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1908 1.31 - 1.44: 3273 1.44 - 1.57: 6774 1.57 - 1.70: 3 1.70 - 1.82: 79 Bond restraints: 12037 Sorted by residual: bond pdb=" OD1 BFD A 560 " pdb="BE BFD A 560 " ideal model delta sigma weight residual 1.737 1.515 0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.60e+00 bond pdb=" C1 BMA D 4 " pdb=" C2 BMA D 4 " ideal model delta sigma weight residual 1.519 1.564 -0.045 2.00e-02 2.50e+03 5.15e+00 bond pdb=" C1 NAG C 503 " pdb=" O5 NAG C 503 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.00e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.25e+00 ... (remaining 12032 not shown) Histogram of bond angle deviations from ideal: 97.07 - 105.06: 194 105.06 - 113.05: 6540 113.05 - 121.05: 6358 121.05 - 129.04: 3127 129.04 - 137.03: 87 Bond angle restraints: 16306 Sorted by residual: angle pdb=" C21 2Y5 A1502 " pdb=" C22 2Y5 A1502 " pdb=" C23 2Y5 A1502 " ideal model delta sigma weight residual 85.82 122.39 -36.57 3.00e+00 1.11e-01 1.49e+02 angle pdb=" C18 2Y5 A1502 " pdb=" C19 2Y5 A1502 " pdb=" C20 2Y5 A1502 " ideal model delta sigma weight residual 152.65 121.88 30.77 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C24 2Y5 A1502 " pdb=" C25 2Y5 A1502 " pdb=" C26 2Y5 A1502 " ideal model delta sigma weight residual 152.70 122.12 30.58 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C15 2Y5 A1502 " pdb=" C16 2Y5 A1502 " pdb=" C17 2Y5 A1502 " ideal model delta sigma weight residual 152.62 123.15 29.47 3.00e+00 1.11e-01 9.65e+01 angle pdb=" N GLY A1283 " pdb=" CA GLY A1283 " pdb=" C GLY A1283 " ideal model delta sigma weight residual 115.80 105.83 9.97 1.74e+00 3.30e-01 3.29e+01 ... (remaining 16301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.99: 7020 33.99 - 67.98: 184 67.98 - 101.98: 27 101.98 - 135.97: 2 135.97 - 169.96: 2 Dihedral angle restraints: 7235 sinusoidal: 2994 harmonic: 4241 Sorted by residual: dihedral pdb=" CA ILE A 670 " pdb=" C ILE A 670 " pdb=" N ILE A 671 " pdb=" CA ILE A 671 " ideal model delta harmonic sigma weight residual 180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA GLU A1191 " pdb=" C GLU A1191 " pdb=" N TYR A1192 " pdb=" CA TYR A1192 " ideal model delta harmonic sigma weight residual -180.00 -154.60 -25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA PHE A1031 " pdb=" C PHE A1031 " pdb=" N ALA A1032 " pdb=" CA ALA A1032 " ideal model delta harmonic sigma weight residual 180.00 155.46 24.54 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 7232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 1807 0.137 - 0.274: 47 0.274 - 0.410: 2 0.410 - 0.547: 0 0.547 - 0.684: 1 Chirality restraints: 1857 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN C 199 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" C5 BMA D 4 " pdb=" C4 BMA D 4 " pdb=" C6 BMA D 4 " pdb=" O5 BMA D 4 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB ILE A 637 " pdb=" CA ILE A 637 " pdb=" CG1 ILE A 637 " pdb=" CG2 ILE A 637 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1854 not shown) Planarity restraints: 2042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 342 " 0.024 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" CD GLU A 342 " -0.083 2.00e-02 2.50e+03 pdb=" OE1 GLU A 342 " 0.029 2.00e-02 2.50e+03 pdb=" OE2 GLU A 342 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A1057 " 0.064 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO A1058 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO A1058 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A1058 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1212 " -0.047 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO A1213 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A1213 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1213 " -0.040 5.00e-02 4.00e+02 ... (remaining 2039 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 23 2.35 - 2.99: 5823 2.99 - 3.62: 17024 3.62 - 4.26: 26766 4.26 - 4.90: 43816 Nonbonded interactions: 93452 Sorted by model distance: nonbonded pdb=" F2 BFD A 560 " pdb="MG MG A1501 " model vdw 1.709 2.120 nonbonded pdb="MG MG A1501 " pdb=" O HOH A1601 " model vdw 1.740 2.170 nonbonded pdb="MG MG A1501 " pdb=" O HOH A1602 " model vdw 1.805 2.170 nonbonded pdb=" O THR A 562 " pdb="MG MG A1501 " model vdw 1.999 2.170 nonbonded pdb=" OD2 BFD A 560 " pdb="MG MG A1501 " model vdw 2.076 2.170 ... (remaining 93447 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.000 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 35.810 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.008 0.222 12037 Z= 0.532 Angle : 1.135 36.575 16306 Z= 0.578 Chirality : 0.061 0.684 1857 Planarity : 0.007 0.095 2039 Dihedral : 16.647 169.959 4495 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.23 % Allowed : 9.47 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.18 (0.16), residues: 1438 helix: -4.68 (0.08), residues: 537 sheet: -2.28 (0.33), residues: 201 loop : -2.65 (0.18), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP C 111 HIS 0.007 0.001 HIS A 634 PHE 0.042 0.003 PHE A 605 TYR 0.046 0.002 TYR A1192 ARG 0.007 0.001 ARG A1219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 231 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 233 average time/residue: 0.2717 time to fit residues: 87.9511 Evaluate side-chains 154 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1056 time to fit residues: 2.1646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN A 376 ASN A 409 ASN A 613 ASN ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN ** A 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 ASN A1050 ASN A1100 ASN A1245 ASN ** A1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN C 116 ASN ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12037 Z= 0.217 Angle : 0.633 13.991 16306 Z= 0.322 Chirality : 0.045 0.381 1857 Planarity : 0.005 0.065 2039 Dihedral : 10.651 151.293 1710 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.72 % Allowed : 16.82 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.09 (0.18), residues: 1438 helix: -3.57 (0.15), residues: 536 sheet: -1.94 (0.33), residues: 220 loop : -2.12 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1028 HIS 0.009 0.001 HIS A1236 PHE 0.017 0.001 PHE C 51 TYR 0.030 0.002 TYR A1192 ARG 0.005 0.000 ARG A1117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 176 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 17 residues processed: 188 average time/residue: 0.2259 time to fit residues: 63.4891 Evaluate side-chains 175 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1151 time to fit residues: 5.5756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 0.0020 chunk 40 optimal weight: 0.7980 chunk 108 optimal weight: 0.0770 chunk 88 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.7750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 GLN A1100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12037 Z= 0.199 Angle : 0.590 12.961 16306 Z= 0.298 Chirality : 0.044 0.321 1857 Planarity : 0.004 0.062 2039 Dihedral : 10.157 144.122 1710 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.56 % Allowed : 19.25 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.46 (0.20), residues: 1438 helix: -2.93 (0.18), residues: 537 sheet: -1.68 (0.34), residues: 219 loop : -1.82 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1028 HIS 0.008 0.001 HIS A 634 PHE 0.018 0.001 PHE C 51 TYR 0.022 0.001 TYR C 77 ARG 0.004 0.000 ARG A1117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 171 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 183 average time/residue: 0.2353 time to fit residues: 63.4773 Evaluate side-chains 158 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 149 time to evaluate : 1.291 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1150 time to fit residues: 3.8668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 2.9990 chunk 97 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 GLN A 839 GLN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12037 Z= 0.311 Angle : 0.634 13.065 16306 Z= 0.322 Chirality : 0.046 0.368 1857 Planarity : 0.004 0.058 2039 Dihedral : 10.092 144.448 1710 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.66 % Allowed : 20.89 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.16 (0.20), residues: 1438 helix: -2.57 (0.19), residues: 536 sheet: -1.72 (0.33), residues: 224 loop : -1.67 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 36 HIS 0.010 0.001 HIS A 634 PHE 0.021 0.002 PHE C 51 TYR 0.026 0.002 TYR A1192 ARG 0.007 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 23 residues processed: 182 average time/residue: 0.2230 time to fit residues: 61.3117 Evaluate side-chains 175 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1164 time to fit residues: 6.6265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.0870 chunk 124 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12037 Z= 0.164 Angle : 0.556 12.752 16306 Z= 0.280 Chirality : 0.043 0.312 1857 Planarity : 0.004 0.055 2039 Dihedral : 9.605 142.341 1710 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.33 % Allowed : 21.83 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.79 (0.21), residues: 1438 helix: -2.16 (0.21), residues: 533 sheet: -1.53 (0.33), residues: 221 loop : -1.56 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1028 HIS 0.008 0.001 HIS A 634 PHE 0.018 0.001 PHE C 51 TYR 0.017 0.001 TYR C 77 ARG 0.005 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 161 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 175 average time/residue: 0.2162 time to fit residues: 57.5050 Evaluate side-chains 154 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 1.255 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.1093 time to fit residues: 4.0290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 0.0060 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12037 Z= 0.251 Angle : 0.589 12.951 16306 Z= 0.296 Chirality : 0.045 0.337 1857 Planarity : 0.004 0.055 2039 Dihedral : 9.605 141.995 1710 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.72 % Allowed : 23.16 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.68 (0.21), residues: 1438 helix: -2.03 (0.21), residues: 534 sheet: -1.48 (0.34), residues: 220 loop : -1.54 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1028 HIS 0.009 0.001 HIS A 634 PHE 0.021 0.002 PHE C 51 TYR 0.022 0.001 TYR A1292 ARG 0.004 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 167 average time/residue: 0.2257 time to fit residues: 56.9840 Evaluate side-chains 162 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 1.373 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.1215 time to fit residues: 5.0098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 137 optimal weight: 0.0570 chunk 86 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12037 Z= 0.181 Angle : 0.561 12.769 16306 Z= 0.281 Chirality : 0.043 0.315 1857 Planarity : 0.003 0.052 2039 Dihedral : 9.276 140.374 1710 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.78 % Allowed : 23.79 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.39 (0.21), residues: 1438 helix: -1.72 (0.22), residues: 529 sheet: -1.35 (0.34), residues: 220 loop : -1.43 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 412 HIS 0.008 0.001 HIS A 634 PHE 0.020 0.001 PHE C 51 TYR 0.018 0.001 TYR A1292 ARG 0.004 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 164 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 172 average time/residue: 0.2408 time to fit residues: 60.9491 Evaluate side-chains 156 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 149 time to evaluate : 1.430 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1273 time to fit residues: 3.6459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 87 optimal weight: 0.0770 chunk 93 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12037 Z= 0.182 Angle : 0.565 12.771 16306 Z= 0.283 Chirality : 0.043 0.312 1857 Planarity : 0.003 0.050 2039 Dihedral : 9.131 139.401 1710 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.02 % Allowed : 24.80 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.25 (0.21), residues: 1438 helix: -1.56 (0.22), residues: 535 sheet: -1.33 (0.34), residues: 220 loop : -1.35 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 412 HIS 0.007 0.001 HIS A 634 PHE 0.023 0.001 PHE A 219 TYR 0.019 0.001 TYR A1192 ARG 0.003 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 162 average time/residue: 0.2250 time to fit residues: 55.2392 Evaluate side-chains 155 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 1.436 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.1121 time to fit residues: 3.9405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1279 GLN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12037 Z= 0.199 Angle : 0.574 12.799 16306 Z= 0.285 Chirality : 0.044 0.319 1857 Planarity : 0.003 0.045 2039 Dihedral : 9.010 138.181 1710 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.39 % Allowed : 24.73 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.10 (0.21), residues: 1438 helix: -1.39 (0.22), residues: 529 sheet: -1.30 (0.34), residues: 223 loop : -1.29 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 412 HIS 0.008 0.001 HIS A 634 PHE 0.022 0.001 PHE C 51 TYR 0.018 0.001 TYR A1192 ARG 0.003 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 156 average time/residue: 0.2192 time to fit residues: 52.1716 Evaluate side-chains 151 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1110 time to fit residues: 2.4641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 113 optimal weight: 0.0570 chunk 11 optimal weight: 3.9990 chunk 87 optimal weight: 0.2980 chunk 69 optimal weight: 0.0770 chunk 90 optimal weight: 1.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12037 Z= 0.183 Angle : 0.568 12.782 16306 Z= 0.281 Chirality : 0.044 0.362 1857 Planarity : 0.003 0.040 2039 Dihedral : 8.885 136.718 1710 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.23 % Allowed : 25.12 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.00 (0.21), residues: 1438 helix: -1.29 (0.22), residues: 531 sheet: -1.26 (0.34), residues: 223 loop : -1.25 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 412 HIS 0.007 0.001 HIS A 634 PHE 0.026 0.001 PHE A 219 TYR 0.018 0.001 TYR A1192 ARG 0.003 0.000 ARG A 351 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 158 average time/residue: 0.2154 time to fit residues: 51.7511 Evaluate side-chains 150 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.321 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1184 time to fit residues: 2.2089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 113 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 14 optimal weight: 0.0870 chunk 20 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.156770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.126793 restraints weight = 15235.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126517 restraints weight = 16189.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127980 restraints weight = 13828.989| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12037 Z= 0.178 Angle : 0.569 12.769 16306 Z= 0.282 Chirality : 0.044 0.375 1857 Planarity : 0.003 0.044 2039 Dihedral : 8.710 135.284 1710 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 25.74 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.88 (0.22), residues: 1438 helix: -1.19 (0.23), residues: 530 sheet: -1.20 (0.34), residues: 223 loop : -1.17 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 412 HIS 0.008 0.001 HIS A 634 PHE 0.022 0.001 PHE C 51 TYR 0.017 0.001 TYR A1192 ARG 0.003 0.000 ARG A 351 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2373.23 seconds wall clock time: 44 minutes 20.82 seconds (2660.82 seconds total)