Starting phenix.real_space_refine on Wed Jun 18 15:02:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pqo_20449/06_2025/6pqo_20449.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqo_20449/06_2025/6pqo_20449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pqo_20449/06_2025/6pqo_20449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqo_20449/06_2025/6pqo_20449.map" model { file = "/net/cci-nas-00/data/ceres_data/6pqo_20449/06_2025/6pqo_20449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqo_20449/06_2025/6pqo_20449.cif" } resolution = 2.88 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 ------------------------------------------------------------------------------- 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= 0.008 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 144 5.16 5 C 13360 2.51 5 N 3208 2.21 5 O 3576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20312 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 4813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4813 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 4813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4813 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "B" Number of atoms: 4813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4813 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 4813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4813 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "E" 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: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 278 Unusual residues: {'6OU': 5, 'JT0': 1, 'LBN': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 3} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 196 Unusual residues: {'6OU': 3, 'JT0': 1, 'LBN': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 83 Planarities with less than four sites: {'6OU:plan-1': 3, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 237 Unusual residues: {'6OU': 4, 'JT0': 1, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 91 Planarities with less than four sites: {'6OU:plan-1': 3, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 237 Unusual residues: {'6OU': 4, 'JT0': 1, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 91 Planarities with less than four sites: {'6OU:plan-1': 3, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 9 Restraints were copied for chains: F, G, H Time building chain proxies: 14.57, per 1000 atoms: 0.72 Number of scatterers: 20312 At special positions: 0 Unit cell: (113.4, 113.4, 149.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 144 16.00 P 24 15.00 O 3576 8.00 N 3208 7.00 C 13360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN D 747 " " NAG F 1 " - " ASN A 747 " " NAG G 1 " - " ASN B 747 " " NAG H 1 " - " ASN C 747 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.86 Conformation dependent library (CDL) restraints added in 3.2 seconds 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4696 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 71.9% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'D' and resid 446 through 455 Processing helix chain 'D' and resid 458 through 466 Processing helix chain 'D' and resid 484 through 492 removed outlier: 3.674A pdb=" N ASN D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 516 through 525 Processing helix chain 'D' and resid 526 through 537 Processing helix chain 'D' and resid 550 through 558 removed outlier: 3.551A pdb=" N PHE D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 removed outlier: 3.522A pdb=" N HIS D 570 " --> pdb=" O LEU D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 589 Processing helix chain 'D' and resid 592 through 601 removed outlier: 3.613A pdb=" N VAL D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 611 removed outlier: 3.952A pdb=" N ILE D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 629 Processing helix chain 'D' and resid 630 through 640 removed outlier: 3.591A pdb=" N MET D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 670 Processing helix chain 'D' and resid 683 through 691 Processing helix chain 'D' and resid 694 through 699 Processing helix chain 'D' and resid 700 through 714 removed outlier: 3.645A pdb=" N TYR D 714 " --> pdb=" O LYS D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 739 removed outlier: 3.797A pdb=" N TYR D 726 " --> pdb=" O ASN D 722 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY D 729 " --> pdb=" O SER D 725 " (cutoff:3.500A) Proline residue: D 732 - end of helix Processing helix chain 'D' and resid 766 through 796 removed outlier: 3.698A pdb=" N THR D 772 " --> pdb=" O TYR D 768 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS D 796 " --> pdb=" O ILE D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 802 through 820 removed outlier: 3.927A pdb=" N VAL D 806 " --> pdb=" O ASP D 802 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 819 " --> pdb=" O GLY D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 823 No H-bonds generated for 'chain 'D' and resid 821 through 823' Processing helix chain 'D' and resid 827 through 846 removed outlier: 3.706A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP D 843 " --> pdb=" O VAL D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 847 through 853 removed outlier: 3.719A pdb=" N GLN D 851 " --> pdb=" O LEU D 848 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG D 852 " --> pdb=" O TYR D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 892 removed outlier: 3.663A pdb=" N ILE D 860 " --> pdb=" O CYS D 856 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL D 876 " --> pdb=" O ARG D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 899 removed outlier: 3.540A pdb=" N SER D 899 " --> pdb=" O ASP D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 912 Processing helix chain 'D' and resid 917 through 922 Processing helix chain 'D' and resid 922 through 927 Processing helix chain 'D' and resid 933 through 948 Processing helix chain 'D' and resid 950 through 969 Processing helix chain 'D' and resid 970 through 987 removed outlier: 3.782A pdb=" N ILE D 976 " --> pdb=" O SER D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 999 Processing helix chain 'D' and resid 1016 through 1024 Processing helix chain 'D' and resid 1040 through 1072 Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 484 through 492 removed outlier: 3.675A pdb=" N ASN A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 516 through 525 Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 550 through 558 removed outlier: 3.551A pdb=" N PHE A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 removed outlier: 3.522A pdb=" N HIS A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 589 Processing helix chain 'A' and resid 592 through 601 removed outlier: 3.613A pdb=" N VAL A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 611 removed outlier: 3.953A pdb=" N ILE A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 630 through 640 removed outlier: 3.592A pdb=" N MET A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 670 Processing helix chain 'A' and resid 683 through 691 Processing helix chain 'A' and resid 694 through 699 Processing helix chain 'A' and resid 700 through 714 removed outlier: 3.644A pdb=" N TYR A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 739 removed outlier: 3.796A pdb=" N TYR A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 766 through 796 removed outlier: 3.697A pdb=" N THR A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 796 " --> pdb=" O ILE A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 820 removed outlier: 3.927A pdb=" N VAL A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 827 through 846 removed outlier: 3.707A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 853 removed outlier: 3.719A pdb=" N GLN A 851 " --> pdb=" O LEU A 848 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 852 " --> pdb=" O TYR A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 892 removed outlier: 3.663A pdb=" N ILE A 860 " --> pdb=" O CYS A 856 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 removed outlier: 3.540A pdb=" N SER A 899 " --> pdb=" O ASP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 912 Processing helix chain 'A' and resid 917 through 922 Processing helix chain 'A' and resid 922 through 927 Processing helix chain 'A' and resid 933 through 948 Processing helix chain 'A' and resid 950 through 969 Processing helix chain 'A' and resid 970 through 987 removed outlier: 3.782A pdb=" N ILE A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 999 Processing helix chain 'A' and resid 1016 through 1024 Processing helix chain 'A' and resid 1040 through 1072 Processing helix chain 'B' and resid 447 through 455 Processing helix chain 'B' and resid 458 through 466 Processing helix chain 'B' and resid 484 through 492 removed outlier: 3.675A pdb=" N ASN B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 516 through 525 Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'B' and resid 550 through 558 removed outlier: 3.551A pdb=" N PHE B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 570 removed outlier: 3.521A pdb=" N HIS B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 589 Processing helix chain 'B' and resid 592 through 601 removed outlier: 3.614A pdb=" N VAL B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 611 removed outlier: 3.953A pdb=" N ILE B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 629 Processing helix chain 'B' and resid 630 through 640 removed outlier: 3.590A pdb=" N MET B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 670 Processing helix chain 'B' and resid 683 through 691 Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'B' and resid 700 through 714 removed outlier: 3.644A pdb=" N TYR B 714 " --> pdb=" O LYS B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 739 removed outlier: 3.797A pdb=" N TYR B 726 " --> pdb=" O ASN B 722 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 766 through 796 removed outlier: 3.698A pdb=" N THR B 772 " --> pdb=" O TYR B 768 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 796 " --> pdb=" O ILE B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 820 removed outlier: 3.927A pdb=" N VAL B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 819 " --> pdb=" O GLY B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 823 No H-bonds generated for 'chain 'B' and resid 821 through 823' Processing helix chain 'B' and resid 827 through 846 removed outlier: 3.706A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 853 removed outlier: 3.720A pdb=" N GLN B 851 " --> pdb=" O LEU B 848 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG B 852 " --> pdb=" O TYR B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 892 removed outlier: 3.663A pdb=" N ILE B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL B 876 " --> pdb=" O ARG B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 899 removed outlier: 3.540A pdb=" N SER B 899 " --> pdb=" O ASP B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 912 Processing helix chain 'B' and resid 917 through 922 Processing helix chain 'B' and resid 922 through 927 Processing helix chain 'B' and resid 933 through 948 Processing helix chain 'B' and resid 950 through 969 Processing helix chain 'B' and resid 970 through 987 removed outlier: 3.782A pdb=" N ILE B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 999 Processing helix chain 'B' and resid 1016 through 1024 Processing helix chain 'B' and resid 1040 through 1072 Processing helix chain 'C' and resid 447 through 455 Processing helix chain 'C' and resid 458 through 466 Processing helix chain 'C' and resid 484 through 492 removed outlier: 3.675A pdb=" N ASN C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 516 through 525 Processing helix chain 'C' and resid 526 through 537 Processing helix chain 'C' and resid 550 through 558 removed outlier: 3.551A pdb=" N PHE C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 570 removed outlier: 3.522A pdb=" N HIS C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 589 Processing helix chain 'C' and resid 592 through 601 removed outlier: 3.613A pdb=" N VAL C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 611 removed outlier: 3.952A pdb=" N ILE C 611 " --> pdb=" O GLU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 629 Processing helix chain 'C' and resid 630 through 640 removed outlier: 3.590A pdb=" N MET C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 670 Processing helix chain 'C' and resid 683 through 691 Processing helix chain 'C' and resid 694 through 699 Processing helix chain 'C' and resid 700 through 714 removed outlier: 3.646A pdb=" N TYR C 714 " --> pdb=" O LYS C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 739 removed outlier: 3.797A pdb=" N TYR C 726 " --> pdb=" O ASN C 722 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY C 729 " --> pdb=" O SER C 725 " (cutoff:3.500A) Proline residue: C 732 - end of helix Processing helix chain 'C' and resid 766 through 796 removed outlier: 3.698A pdb=" N THR C 772 " --> pdb=" O TYR C 768 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 796 " --> pdb=" O ILE C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 820 removed outlier: 3.927A pdb=" N VAL C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 823 No H-bonds generated for 'chain 'C' and resid 821 through 823' Processing helix chain 'C' and resid 827 through 846 removed outlier: 3.706A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP C 843 " --> pdb=" O VAL C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 853 removed outlier: 3.719A pdb=" N GLN C 851 " --> pdb=" O LEU C 848 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG C 852 " --> pdb=" O TYR C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 892 removed outlier: 3.663A pdb=" N ILE C 860 " --> pdb=" O CYS C 856 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL C 875 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL C 876 " --> pdb=" O ARG C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 899 removed outlier: 3.539A pdb=" N SER C 899 " --> pdb=" O ASP C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 912 Processing helix chain 'C' and resid 917 through 922 Processing helix chain 'C' and resid 922 through 927 Processing helix chain 'C' and resid 933 through 948 Processing helix chain 'C' and resid 950 through 969 Processing helix chain 'C' and resid 970 through 987 removed outlier: 3.782A pdb=" N ILE C 976 " --> pdb=" O SER C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 999 Processing helix chain 'C' and resid 1016 through 1024 Processing helix chain 'C' and resid 1040 through 1072 Processing sheet with id=AA1, first strand: chain 'D' and resid 642 through 644 Processing sheet with id=AA2, first strand: chain 'D' and resid 745 through 747 removed outlier: 4.001A pdb=" N ALA D 745 " --> pdb=" O ILE D 752 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 642 through 644 Processing sheet with id=AA4, first strand: chain 'A' and resid 745 through 747 removed outlier: 4.002A pdb=" N ALA A 745 " --> pdb=" O ILE A 752 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 642 through 644 Processing sheet with id=AA6, first strand: chain 'B' and resid 745 through 747 removed outlier: 4.002A pdb=" N ALA B 745 " --> pdb=" O ILE B 752 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 642 through 644 Processing sheet with id=AA8, first strand: chain 'C' and resid 745 through 747 removed outlier: 4.002A pdb=" N ALA C 745 " --> pdb=" O ILE C 752 " (cutoff:3.500A) 1165 hydrogen bonds defined for protein. 3411 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: 6.33 Time building geometry restraints manager: 5.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3060 1.30 - 1.43: 5286 1.43 - 1.56: 11863 1.56 - 1.69: 235 1.69 - 1.81: 276 Bond restraints: 20720 Sorted by residual: bond pdb=" O2 LBN B1205 " pdb=" P1 LBN B1205 " ideal model delta sigma weight residual 1.650 1.770 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" O2 LBN A1205 " pdb=" P1 LBN A1205 " ideal model delta sigma weight residual 1.650 1.770 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" O2 LBN D1304 " pdb=" P1 LBN D1304 " ideal model delta sigma weight residual 1.650 1.770 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" O2 LBN C1206 " pdb=" P1 LBN C1206 " ideal model delta sigma weight residual 1.650 1.770 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" O2 LBN A1206 " pdb=" P1 LBN A1206 " ideal model delta sigma weight residual 1.650 1.767 -0.117 2.00e-02 2.50e+03 3.42e+01 ... (remaining 20715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 26984 3.19 - 6.37: 796 6.37 - 9.56: 112 9.56 - 12.75: 36 12.75 - 15.94: 16 Bond angle restraints: 27944 Sorted by residual: angle pdb=" N ILE D 611 " pdb=" CA ILE D 611 " pdb=" C ILE D 611 " ideal model delta sigma weight residual 107.73 123.67 -15.94 1.56e+00 4.11e-01 1.04e+02 angle pdb=" N ILE B 611 " pdb=" CA ILE B 611 " pdb=" C ILE B 611 " ideal model delta sigma weight residual 107.73 123.67 -15.94 1.56e+00 4.11e-01 1.04e+02 angle pdb=" N ILE A 611 " pdb=" CA ILE A 611 " pdb=" C ILE A 611 " ideal model delta sigma weight residual 107.73 123.66 -15.93 1.56e+00 4.11e-01 1.04e+02 angle pdb=" N ILE C 611 " pdb=" CA ILE C 611 " pdb=" C ILE C 611 " ideal model delta sigma weight residual 107.73 123.66 -15.93 1.56e+00 4.11e-01 1.04e+02 angle pdb=" C ILE B 611 " pdb=" CA ILE B 611 " pdb=" CB ILE B 611 " ideal model delta sigma weight residual 111.25 103.78 7.47 1.27e+00 6.20e-01 3.46e+01 ... (remaining 27939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 12268 35.43 - 70.86: 336 70.86 - 106.29: 56 106.29 - 141.72: 20 141.72 - 177.15: 12 Dihedral angle restraints: 12692 sinusoidal: 5472 harmonic: 7220 Sorted by residual: dihedral pdb=" C1 LBN A1206 " pdb=" O1 LBN A1206 " pdb=" P1 LBN A1206 " pdb=" O3 LBN A1206 " ideal model delta sinusoidal sigma weight residual 275.40 98.25 177.15 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 LBN C1207 " pdb=" O1 LBN C1207 " pdb=" P1 LBN C1207 " pdb=" O3 LBN C1207 " ideal model delta sinusoidal sigma weight residual 275.40 98.27 177.13 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 LBN D1305 " pdb=" O1 LBN D1305 " pdb=" P1 LBN D1305 " pdb=" O3 LBN D1305 " ideal model delta sinusoidal sigma weight residual 275.40 98.28 177.12 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 3180 0.182 - 0.364: 8 0.364 - 0.546: 8 0.546 - 0.728: 12 0.728 - 0.910: 4 Chirality restraints: 3212 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.23e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.16e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.15e+01 ... (remaining 3209 not shown) Planarity restraints: 3368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 JT0 C1205 " 0.148 2.00e-02 2.50e+03 6.51e-01 6.36e+03 pdb=" C04 JT0 C1205 " -0.641 2.00e-02 2.50e+03 pdb=" C09 JT0 C1205 " 0.471 2.00e-02 2.50e+03 pdb=" C22 JT0 C1205 " -1.000 2.00e-02 2.50e+03 pdb=" N03 JT0 C1205 " 0.081 2.00e-02 2.50e+03 pdb=" O01 JT0 C1205 " 0.940 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 JT0 D1303 " 0.148 2.00e-02 2.50e+03 6.51e-01 6.36e+03 pdb=" C04 JT0 D1303 " -0.641 2.00e-02 2.50e+03 pdb=" C09 JT0 D1303 " 0.472 2.00e-02 2.50e+03 pdb=" C22 JT0 D1303 " -1.000 2.00e-02 2.50e+03 pdb=" N03 JT0 D1303 " 0.081 2.00e-02 2.50e+03 pdb=" O01 JT0 D1303 " 0.940 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 JT0 B1204 " 0.148 2.00e-02 2.50e+03 6.51e-01 6.36e+03 pdb=" C04 JT0 B1204 " -0.642 2.00e-02 2.50e+03 pdb=" C09 JT0 B1204 " 0.472 2.00e-02 2.50e+03 pdb=" C22 JT0 B1204 " -0.999 2.00e-02 2.50e+03 pdb=" N03 JT0 B1204 " 0.081 2.00e-02 2.50e+03 pdb=" O01 JT0 B1204 " 0.939 2.00e-02 2.50e+03 ... (remaining 3365 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3044 2.76 - 3.29: 18154 3.29 - 3.83: 31360 3.83 - 4.36: 36391 4.36 - 4.90: 62978 Nonbonded interactions: 151927 Sorted by model distance: nonbonded pdb=" OD1 ASN B 747 " pdb=" N SER B 748 " model vdw 2.222 3.120 nonbonded pdb=" OD1 ASN D 747 " pdb=" N SER D 748 " model vdw 2.222 3.120 nonbonded pdb=" OD1 ASN A 747 " pdb=" N SER A 748 " model vdw 2.222 3.120 nonbonded pdb=" OD1 ASN C 747 " pdb=" N SER C 748 " model vdw 2.223 3.120 nonbonded pdb=" O ILE A 810 " pdb=" OG1 THR A 814 " model vdw 2.301 3.040 ... (remaining 151922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 446 through 1079 or (resid 1208 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name O17 or name O18 or name O22 \ or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)))) selection = (chain 'B' and (resid 446 through 1079 or resid 1208)) selection = (chain 'C' and (resid 446 through 1079 or (resid 1208 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name O17 or name O18 or name O22 \ or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)))) selection = (chain 'D' and (resid 446 through 1079 or (resid 1308 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name O17 or name O18 or name O22 \ or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 49.310 Find NCS groups from input model: 1.360 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:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 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 : 0.012 0.339 20732 Z= 0.583 Angle : 1.300 15.937 27968 Z= 0.578 Chirality : 0.079 0.910 3212 Planarity : 0.026 0.651 3364 Dihedral : 18.204 177.148 7996 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.58 % Allowed : 4.09 % Favored : 95.33 % 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: -2.93 (0.14), residues: 2416 helix: -2.04 (0.10), residues: 1732 sheet: 0.83 (0.76), residues: 68 loop : -1.27 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP C 515 HIS 0.011 0.002 HIS A 585 PHE 0.027 0.003 PHE C 783 TYR 0.034 0.003 TYR B 785 ARG 0.015 0.001 ARG C 919 Details of bonding type rmsd link_NAG-ASN : bond 0.33856 ( 4) link_NAG-ASN : angle 8.64155 ( 12) link_BETA1-4 : bond 0.00095 ( 4) link_BETA1-4 : angle 0.22966 ( 12) hydrogen bonds : bond 0.15245 ( 1165) hydrogen bonds : angle 5.35433 ( 3411) covalent geometry : bond 0.01134 (20720) covalent geometry : angle 1.28845 (27944) Misc. bond : bond 0.00116 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 602 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 483 MET cc_start: 0.7988 (mtt) cc_final: 0.7435 (mtm) REVERT: D 558 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7080 (mm-30) REVERT: D 591 LYS cc_start: 0.8962 (mttt) cc_final: 0.8639 (mtmm) REVERT: D 669 PHE cc_start: 0.7510 (m-80) cc_final: 0.7210 (m-80) REVERT: D 717 ARG cc_start: 0.6931 (ttt180) cc_final: 0.6367 (ttt90) REVERT: D 721 MET cc_start: 0.7408 (ttm) cc_final: 0.6878 (mmp) REVERT: D 768 TYR cc_start: 0.7736 (t80) cc_final: 0.7454 (t80) REVERT: D 864 GLU cc_start: 0.7202 (tt0) cc_final: 0.6812 (tt0) REVERT: D 920 GLU cc_start: 0.8021 (tt0) cc_final: 0.7650 (mp0) REVERT: D 924 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7370 (mt-10) REVERT: D 928 ARG cc_start: 0.7927 (mtm180) cc_final: 0.7721 (mtm-85) REVERT: D 963 ASP cc_start: 0.7393 (m-30) cc_final: 0.7112 (m-30) REVERT: D 969 LYS cc_start: 0.7667 (tttt) cc_final: 0.7318 (ttpp) REVERT: D 981 GLU cc_start: 0.7512 (tp30) cc_final: 0.7173 (tp30) REVERT: D 1049 TYR cc_start: 0.8094 (m-10) cc_final: 0.7862 (m-10) REVERT: A 483 MET cc_start: 0.8211 (mtt) cc_final: 0.7670 (mtm) REVERT: A 523 MET cc_start: 0.8180 (tpt) cc_final: 0.7924 (tpt) REVERT: A 558 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7460 (mm-30) REVERT: A 562 LYS cc_start: 0.7755 (mttt) cc_final: 0.7533 (mptp) REVERT: A 579 GLN cc_start: 0.8400 (mt0) cc_final: 0.8195 (mm-40) REVERT: A 591 LYS cc_start: 0.8986 (mttt) cc_final: 0.8701 (mtmm) REVERT: A 657 GLU cc_start: 0.7138 (tt0) cc_final: 0.6866 (tm-30) REVERT: A 669 PHE cc_start: 0.7609 (m-80) cc_final: 0.7290 (m-80) REVERT: A 705 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7155 (mm-30) REVERT: A 717 ARG cc_start: 0.6691 (ttt180) cc_final: 0.6120 (ttt90) REVERT: A 720 MET cc_start: 0.6859 (mmm) cc_final: 0.6626 (mmm) REVERT: A 721 MET cc_start: 0.7208 (ttm) cc_final: 0.6760 (mmp) REVERT: A 768 TYR cc_start: 0.7747 (t80) cc_final: 0.7424 (t80) REVERT: A 825 GLU cc_start: 0.8246 (tt0) cc_final: 0.7991 (tm-30) REVERT: A 852 ARG cc_start: 0.7669 (mtt90) cc_final: 0.7456 (mmt90) REVERT: A 864 GLU cc_start: 0.7065 (tt0) cc_final: 0.6701 (tt0) REVERT: A 920 GLU cc_start: 0.8278 (tt0) cc_final: 0.7464 (mp0) REVERT: A 924 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7772 (mt-10) REVERT: A 928 ARG cc_start: 0.8072 (mtm180) cc_final: 0.7853 (mtm-85) REVERT: A 981 GLU cc_start: 0.7438 (tp30) cc_final: 0.7113 (tp30) REVERT: A 1042 MET cc_start: 0.7190 (ppp) cc_final: 0.6736 (mmp) REVERT: A 1049 TYR cc_start: 0.8057 (m-10) cc_final: 0.7843 (m-10) REVERT: A 1050 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.7319 (ttm110) REVERT: B 483 MET cc_start: 0.8033 (mtt) cc_final: 0.7497 (mtm) REVERT: B 523 MET cc_start: 0.7845 (tpt) cc_final: 0.7581 (tpt) REVERT: B 558 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7066 (mm-30) REVERT: B 562 LYS cc_start: 0.7720 (mttt) cc_final: 0.7512 (mptp) REVERT: B 591 LYS cc_start: 0.8970 (mttt) cc_final: 0.8683 (mtmm) REVERT: B 603 LYS cc_start: 0.8817 (mttt) cc_final: 0.8592 (mtpt) REVERT: B 657 GLU cc_start: 0.7116 (tt0) cc_final: 0.6841 (tm-30) REVERT: B 669 PHE cc_start: 0.7651 (m-80) cc_final: 0.7225 (m-80) REVERT: B 689 MET cc_start: 0.7853 (mtm) cc_final: 0.7648 (mtp) REVERT: B 705 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6940 (mm-30) REVERT: B 717 ARG cc_start: 0.6742 (ttt180) cc_final: 0.6213 (ttt90) REVERT: B 720 MET cc_start: 0.6809 (mmm) cc_final: 0.6550 (mmm) REVERT: B 721 MET cc_start: 0.7262 (ttm) cc_final: 0.6729 (mmp) REVERT: B 768 TYR cc_start: 0.7864 (t80) cc_final: 0.7540 (t80) REVERT: B 825 GLU cc_start: 0.8299 (tt0) cc_final: 0.8050 (tm-30) REVERT: B 864 GLU cc_start: 0.7171 (tt0) cc_final: 0.6791 (tt0) REVERT: B 920 GLU cc_start: 0.8171 (tt0) cc_final: 0.7661 (mp0) REVERT: B 924 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7468 (mt-10) REVERT: B 963 ASP cc_start: 0.7550 (m-30) cc_final: 0.7282 (m-30) REVERT: B 969 LYS cc_start: 0.7734 (tttt) cc_final: 0.7385 (ttpp) REVERT: B 981 GLU cc_start: 0.7420 (tp30) cc_final: 0.7096 (tp30) REVERT: B 1049 TYR cc_start: 0.8148 (m-10) cc_final: 0.7869 (m-10) REVERT: B 1050 ARG cc_start: 0.7487 (ttm-80) cc_final: 0.7234 (ttm110) REVERT: C 562 LYS cc_start: 0.8349 (mttt) cc_final: 0.8093 (mptp) REVERT: C 571 ASN cc_start: 0.8525 (m110) cc_final: 0.8290 (m-40) REVERT: C 591 LYS cc_start: 0.8983 (mttt) cc_final: 0.8739 (mttm) REVERT: C 594 GLU cc_start: 0.7774 (tp30) cc_final: 0.7313 (tp30) REVERT: C 630 LEU cc_start: 0.8077 (mt) cc_final: 0.7823 (mt) REVERT: C 635 LYS cc_start: 0.7137 (tttt) cc_final: 0.6776 (tptm) REVERT: C 699 ASN cc_start: 0.8293 (m-40) cc_final: 0.8009 (m-40) REVERT: C 704 LYS cc_start: 0.7073 (mttt) cc_final: 0.6801 (mtpp) REVERT: C 719 HIS cc_start: 0.6772 (t-90) cc_final: 0.6550 (t70) REVERT: C 720 MET cc_start: 0.7096 (mmm) cc_final: 0.6677 (mmm) REVERT: C 768 TYR cc_start: 0.8179 (t80) cc_final: 0.7900 (t80) REVERT: C 825 GLU cc_start: 0.7973 (tt0) cc_final: 0.7601 (tm-30) REVERT: C 852 ARG cc_start: 0.7544 (mtt90) cc_final: 0.7240 (mmt90) REVERT: C 864 GLU cc_start: 0.7215 (tt0) cc_final: 0.7000 (tt0) REVERT: C 900 SER cc_start: 0.8421 (m) cc_final: 0.8082 (t) REVERT: C 969 LYS cc_start: 0.7641 (tttt) cc_final: 0.7264 (ttpp) REVERT: C 1050 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.6905 (ttp-110) REVERT: C 1073 GLU cc_start: 0.7748 (tt0) cc_final: 0.7547 (tt0) outliers start: 12 outliers final: 3 residues processed: 610 average time/residue: 1.3610 time to fit residues: 934.0342 Evaluate side-chains 312 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 309 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain B residue 465 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 8.9990 chunk 184 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 191 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 221 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 451 HIS D 512 HIS D 519 HIS D 549 ASN D 644 HIS D 700 HIS D 719 HIS D 805 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A 460 ASN A 512 HIS A 519 HIS A 549 ASN A 644 HIS A 700 HIS A 719 HIS A 805 ASN A 851 GLN A 970 HIS B 451 HIS B 512 HIS B 519 HIS B 549 ASN B 644 HIS B 700 HIS B 719 HIS B 805 ASN B 851 GLN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 460 ASN C 463 GLN C 512 HIS C 519 HIS C 570 HIS C 577 ASN C 644 HIS C 700 HIS C 719 HIS C 739 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.143317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.101766 restraints weight = 25260.274| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.21 r_work: 0.2976 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20732 Z= 0.150 Angle : 0.665 12.832 27968 Z= 0.318 Chirality : 0.042 0.159 3212 Planarity : 0.005 0.064 3364 Dihedral : 19.709 156.020 3530 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.94 % Allowed : 12.35 % Favored : 83.71 % 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: -0.37 (0.17), residues: 2416 helix: -0.07 (0.12), residues: 1720 sheet: 1.42 (0.73), residues: 68 loop : -0.52 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 515 HIS 0.007 0.001 HIS D 585 PHE 0.011 0.001 PHE C 823 TYR 0.016 0.001 TYR A 785 ARG 0.007 0.001 ARG C 601 Details of bonding type rmsd link_NAG-ASN : bond 0.01017 ( 4) link_NAG-ASN : angle 7.78722 ( 12) link_BETA1-4 : bond 0.02058 ( 4) link_BETA1-4 : angle 1.93535 ( 12) hydrogen bonds : bond 0.06253 ( 1165) hydrogen bonds : angle 3.90052 ( 3411) covalent geometry : bond 0.00324 (20720) covalent geometry : angle 0.64436 (27944) Misc. bond : bond 0.00946 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 320 time to evaluate : 2.405 Fit side-chains revert: symmetry clash REVERT: D 483 MET cc_start: 0.8623 (mtt) cc_final: 0.8313 (mtm) REVERT: D 547 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7911 (t0) REVERT: D 669 PHE cc_start: 0.7855 (m-80) cc_final: 0.7355 (m-80) REVERT: D 717 ARG cc_start: 0.7846 (ttt180) cc_final: 0.7421 (ttt90) REVERT: D 721 MET cc_start: 0.8430 (ttm) cc_final: 0.7995 (mmp) REVERT: D 768 TYR cc_start: 0.8038 (t80) cc_final: 0.7757 (t80) REVERT: D 920 GLU cc_start: 0.8921 (tt0) cc_final: 0.8548 (mp0) REVERT: D 966 GLU cc_start: 0.8425 (tt0) cc_final: 0.8099 (mm-30) REVERT: D 981 GLU cc_start: 0.8336 (tp30) cc_final: 0.8072 (tp30) REVERT: A 669 PHE cc_start: 0.8040 (m-80) cc_final: 0.7613 (m-80) REVERT: A 696 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8335 (pm20) REVERT: A 717 ARG cc_start: 0.7789 (ttt180) cc_final: 0.7382 (ttt90) REVERT: A 720 MET cc_start: 0.7978 (mmm) cc_final: 0.7744 (mmm) REVERT: A 721 MET cc_start: 0.8331 (ttm) cc_final: 0.7844 (mmp) REVERT: A 768 TYR cc_start: 0.8093 (t80) cc_final: 0.7877 (t80) REVERT: A 808 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8251 (mp0) REVERT: A 920 GLU cc_start: 0.9093 (tt0) cc_final: 0.8595 (mp0) REVERT: A 981 GLU cc_start: 0.8344 (tp30) cc_final: 0.8075 (tp30) REVERT: A 1050 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.7802 (ttp-110) REVERT: A 1063 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: A 1067 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8607 (tp) REVERT: B 483 MET cc_start: 0.8686 (mtt) cc_final: 0.8350 (mtm) REVERT: B 547 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7936 (t0) REVERT: B 669 PHE cc_start: 0.7932 (m-80) cc_final: 0.7452 (m-80) REVERT: B 717 ARG cc_start: 0.7831 (ttt180) cc_final: 0.7428 (ttt90) REVERT: B 720 MET cc_start: 0.7957 (mmm) cc_final: 0.7711 (mmm) REVERT: B 721 MET cc_start: 0.8366 (ttm) cc_final: 0.7808 (mmp) REVERT: B 768 TYR cc_start: 0.8181 (t80) cc_final: 0.7940 (t80) REVERT: B 920 GLU cc_start: 0.8967 (tt0) cc_final: 0.8557 (mp0) REVERT: B 966 GLU cc_start: 0.8406 (tt0) cc_final: 0.8077 (mm-30) REVERT: B 969 LYS cc_start: 0.8090 (tttt) cc_final: 0.7727 (ttpp) REVERT: B 981 GLU cc_start: 0.8353 (tp30) cc_final: 0.8081 (tp30) REVERT: B 1049 TYR cc_start: 0.8487 (m-10) cc_final: 0.8271 (m-10) REVERT: B 1050 ARG cc_start: 0.8100 (ttm-80) cc_final: 0.7868 (ttm110) REVERT: B 1067 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8724 (tp) REVERT: C 530 MET cc_start: 0.8492 (ttp) cc_final: 0.8220 (mtp) REVERT: C 544 LEU cc_start: 0.8862 (mt) cc_final: 0.8390 (mm) REVERT: C 594 GLU cc_start: 0.8421 (tp30) cc_final: 0.7990 (tp30) REVERT: C 704 LYS cc_start: 0.8078 (mttt) cc_final: 0.7806 (mttp) REVERT: C 719 HIS cc_start: 0.7792 (t70) cc_final: 0.7524 (t70) REVERT: C 768 TYR cc_start: 0.8392 (t80) cc_final: 0.8183 (t80) REVERT: C 825 GLU cc_start: 0.8392 (tt0) cc_final: 0.8167 (tm-30) REVERT: C 920 GLU cc_start: 0.8914 (tt0) cc_final: 0.8569 (mp0) REVERT: C 974 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8202 (tmtt) REVERT: C 981 GLU cc_start: 0.8264 (tp30) cc_final: 0.7840 (tm-30) REVERT: C 1000 GLN cc_start: 0.8623 (mt0) cc_final: 0.8237 (mm110) outliers start: 81 outliers final: 28 residues processed: 383 average time/residue: 1.4533 time to fit residues: 624.4558 Evaluate side-chains 290 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 255 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 606 ASP Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 873 SER Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 787 LYS Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 974 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 113 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 chunk 178 optimal weight: 9.9990 chunk 45 optimal weight: 0.1980 chunk 91 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 chunk 55 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 691 GLN D 983 HIS ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 HIS B 855 ASN B 983 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 577 ASN C 805 ASN C 970 HIS C 983 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.144060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.102849 restraints weight = 24978.603| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.18 r_work: 0.3011 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20732 Z= 0.116 Angle : 0.538 7.758 27968 Z= 0.268 Chirality : 0.039 0.166 3212 Planarity : 0.004 0.063 3364 Dihedral : 17.797 165.214 3524 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.04 % Allowed : 14.11 % Favored : 81.86 % 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: 0.85 (0.17), residues: 2416 helix: 0.94 (0.12), residues: 1704 sheet: 2.78 (0.85), residues: 48 loop : -0.40 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 515 HIS 0.004 0.001 HIS D 585 PHE 0.010 0.001 PHE C 823 TYR 0.013 0.001 TYR A 785 ARG 0.006 0.001 ARG C 601 Details of bonding type rmsd link_NAG-ASN : bond 0.00895 ( 4) link_NAG-ASN : angle 4.95033 ( 12) link_BETA1-4 : bond 0.00996 ( 4) link_BETA1-4 : angle 1.40959 ( 12) hydrogen bonds : bond 0.04958 ( 1165) hydrogen bonds : angle 3.55631 ( 3411) covalent geometry : bond 0.00242 (20720) covalent geometry : angle 0.52749 (27944) Misc. bond : bond 0.00361 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 300 time to evaluate : 3.261 Fit side-chains revert: symmetry clash REVERT: D 483 MET cc_start: 0.8531 (mtt) cc_final: 0.8305 (mtp) REVERT: D 547 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7936 (t0) REVERT: D 669 PHE cc_start: 0.7990 (m-80) cc_final: 0.7512 (m-80) REVERT: D 717 ARG cc_start: 0.7870 (ttt180) cc_final: 0.7448 (ttt90) REVERT: D 721 MET cc_start: 0.8353 (ttm) cc_final: 0.7856 (mmp) REVERT: D 768 TYR cc_start: 0.7881 (t80) cc_final: 0.7609 (t80) REVERT: D 822 LEU cc_start: 0.7765 (pt) cc_final: 0.7507 (pp) REVERT: D 920 GLU cc_start: 0.8853 (tt0) cc_final: 0.8447 (mp0) REVERT: D 941 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8279 (tp) REVERT: D 966 GLU cc_start: 0.8295 (tt0) cc_final: 0.7991 (mm-30) REVERT: D 981 GLU cc_start: 0.8278 (tp30) cc_final: 0.7982 (tp30) REVERT: A 544 LEU cc_start: 0.8939 (mt) cc_final: 0.8714 (mm) REVERT: A 669 PHE cc_start: 0.7890 (m-80) cc_final: 0.7427 (m-80) REVERT: A 717 ARG cc_start: 0.7765 (ttt180) cc_final: 0.7346 (ttt90) REVERT: A 720 MET cc_start: 0.7887 (mmm) cc_final: 0.7684 (mmm) REVERT: A 721 MET cc_start: 0.8262 (ttm) cc_final: 0.7834 (mmp) REVERT: A 768 TYR cc_start: 0.7957 (t80) cc_final: 0.7752 (t80) REVERT: A 808 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8280 (mp0) REVERT: A 920 GLU cc_start: 0.9012 (tt0) cc_final: 0.8540 (mp0) REVERT: A 941 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8413 (tp) REVERT: A 981 GLU cc_start: 0.8273 (tp30) cc_final: 0.8001 (tp30) REVERT: B 523 MET cc_start: 0.8757 (tpt) cc_final: 0.8547 (tpt) REVERT: B 544 LEU cc_start: 0.8885 (mt) cc_final: 0.8621 (mm) REVERT: B 547 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7903 (t0) REVERT: B 669 PHE cc_start: 0.8009 (m-80) cc_final: 0.7484 (m-80) REVERT: B 717 ARG cc_start: 0.7803 (ttt180) cc_final: 0.7373 (ttt90) REVERT: B 720 MET cc_start: 0.7953 (mmm) cc_final: 0.7731 (mmm) REVERT: B 721 MET cc_start: 0.8277 (ttm) cc_final: 0.7761 (mmp) REVERT: B 768 TYR cc_start: 0.8048 (t80) cc_final: 0.7826 (t80) REVERT: B 864 GLU cc_start: 0.8423 (tt0) cc_final: 0.8215 (tt0) REVERT: B 920 GLU cc_start: 0.8892 (tt0) cc_final: 0.8458 (mp0) REVERT: B 941 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8324 (tp) REVERT: B 966 GLU cc_start: 0.8285 (tt0) cc_final: 0.8055 (mm-30) REVERT: B 981 GLU cc_start: 0.8236 (tp30) cc_final: 0.7965 (tp30) REVERT: C 500 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7731 (tp) REVERT: C 530 MET cc_start: 0.8539 (ttp) cc_final: 0.8318 (mtp) REVERT: C 544 LEU cc_start: 0.8763 (mt) cc_final: 0.8413 (mm) REVERT: C 604 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.5825 (mtm-85) REVERT: C 704 LYS cc_start: 0.8096 (mttt) cc_final: 0.7820 (mttp) REVERT: C 768 TYR cc_start: 0.8360 (t80) cc_final: 0.8150 (t80) REVERT: C 825 GLU cc_start: 0.8472 (tt0) cc_final: 0.8249 (tm-30) REVERT: C 881 LEU cc_start: 0.8668 (tt) cc_final: 0.8253 (tp) REVERT: C 920 GLU cc_start: 0.8852 (tt0) cc_final: 0.8497 (mp0) REVERT: C 941 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8029 (tp) REVERT: C 966 GLU cc_start: 0.8406 (tp30) cc_final: 0.8205 (mm-30) REVERT: C 969 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7669 (ttpp) REVERT: C 1067 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8381 (tp) outliers start: 83 outliers final: 26 residues processed: 364 average time/residue: 1.5594 time to fit residues: 646.5814 Evaluate side-chains 297 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 261 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 855 ASN Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 855 ASN Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 787 LYS Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 1067 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 chunk 128 optimal weight: 0.0370 chunk 108 optimal weight: 0.6980 chunk 173 optimal weight: 0.4980 chunk 176 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 691 GLN D 907 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN B 970 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN C 907 GLN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.143775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.102155 restraints weight = 25236.114| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.21 r_work: 0.2995 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20732 Z= 0.106 Angle : 0.506 7.221 27968 Z= 0.254 Chirality : 0.039 0.203 3212 Planarity : 0.004 0.061 3364 Dihedral : 17.066 169.767 3524 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.65 % Allowed : 15.71 % Favored : 80.64 % 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: 1.41 (0.17), residues: 2416 helix: 1.35 (0.13), residues: 1712 sheet: 2.92 (0.86), residues: 48 loop : -0.19 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 832 HIS 0.004 0.001 HIS D 585 PHE 0.008 0.001 PHE C 746 TYR 0.010 0.001 TYR B 785 ARG 0.004 0.000 ARG C 601 Details of bonding type rmsd link_NAG-ASN : bond 0.00718 ( 4) link_NAG-ASN : angle 4.17898 ( 12) link_BETA1-4 : bond 0.00876 ( 4) link_BETA1-4 : angle 1.25450 ( 12) hydrogen bonds : bond 0.04627 ( 1165) hydrogen bonds : angle 3.44365 ( 3411) covalent geometry : bond 0.00215 (20720) covalent geometry : angle 0.49814 (27944) Misc. bond : bond 0.00016 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 271 time to evaluate : 2.267 Fit side-chains revert: symmetry clash REVERT: D 547 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7926 (t0) REVERT: D 669 PHE cc_start: 0.8023 (m-80) cc_final: 0.7522 (m-80) REVERT: D 717 ARG cc_start: 0.7875 (ttt180) cc_final: 0.7387 (ttt90) REVERT: D 721 MET cc_start: 0.8374 (ttm) cc_final: 0.7808 (mmp) REVERT: D 768 TYR cc_start: 0.7897 (t80) cc_final: 0.7574 (t80) REVERT: D 920 GLU cc_start: 0.8849 (tt0) cc_final: 0.8446 (mp0) REVERT: D 941 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8280 (tp) REVERT: D 966 GLU cc_start: 0.8307 (tt0) cc_final: 0.8003 (mm-30) REVERT: D 981 GLU cc_start: 0.8281 (tp30) cc_final: 0.7996 (tp30) REVERT: A 483 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8451 (mtm) REVERT: A 544 LEU cc_start: 0.8941 (mt) cc_final: 0.8717 (mm) REVERT: A 669 PHE cc_start: 0.7834 (m-80) cc_final: 0.7363 (m-80) REVERT: A 717 ARG cc_start: 0.7771 (ttt180) cc_final: 0.7367 (ttt90) REVERT: A 721 MET cc_start: 0.8329 (ttm) cc_final: 0.7852 (mmp) REVERT: A 768 TYR cc_start: 0.7932 (t80) cc_final: 0.7715 (t80) REVERT: A 920 GLU cc_start: 0.8983 (tt0) cc_final: 0.8548 (mp0) REVERT: A 941 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8432 (tp) REVERT: A 981 GLU cc_start: 0.8259 (tp30) cc_final: 0.7987 (tp30) REVERT: A 1067 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8416 (tp) REVERT: B 483 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8433 (mtp) REVERT: B 544 LEU cc_start: 0.8892 (mt) cc_final: 0.8610 (mm) REVERT: B 547 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7921 (t0) REVERT: B 669 PHE cc_start: 0.7893 (m-80) cc_final: 0.7329 (m-80) REVERT: B 717 ARG cc_start: 0.7780 (ttt180) cc_final: 0.7364 (ttt90) REVERT: B 721 MET cc_start: 0.8377 (ttm) cc_final: 0.7802 (mmp) REVERT: B 768 TYR cc_start: 0.8012 (t80) cc_final: 0.7790 (t80) REVERT: B 864 GLU cc_start: 0.8500 (tt0) cc_final: 0.8298 (tt0) REVERT: B 920 GLU cc_start: 0.8865 (tt0) cc_final: 0.8468 (mp0) REVERT: B 941 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8320 (tp) REVERT: B 966 GLU cc_start: 0.8254 (tt0) cc_final: 0.7980 (mm-30) REVERT: B 981 GLU cc_start: 0.8261 (tp30) cc_final: 0.7986 (tp30) REVERT: B 1067 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8484 (tp) REVERT: C 500 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7782 (tp) REVERT: C 544 LEU cc_start: 0.8771 (mt) cc_final: 0.8406 (mm) REVERT: C 604 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.5897 (mtm-85) REVERT: C 704 LYS cc_start: 0.7993 (mttt) cc_final: 0.7698 (mttp) REVERT: C 768 TYR cc_start: 0.8366 (t80) cc_final: 0.8139 (t80) REVERT: C 808 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8155 (mp0) REVERT: C 825 GLU cc_start: 0.8474 (tt0) cc_final: 0.8250 (tm-30) REVERT: C 881 LEU cc_start: 0.8693 (tt) cc_final: 0.8243 (tp) REVERT: C 920 GLU cc_start: 0.8817 (tt0) cc_final: 0.8467 (mp0) REVERT: C 941 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8048 (tp) REVERT: C 981 GLU cc_start: 0.8331 (tp30) cc_final: 0.7778 (tm-30) REVERT: C 1067 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8384 (tp) outliers start: 75 outliers final: 29 residues processed: 322 average time/residue: 1.2958 time to fit residues: 473.0031 Evaluate side-chains 298 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 256 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 912 MET Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 825 GLU Chi-restraints excluded: chain B residue 912 MET Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 787 LYS Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1067 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 120 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 234 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 119 optimal weight: 0.6980 chunk 219 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 460 ASN D 691 GLN D 855 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN A 907 GLN B 460 ASN C 549 ASN C 719 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.095932 restraints weight = 24965.201| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.51 r_work: 0.2849 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20732 Z= 0.141 Angle : 0.550 7.001 27968 Z= 0.274 Chirality : 0.040 0.156 3212 Planarity : 0.004 0.061 3364 Dihedral : 16.195 171.156 3524 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.62 % Allowed : 15.76 % Favored : 79.62 % 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: 1.62 (0.17), residues: 2416 helix: 1.52 (0.13), residues: 1720 sheet: 3.01 (0.84), residues: 48 loop : -0.15 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 515 HIS 0.007 0.001 HIS C 494 PHE 0.013 0.001 PHE A 818 TYR 0.015 0.001 TYR B 785 ARG 0.004 0.001 ARG B 458 Details of bonding type rmsd link_NAG-ASN : bond 0.00459 ( 4) link_NAG-ASN : angle 3.82906 ( 12) link_BETA1-4 : bond 0.00671 ( 4) link_BETA1-4 : angle 1.00015 ( 12) hydrogen bonds : bond 0.05645 ( 1165) hydrogen bonds : angle 3.49376 ( 3411) covalent geometry : bond 0.00328 (20720) covalent geometry : angle 0.54392 (27944) Misc. bond : bond 0.00013 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 275 time to evaluate : 2.676 Fit side-chains revert: symmetry clash REVERT: D 544 LEU cc_start: 0.8965 (mt) cc_final: 0.8718 (mm) REVERT: D 547 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7952 (t0) REVERT: D 669 PHE cc_start: 0.8037 (m-80) cc_final: 0.7491 (m-80) REVERT: D 717 ARG cc_start: 0.7784 (ttt180) cc_final: 0.7371 (ttt90) REVERT: D 721 MET cc_start: 0.8285 (ttm) cc_final: 0.7723 (mmp) REVERT: D 768 TYR cc_start: 0.7842 (t80) cc_final: 0.7621 (t80) REVERT: D 920 GLU cc_start: 0.8704 (tt0) cc_final: 0.8414 (mp0) REVERT: D 941 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8274 (tp) REVERT: D 966 GLU cc_start: 0.8235 (tt0) cc_final: 0.7996 (mm-30) REVERT: D 981 GLU cc_start: 0.8116 (tp30) cc_final: 0.7845 (tp30) REVERT: A 523 MET cc_start: 0.8895 (tpt) cc_final: 0.8691 (tpt) REVERT: A 544 LEU cc_start: 0.8980 (mt) cc_final: 0.8741 (mm) REVERT: A 669 PHE cc_start: 0.7981 (m-80) cc_final: 0.7493 (m-80) REVERT: A 717 ARG cc_start: 0.7744 (ttt180) cc_final: 0.7320 (ttt90) REVERT: A 721 MET cc_start: 0.8233 (ttm) cc_final: 0.7670 (mmp) REVERT: A 723 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7981 (tp) REVERT: A 768 TYR cc_start: 0.7983 (t80) cc_final: 0.7766 (t80) REVERT: A 808 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8188 (mp0) REVERT: A 920 GLU cc_start: 0.8839 (tt0) cc_final: 0.8534 (mp0) REVERT: A 941 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8332 (tp) REVERT: A 981 GLU cc_start: 0.8129 (tp30) cc_final: 0.7872 (tp30) REVERT: A 1059 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8164 (mt-10) REVERT: A 1063 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: A 1067 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8595 (tp) REVERT: B 463 GLN cc_start: 0.8088 (mt0) cc_final: 0.7846 (mt0) REVERT: B 544 LEU cc_start: 0.9000 (mt) cc_final: 0.8722 (mm) REVERT: B 547 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7913 (t0) REVERT: B 669 PHE cc_start: 0.7934 (m-80) cc_final: 0.7329 (m-80) REVERT: B 717 ARG cc_start: 0.7788 (ttt180) cc_final: 0.7375 (ttt90) REVERT: B 721 MET cc_start: 0.8241 (ttm) cc_final: 0.7636 (mmp) REVERT: B 768 TYR cc_start: 0.7986 (t80) cc_final: 0.7773 (t80) REVERT: B 864 GLU cc_start: 0.8363 (tt0) cc_final: 0.8143 (tt0) REVERT: B 920 GLU cc_start: 0.8689 (tt0) cc_final: 0.8406 (mp0) REVERT: B 941 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8351 (tp) REVERT: B 966 GLU cc_start: 0.8236 (tt0) cc_final: 0.8028 (mm-30) REVERT: B 981 GLU cc_start: 0.8132 (tp30) cc_final: 0.7863 (tp30) REVERT: B 1067 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8657 (tp) REVERT: C 544 LEU cc_start: 0.8844 (mt) cc_final: 0.8483 (mm) REVERT: C 604 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.6044 (mtm-85) REVERT: C 606 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8101 (m-30) REVERT: C 768 TYR cc_start: 0.8271 (t80) cc_final: 0.8007 (t80) REVERT: C 808 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8061 (mp0) REVERT: C 825 GLU cc_start: 0.8405 (tt0) cc_final: 0.8191 (tm-30) REVERT: C 920 GLU cc_start: 0.8720 (tt0) cc_final: 0.8505 (mp0) REVERT: C 941 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8206 (tp) REVERT: C 981 GLU cc_start: 0.8341 (tp30) cc_final: 0.8047 (tp30) REVERT: C 1059 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8101 (mt-10) REVERT: C 1063 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: C 1067 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8569 (tp) outliers start: 95 outliers final: 35 residues processed: 342 average time/residue: 1.5173 time to fit residues: 594.7780 Evaluate side-chains 303 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 254 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 912 MET Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 825 GLU Chi-restraints excluded: chain B residue 912 MET Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 787 LYS Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 1063 GLU Chi-restraints excluded: chain C residue 1067 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 54 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 214 optimal weight: 0.1980 chunk 87 optimal weight: 0.8980 chunk 144 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 232 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 719 HIS D 855 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 HIS ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN B 719 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN C 719 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.142372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.097689 restraints weight = 24878.075| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.52 r_work: 0.2886 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20732 Z= 0.109 Angle : 0.499 7.020 27968 Z= 0.253 Chirality : 0.039 0.158 3212 Planarity : 0.004 0.060 3364 Dihedral : 15.755 176.110 3524 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.60 % Allowed : 17.17 % Favored : 79.23 % 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: 1.84 (0.18), residues: 2416 helix: 1.67 (0.13), residues: 1728 sheet: 3.03 (0.84), residues: 48 loop : -0.04 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 832 HIS 0.004 0.001 HIS D 585 PHE 0.007 0.001 PHE C 746 TYR 0.008 0.001 TYR B 785 ARG 0.004 0.000 ARG A 852 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 4) link_NAG-ASN : angle 3.04849 ( 12) link_BETA1-4 : bond 0.00759 ( 4) link_BETA1-4 : angle 0.94441 ( 12) hydrogen bonds : bond 0.04797 ( 1165) hydrogen bonds : angle 3.40163 ( 3411) covalent geometry : bond 0.00228 (20720) covalent geometry : angle 0.49466 (27944) Misc. bond : bond 0.00025 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 270 time to evaluate : 2.187 Fit side-chains REVERT: D 544 LEU cc_start: 0.8946 (mt) cc_final: 0.8691 (mm) REVERT: D 547 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7925 (t0) REVERT: D 669 PHE cc_start: 0.7913 (m-80) cc_final: 0.7298 (m-80) REVERT: D 717 ARG cc_start: 0.7734 (ttt180) cc_final: 0.7263 (ttt90) REVERT: D 721 MET cc_start: 0.8189 (ttm) cc_final: 0.7600 (mmp) REVERT: D 768 TYR cc_start: 0.7801 (t80) cc_final: 0.7574 (t80) REVERT: D 920 GLU cc_start: 0.8679 (tt0) cc_final: 0.8385 (mp0) REVERT: D 981 GLU cc_start: 0.8089 (tp30) cc_final: 0.7833 (tp30) REVERT: D 999 ASP cc_start: 0.8583 (t70) cc_final: 0.8110 (t0) REVERT: A 483 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8448 (mtp) REVERT: A 544 LEU cc_start: 0.8965 (mt) cc_final: 0.8722 (mm) REVERT: A 669 PHE cc_start: 0.7959 (m-80) cc_final: 0.7452 (m-80) REVERT: A 717 ARG cc_start: 0.7686 (ttt180) cc_final: 0.7265 (ttt90) REVERT: A 721 MET cc_start: 0.8203 (ttm) cc_final: 0.7692 (mmp) REVERT: A 723 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7980 (tp) REVERT: A 808 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8190 (mp0) REVERT: A 855 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8144 (p0) REVERT: A 920 GLU cc_start: 0.8790 (tt0) cc_final: 0.8496 (mp0) REVERT: A 981 GLU cc_start: 0.8105 (tp30) cc_final: 0.7859 (tp30) REVERT: A 1063 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: A 1067 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8535 (tp) REVERT: B 463 GLN cc_start: 0.8068 (mt0) cc_final: 0.7823 (mt0) REVERT: B 483 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8357 (mtm) REVERT: B 544 LEU cc_start: 0.8975 (mt) cc_final: 0.8700 (mm) REVERT: B 669 PHE cc_start: 0.7911 (m-80) cc_final: 0.7275 (m-80) REVERT: B 717 ARG cc_start: 0.7690 (ttt180) cc_final: 0.7285 (ttt90) REVERT: B 721 MET cc_start: 0.8186 (ttm) cc_final: 0.7589 (mmp) REVERT: B 864 GLU cc_start: 0.8289 (tt0) cc_final: 0.8067 (tt0) REVERT: B 920 GLU cc_start: 0.8664 (tt0) cc_final: 0.8380 (mp0) REVERT: B 966 GLU cc_start: 0.8204 (tt0) cc_final: 0.7999 (mm-30) REVERT: B 981 GLU cc_start: 0.8086 (tp30) cc_final: 0.7842 (tp30) REVERT: B 1067 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8549 (tp) REVERT: C 544 LEU cc_start: 0.8839 (mt) cc_final: 0.8466 (mm) REVERT: C 597 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8226 (mt) REVERT: C 604 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.6051 (mtm-85) REVERT: C 606 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: C 768 TYR cc_start: 0.8234 (t80) cc_final: 0.8006 (t80) REVERT: C 808 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7952 (mp0) REVERT: C 825 GLU cc_start: 0.8395 (tt0) cc_final: 0.8187 (tm-30) REVERT: C 920 GLU cc_start: 0.8706 (tt0) cc_final: 0.8480 (mp0) REVERT: C 941 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8233 (tp) REVERT: C 981 GLU cc_start: 0.8292 (tp30) cc_final: 0.8011 (tp30) REVERT: C 1059 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7982 (mt-10) REVERT: C 1063 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: C 1067 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8544 (tp) outliers start: 74 outliers final: 32 residues processed: 317 average time/residue: 1.2550 time to fit residues: 451.8929 Evaluate side-chains 304 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 258 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 825 GLU Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 1063 GLU Chi-restraints excluded: chain C residue 1067 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.5116 > 50: distance: 60 - 83: 22.364 distance: 70 - 109: 8.064 distance: 78 - 83: 20.203 distance: 79 - 117: 33.033 distance: 83 - 84: 30.908 distance: 84 - 85: 25.041 distance: 84 - 87: 22.210 distance: 85 - 86: 12.066 distance: 85 - 95: 26.616 distance: 86 - 125: 22.924 distance: 87 - 88: 23.806 distance: 88 - 89: 19.246 distance: 88 - 90: 16.298 distance: 89 - 91: 30.588 distance: 90 - 92: 13.076 distance: 91 - 93: 7.911 distance: 92 - 93: 23.108 distance: 93 - 94: 23.749 distance: 95 - 96: 22.974 distance: 96 - 97: 17.177 distance: 96 - 99: 22.294 distance: 97 - 98: 25.464 distance: 97 - 109: 20.166 distance: 99 - 100: 16.737 distance: 100 - 101: 24.956 distance: 100 - 102: 16.162 distance: 101 - 103: 10.017 distance: 102 - 104: 7.913 distance: 102 - 105: 5.855 distance: 104 - 106: 8.335 distance: 105 - 107: 10.754 distance: 106 - 108: 6.654 distance: 107 - 108: 3.788 distance: 109 - 110: 16.619 distance: 110 - 111: 20.522 distance: 110 - 113: 20.538 distance: 111 - 112: 31.163 distance: 111 - 117: 28.037 distance: 113 - 114: 45.644 distance: 114 - 115: 20.387 distance: 115 - 116: 4.718 distance: 117 - 118: 35.827 distance: 118 - 119: 18.783 distance: 118 - 121: 21.787 distance: 119 - 120: 54.489 distance: 119 - 125: 41.625 distance: 121 - 122: 41.940 distance: 122 - 123: 8.025 distance: 122 - 124: 44.191 distance: 125 - 126: 19.394 distance: 126 - 127: 42.425 distance: 126 - 129: 10.662 distance: 127 - 128: 36.626 distance: 127 - 136: 50.891 distance: 129 - 130: 37.129 distance: 130 - 131: 19.008 distance: 130 - 132: 8.899 distance: 131 - 133: 28.983 distance: 132 - 134: 9.120 distance: 133 - 135: 13.909 distance: 134 - 135: 30.021 distance: 136 - 137: 17.906 distance: 137 - 138: 14.322 distance: 137 - 140: 26.283 distance: 138 - 139: 26.686 distance: 138 - 144: 29.071 distance: 139 - 164: 26.628 distance: 140 - 141: 44.600 distance: 141 - 142: 22.721 distance: 141 - 143: 15.960 distance: 144 - 145: 19.243 distance: 145 - 146: 32.102 distance: 145 - 148: 21.607 distance: 146 - 147: 22.908 distance: 146 - 152: 8.020 distance: 148 - 149: 25.596 distance: 149 - 150: 10.980 distance: 149 - 151: 14.619 distance: 152 - 153: 22.918 distance: 153 - 154: 13.929 distance: 153 - 156: 20.808 distance: 154 - 155: 8.432 distance: 154 - 164: 5.632 distance: 156 - 157: 23.147 distance: 157 - 158: 9.465 distance: 158 - 160: 4.446 distance: 159 - 161: 6.193 distance: 160 - 162: 5.362 distance: 161 - 162: 5.288 distance: 162 - 163: 8.196 distance: 164 - 165: 6.640 distance: 165 - 166: 6.773 distance: 165 - 168: 11.544 distance: 166 - 167: 26.121 distance: 166 - 172: 26.462 distance: 167 - 192: 26.877 distance: 168 - 169: 12.766 distance: 169 - 170: 9.076 distance: 169 - 171: 13.029 distance: 172 - 173: 45.522 distance: 173 - 174: 13.009 distance: 173 - 176: 29.116 distance: 174 - 175: 28.264 distance: 174 - 181: 22.261 distance: 176 - 177: 43.526 distance: 177 - 178: 40.365 distance: 178 - 179: 12.810 distance: 178 - 180: 21.294 distance: 231 - 244: 3.007