Starting phenix.real_space_refine on Mon Aug 5 06:46:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3y_41016/08_2024/8t3y_41016.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3y_41016/08_2024/8t3y_41016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3y_41016/08_2024/8t3y_41016.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3y_41016/08_2024/8t3y_41016.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3y_41016/08_2024/8t3y_41016.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3y_41016/08_2024/8t3y_41016.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 292 5.49 5 S 32 5.16 5 C 7249 2.51 5 N 2425 2.21 5 O 2999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 133": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13001 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 543 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "L" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 543 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12166 SG CYS K 663 94.355 72.816 65.837 1.00139.73 S ATOM 12325 SG CYS K 683 93.142 74.641 62.690 1.00119.37 S ATOM 12345 SG CYS K 686 96.345 72.628 62.545 1.00125.56 S ATOM 12049 SG CYS K 648 85.738 81.611 66.914 1.00162.60 S ATOM 12069 SG CYS K 651 83.084 84.229 67.970 1.00163.36 S ATOM 12204 SG CYS K 668 82.674 80.608 68.908 1.00143.24 S ATOM 12227 SG CYS K 671 81.963 81.360 65.671 1.00136.31 S ATOM 12709 SG CYS L 663 91.116 70.796 85.897 1.00172.78 S ATOM 12868 SG CYS L 683 92.443 70.565 89.900 1.00186.18 S ATOM 12888 SG CYS L 686 89.213 70.114 89.733 1.00190.44 S ATOM 12592 SG CYS L 648 100.439 80.745 85.760 1.00189.02 S ATOM 12612 SG CYS L 651 103.664 82.864 85.645 1.00190.09 S ATOM 12747 SG CYS L 668 103.350 79.634 83.727 1.00189.67 S ATOM 12770 SG CYS L 671 103.665 79.459 87.442 1.00190.98 S Time building chain proxies: 8.09, per 1000 atoms: 0.62 Number of scatterers: 13001 At special positions: 0 Unit cell: (127.395, 115.425, 117.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 32 16.00 P 292 15.00 O 2999 8.00 N 2425 7.00 C 7249 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.86 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 801 " pdb="ZN ZN K 801 " - pdb=" ND1 HIS K 665 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 683 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 686 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 663 " pdb=" ZN K 802 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 668 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 671 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 651 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 648 " pdb=" ZN L 801 " pdb="ZN ZN L 801 " - pdb=" ND1 HIS L 665 " pdb="ZN ZN L 801 " - pdb=" SG CYS L 663 " pdb="ZN ZN L 801 " - pdb=" SG CYS L 683 " pdb="ZN ZN L 801 " - pdb=" SG CYS L 686 " pdb=" ZN L 802 " pdb="ZN ZN L 802 " - pdb=" SG CYS L 668 " pdb="ZN ZN L 802 " - pdb=" SG CYS L 648 " pdb="ZN ZN L 802 " - pdb=" SG CYS L 671 " pdb="ZN ZN L 802 " - pdb=" SG CYS L 651 " Number of angles added : 18 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1672 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 10 sheets defined 65.7% alpha, 3.4% beta 134 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 5.49 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.713A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.544A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.759A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.505A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.701A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.527A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.562A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 35 removed outlier: 3.665A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.585A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.866A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.604A pdb=" N LEU C 116 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.719A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.716A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 100 removed outlier: 3.689A pdb=" N ARG D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.647A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 removed outlier: 3.788A pdb=" N ILE E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.562A pdb=" N ALA E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER E 96 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN E 108 " --> pdb=" O PHE E 104 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.988A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.885A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.516A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.009A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL F 57 " --> pdb=" O GLU F 53 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE F 66 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 4.137A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.851A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 73 removed outlier: 3.978A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 85 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.873A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.686A pdb=" N VAL H 66 " --> pdb=" O MET H 62 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU H 80 " --> pdb=" O GLU H 76 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.858A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 123 removed outlier: 4.318A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 633 through 647 removed outlier: 3.758A pdb=" N LEU K 645 " --> pdb=" O ASN K 641 " (cutoff:3.500A) Processing helix chain 'K' and resid 668 through 677 removed outlier: 3.699A pdb=" N GLU K 674 " --> pdb=" O ASN K 670 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG K 675 " --> pdb=" O CYS K 671 " (cutoff:3.500A) Processing helix chain 'K' and resid 691 through 693 No H-bonds generated for 'chain 'K' and resid 691 through 693' Processing helix chain 'L' and resid 633 through 647 removed outlier: 4.039A pdb=" N GLU L 638 " --> pdb=" O ALA L 634 " (cutoff:3.500A) Processing helix chain 'L' and resid 669 through 678 removed outlier: 3.732A pdb=" N LYS L 673 " --> pdb=" O GLU L 669 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU L 674 " --> pdb=" O ASN L 670 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG L 675 " --> pdb=" O CYS L 671 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU L 676 " --> pdb=" O CYS L 672 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA L 678 " --> pdb=" O GLU L 674 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.587A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 7.073A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.521A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.715A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.852A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.561A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.455A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 666 through 667 Processing sheet with id=AB1, first strand: chain 'L' and resid 666 through 667 331 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 696 hydrogen bond angles 0 basepair planarities 134 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 4.26 Time building geometry restraints manager: 6.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1728 1.32 - 1.45: 5025 1.45 - 1.57: 6440 1.57 - 1.70: 582 1.70 - 1.82: 46 Bond restraints: 13821 Sorted by residual: bond pdb=" CA ARG A 53 " pdb=" C ARG A 53 " ideal model delta sigma weight residual 1.524 1.489 0.035 1.29e-02 6.01e+03 7.38e+00 bond pdb=" C TYR A 54 " pdb=" O TYR A 54 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.31e-02 5.83e+03 7.26e+00 bond pdb=" O3' DT J 140 " pdb=" P DT J 141 " ideal model delta sigma weight residual 1.607 1.644 -0.037 1.50e-02 4.44e+03 6.24e+00 bond pdb=" C ARG A 53 " pdb=" O ARG A 53 " ideal model delta sigma weight residual 1.236 1.207 0.029 1.19e-02 7.06e+03 5.92e+00 bond pdb=" C LYS H 120 " pdb=" O LYS H 120 " ideal model delta sigma weight residual 1.237 1.208 0.028 1.19e-02 7.06e+03 5.61e+00 ... (remaining 13816 not shown) Histogram of bond angle deviations from ideal: 98.42 - 105.52: 1376 105.52 - 112.62: 7632 112.62 - 119.71: 4689 119.71 - 126.81: 5384 126.81 - 133.90: 837 Bond angle restraints: 19918 Sorted by residual: angle pdb=" N THR L 662 " pdb=" CA THR L 662 " pdb=" C THR L 662 " ideal model delta sigma weight residual 111.36 117.42 -6.06 1.09e+00 8.42e-01 3.09e+01 angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.71 108.49 5.22 9.50e-01 1.11e+00 3.02e+01 angle pdb=" O3' DC I 78 " pdb=" C3' DC I 78 " pdb=" C2' DC I 78 " ideal model delta sigma weight residual 111.50 105.07 6.43 1.50e+00 4.44e-01 1.84e+01 angle pdb=" N GLY E 132 " pdb=" CA GLY E 132 " pdb=" C GLY E 132 " ideal model delta sigma weight residual 113.18 121.62 -8.44 2.37e+00 1.78e-01 1.27e+01 angle pdb=" O3' DT J 99 " pdb=" C3' DT J 99 " pdb=" C2' DT J 99 " ideal model delta sigma weight residual 111.50 106.43 5.07 1.50e+00 4.44e-01 1.14e+01 ... (remaining 19913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 6216 34.73 - 69.47: 1341 69.47 - 104.20: 13 104.20 - 138.94: 0 138.94 - 173.67: 3 Dihedral angle restraints: 7573 sinusoidal: 4993 harmonic: 2580 Sorted by residual: dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 46.33 173.67 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual -140.00 31.72 -171.72 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 69.93 150.07 1 3.50e+01 8.16e-04 1.46e+01 ... (remaining 7570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1973 0.052 - 0.104: 258 0.104 - 0.157: 32 0.157 - 0.209: 5 0.209 - 0.261: 6 Chirality restraints: 2274 Sorted by residual: chirality pdb=" CA ARG E 131 " pdb=" N ARG E 131 " pdb=" C ARG E 131 " pdb=" CB ARG E 131 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ASN L 687 " pdb=" N ASN L 687 " pdb=" C ASN L 687 " pdb=" CB ASN L 687 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA THR A 58 " pdb=" N THR A 58 " pdb=" C THR A 58 " pdb=" CB THR A 58 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2271 not shown) Planarity restraints: 1507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO E 43 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 100 " 0.020 2.00e-02 2.50e+03 8.26e-03 2.05e+00 pdb=" N9 DG I 100 " -0.018 2.00e-02 2.50e+03 pdb=" C8 DG I 100 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 100 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 100 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 100 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 100 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 100 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 100 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 100 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 100 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 100 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " 0.019 2.00e-02 2.50e+03 8.62e-03 2.04e+00 pdb=" N9 DA I 20 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " -0.002 2.00e-02 2.50e+03 ... (remaining 1504 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2801 2.81 - 3.33: 10764 3.33 - 3.85: 22906 3.85 - 4.38: 27619 4.38 - 4.90: 39610 Nonbonded interactions: 103700 Sorted by model distance: nonbonded pdb=" N THR L 662 " pdb=" OD2 ASP L 694 " model vdw 2.284 3.120 nonbonded pdb=" OE2 GLU A 50 " pdb=" NE ARG B 39 " model vdw 2.320 3.120 nonbonded pdb=" N CYS L 683 " pdb=" O LYS L 688 " model vdw 2.320 3.120 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.342 3.040 nonbonded pdb=" O TYR K 647 " pdb=" NZ LYS K 656 " model vdw 2.370 3.120 ... (remaining 103695 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 32 through 124) } ncs_group { reference = chain 'K' selection = chain 'L' } 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: 18.220 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: 0.000 Extract box with map and model: 3.040 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 41.820 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 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 : 0.004 0.047 13821 Z= 0.208 Angle : 0.642 8.441 19918 Z= 0.415 Chirality : 0.039 0.261 2274 Planarity : 0.003 0.045 1507 Dihedral : 26.537 173.671 5901 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.74 % Allowed : 1.21 % Favored : 97.05 % 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: -1.27 (0.28), residues: 866 helix: -0.07 (0.23), residues: 539 sheet: -1.72 (0.98), residues: 30 loop : -2.10 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 655 HIS 0.003 0.001 HIS A 113 PHE 0.020 0.002 PHE L 690 TYR 0.009 0.001 TYR A 54 ARG 0.003 0.001 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 249 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8419 (mmm) cc_final: 0.7945 (mtt) REVERT: B 59 LYS cc_start: 0.9028 (tttm) cc_final: 0.8814 (ttpp) REVERT: E 73 GLU cc_start: 0.7972 (tt0) cc_final: 0.7669 (tt0) REVERT: F 25 ASN cc_start: 0.9112 (m110) cc_final: 0.8673 (m110) REVERT: H 113 GLU cc_start: 0.8196 (tp30) cc_final: 0.7984 (tp30) REVERT: K 647 TYR cc_start: 0.8040 (m-10) cc_final: 0.6852 (m-80) REVERT: K 658 MET cc_start: 0.8527 (tpp) cc_final: 0.8304 (tpp) REVERT: K 693 ASN cc_start: 0.9276 (p0) cc_final: 0.9039 (p0) REVERT: L 693 ASN cc_start: 0.7363 (OUTLIER) cc_final: 0.6977 (m-40) REVERT: L 694 ASP cc_start: 0.6627 (OUTLIER) cc_final: 0.6113 (m-30) outliers start: 13 outliers final: 5 residues processed: 257 average time/residue: 0.3926 time to fit residues: 128.0526 Evaluate side-chains 177 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain L residue 693 ASN Chi-restraints excluded: chain L residue 694 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS B 93 GLN C 104 GLN E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN K 654 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13821 Z= 0.313 Angle : 0.612 9.996 19918 Z= 0.360 Chirality : 0.037 0.129 2274 Planarity : 0.005 0.043 1507 Dihedral : 29.417 172.262 4184 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.68 % Allowed : 8.85 % Favored : 88.47 % 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: -0.50 (0.29), residues: 866 helix: 0.54 (0.23), residues: 563 sheet: -1.91 (1.02), residues: 20 loop : -1.94 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 655 HIS 0.006 0.001 HIS C 31 PHE 0.015 0.002 PHE L 690 TYR 0.019 0.001 TYR K 647 ARG 0.004 0.001 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8546 (mmm) cc_final: 0.8160 (mtt) REVERT: B 84 MET cc_start: 0.8606 (mmt) cc_final: 0.8372 (mmt) REVERT: C 91 GLU cc_start: 0.7127 (pm20) cc_final: 0.6743 (pm20) REVERT: C 92 GLU cc_start: 0.7991 (mp0) cc_final: 0.7750 (mp0) REVERT: D 34 LYS cc_start: 0.9000 (mtmm) cc_final: 0.8722 (mtpt) REVERT: E 73 GLU cc_start: 0.7987 (tt0) cc_final: 0.7669 (tt0) REVERT: F 25 ASN cc_start: 0.9152 (m110) cc_final: 0.8754 (m110) REVERT: G 90 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7842 (p0) REVERT: K 647 TYR cc_start: 0.7437 (m-10) cc_final: 0.7011 (m-80) REVERT: K 658 MET cc_start: 0.8742 (tpp) cc_final: 0.8496 (tpp) REVERT: K 693 ASN cc_start: 0.9306 (p0) cc_final: 0.9039 (p0) REVERT: L 693 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.7129 (p0) outliers start: 20 outliers final: 12 residues processed: 186 average time/residue: 0.3501 time to fit residues: 84.9279 Evaluate side-chains 178 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain L residue 657 ASN Chi-restraints excluded: chain L residue 693 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 47 GLN F 75 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 654 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13821 Z= 0.241 Angle : 0.569 8.111 19918 Z= 0.339 Chirality : 0.035 0.152 2274 Planarity : 0.004 0.071 1507 Dihedral : 29.367 172.095 4176 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.22 % Allowed : 11.80 % Favored : 84.99 % 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: -0.16 (0.29), residues: 866 helix: 0.85 (0.23), residues: 559 sheet: -1.54 (1.07), residues: 20 loop : -1.92 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 655 HIS 0.007 0.001 HIS B 75 PHE 0.014 0.002 PHE K 642 TYR 0.017 0.001 TYR K 647 ARG 0.011 0.001 ARG L 643 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8513 (mmm) cc_final: 0.8103 (mtt) REVERT: D 34 LYS cc_start: 0.9009 (mtmm) cc_final: 0.8745 (mtpt) REVERT: E 73 GLU cc_start: 0.8005 (tt0) cc_final: 0.7700 (tt0) REVERT: F 25 ASN cc_start: 0.9169 (m110) cc_final: 0.8874 (m110) REVERT: K 653 LYS cc_start: 0.8842 (tppt) cc_final: 0.8554 (mmtp) REVERT: K 658 MET cc_start: 0.8834 (tpp) cc_final: 0.8531 (tpp) REVERT: K 693 ASN cc_start: 0.9220 (p0) cc_final: 0.8981 (p0) outliers start: 24 outliers final: 20 residues processed: 178 average time/residue: 0.3430 time to fit residues: 79.6936 Evaluate side-chains 180 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 160 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 654 ASN Chi-restraints excluded: chain L residue 657 ASN Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 60 optimal weight: 0.0970 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN L 654 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13821 Z= 0.364 Angle : 0.624 7.236 19918 Z= 0.368 Chirality : 0.039 0.152 2274 Planarity : 0.005 0.050 1507 Dihedral : 29.487 171.960 4174 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.49 % Allowed : 13.27 % Favored : 83.24 % 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: -0.11 (0.29), residues: 866 helix: 0.90 (0.23), residues: 565 sheet: -1.51 (1.12), residues: 20 loop : -1.97 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 655 HIS 0.007 0.002 HIS C 31 PHE 0.043 0.002 PHE L 642 TYR 0.015 0.001 TYR K 647 ARG 0.021 0.001 ARG K 643 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8578 (mmm) cc_final: 0.7822 (mtt) REVERT: D 34 LYS cc_start: 0.9071 (mtmm) cc_final: 0.8823 (mtpt) REVERT: E 73 GLU cc_start: 0.8035 (tt0) cc_final: 0.7805 (tt0) REVERT: F 25 ASN cc_start: 0.9128 (m110) cc_final: 0.8738 (m110) REVERT: G 90 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7757 (p0) REVERT: K 642 PHE cc_start: 0.7185 (m-80) cc_final: 0.6564 (m-80) REVERT: K 658 MET cc_start: 0.8885 (tpp) cc_final: 0.8597 (tpp) REVERT: K 687 ASN cc_start: 0.8807 (t0) cc_final: 0.8587 (t0) REVERT: K 691 SER cc_start: 0.8190 (t) cc_final: 0.7801 (p) REVERT: K 693 ASN cc_start: 0.9230 (p0) cc_final: 0.8896 (p0) REVERT: K 699 HIS cc_start: 0.7287 (m90) cc_final: 0.7081 (m-70) REVERT: L 642 PHE cc_start: 0.8299 (m-10) cc_final: 0.8015 (m-10) outliers start: 26 outliers final: 22 residues processed: 182 average time/residue: 0.3365 time to fit residues: 80.5279 Evaluate side-chains 183 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 654 ASN Chi-restraints excluded: chain L residue 657 ASN Chi-restraints excluded: chain L residue 662 THR Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 0.0170 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13821 Z= 0.302 Angle : 0.592 5.946 19918 Z= 0.352 Chirality : 0.037 0.167 2274 Planarity : 0.004 0.041 1507 Dihedral : 29.449 171.651 4174 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.49 % Allowed : 13.94 % Favored : 82.57 % 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: 0.08 (0.29), residues: 866 helix: 1.05 (0.22), residues: 565 sheet: -1.47 (1.11), residues: 20 loop : -1.90 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 655 HIS 0.007 0.001 HIS L 699 PHE 0.037 0.002 PHE L 642 TYR 0.008 0.001 TYR L 647 ARG 0.005 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: C 91 GLU cc_start: 0.7220 (pm20) cc_final: 0.6389 (pm20) REVERT: C 92 GLU cc_start: 0.7872 (mp0) cc_final: 0.7415 (mp0) REVERT: F 25 ASN cc_start: 0.9093 (m110) cc_final: 0.8715 (m110) REVERT: K 642 PHE cc_start: 0.7231 (m-80) cc_final: 0.6731 (m-80) REVERT: K 658 MET cc_start: 0.8904 (tpp) cc_final: 0.8605 (tpp) REVERT: K 691 SER cc_start: 0.8115 (t) cc_final: 0.7903 (p) REVERT: K 693 ASN cc_start: 0.9188 (p0) cc_final: 0.8872 (p0) REVERT: L 661 LYS cc_start: 0.9077 (ttmt) cc_final: 0.8838 (mttp) outliers start: 26 outliers final: 20 residues processed: 182 average time/residue: 0.3502 time to fit residues: 84.2048 Evaluate side-chains 181 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 654 ASN Chi-restraints excluded: chain L residue 657 ASN Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS L 654 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13821 Z= 0.219 Angle : 0.565 6.776 19918 Z= 0.337 Chirality : 0.035 0.162 2274 Planarity : 0.004 0.039 1507 Dihedral : 29.407 172.261 4172 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.08 % Allowed : 14.75 % Favored : 82.17 % 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: 0.34 (0.29), residues: 866 helix: 1.26 (0.22), residues: 566 sheet: -1.56 (1.13), residues: 20 loop : -1.82 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP L 655 HIS 0.006 0.001 HIS L 699 PHE 0.038 0.002 PHE L 642 TYR 0.008 0.001 TYR L 647 ARG 0.013 0.000 ARG L 643 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: C 91 GLU cc_start: 0.7183 (pm20) cc_final: 0.6437 (pm20) REVERT: C 92 GLU cc_start: 0.7886 (mp0) cc_final: 0.7347 (mp0) REVERT: E 73 GLU cc_start: 0.8032 (tt0) cc_final: 0.7514 (tt0) REVERT: F 25 ASN cc_start: 0.9018 (m110) cc_final: 0.8534 (m-40) REVERT: K 642 PHE cc_start: 0.7261 (m-80) cc_final: 0.6908 (m-80) REVERT: K 658 MET cc_start: 0.8832 (tpp) cc_final: 0.8544 (tpp) REVERT: K 693 ASN cc_start: 0.8995 (p0) cc_final: 0.8682 (p0) outliers start: 23 outliers final: 18 residues processed: 176 average time/residue: 0.3384 time to fit residues: 78.8746 Evaluate side-chains 181 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 654 ASN Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13821 Z= 0.210 Angle : 0.560 7.143 19918 Z= 0.333 Chirality : 0.035 0.170 2274 Planarity : 0.004 0.051 1507 Dihedral : 29.394 172.424 4170 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.41 % Allowed : 15.95 % Favored : 81.64 % 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: 0.53 (0.29), residues: 866 helix: 1.40 (0.22), residues: 568 sheet: -2.73 (1.67), residues: 10 loop : -1.69 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 655 HIS 0.007 0.001 HIS L 699 PHE 0.041 0.002 PHE L 642 TYR 0.035 0.001 TYR L 647 ARG 0.007 0.000 ARG L 643 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 166 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.7179 (pm20) cc_final: 0.6503 (pm20) REVERT: C 92 GLU cc_start: 0.7864 (mp0) cc_final: 0.7299 (mp0) REVERT: E 73 GLU cc_start: 0.8031 (tt0) cc_final: 0.7545 (tt0) REVERT: F 25 ASN cc_start: 0.8977 (m110) cc_final: 0.8461 (m-40) REVERT: K 642 PHE cc_start: 0.7249 (m-80) cc_final: 0.6805 (m-80) outliers start: 18 outliers final: 16 residues processed: 175 average time/residue: 0.3381 time to fit residues: 77.9154 Evaluate side-chains 178 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 654 ASN Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 0.2980 chunk 84 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13821 Z= 0.224 Angle : 0.564 8.842 19918 Z= 0.334 Chirality : 0.035 0.162 2274 Planarity : 0.004 0.058 1507 Dihedral : 29.388 172.281 4170 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.95 % Allowed : 16.49 % Favored : 80.56 % 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: 0.61 (0.29), residues: 866 helix: 1.50 (0.22), residues: 568 sheet: -1.69 (1.13), residues: 20 loop : -1.78 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 655 HIS 0.007 0.001 HIS L 699 PHE 0.015 0.001 PHE L 642 TYR 0.018 0.001 TYR L 647 ARG 0.009 0.000 ARG L 643 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 164 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.7233 (pm20) cc_final: 0.6573 (pm20) REVERT: C 92 GLU cc_start: 0.7878 (mp0) cc_final: 0.7297 (mp0) REVERT: E 73 GLU cc_start: 0.8032 (tt0) cc_final: 0.7557 (tt0) REVERT: F 25 ASN cc_start: 0.8966 (m110) cc_final: 0.8382 (m110) REVERT: K 642 PHE cc_start: 0.7277 (m-80) cc_final: 0.6871 (m-80) outliers start: 22 outliers final: 20 residues processed: 177 average time/residue: 0.3245 time to fit residues: 75.6725 Evaluate side-chains 184 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 654 ASN Chi-restraints excluded: chain L residue 670 ASN Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 20.0000 chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13821 Z= 0.271 Angle : 0.583 8.225 19918 Z= 0.344 Chirality : 0.036 0.168 2274 Planarity : 0.004 0.061 1507 Dihedral : 29.403 171.749 4170 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.95 % Allowed : 16.22 % Favored : 80.83 % 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: 0.59 (0.29), residues: 866 helix: 1.48 (0.22), residues: 568 sheet: -1.90 (1.13), residues: 20 loop : -1.77 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 655 HIS 0.004 0.001 HIS B 75 PHE 0.015 0.001 PHE L 642 TYR 0.017 0.001 TYR L 647 ARG 0.009 0.000 ARG L 643 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 163 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.7253 (pm20) cc_final: 0.6600 (pm20) REVERT: C 92 GLU cc_start: 0.7873 (mp0) cc_final: 0.7313 (mp0) REVERT: E 73 GLU cc_start: 0.8055 (tt0) cc_final: 0.7609 (tt0) REVERT: F 25 ASN cc_start: 0.8987 (m110) cc_final: 0.8438 (m110) REVERT: K 642 PHE cc_start: 0.7265 (m-80) cc_final: 0.6857 (m-80) outliers start: 22 outliers final: 21 residues processed: 177 average time/residue: 0.3324 time to fit residues: 78.0666 Evaluate side-chains 183 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 654 ASN Chi-restraints excluded: chain L residue 670 ASN Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13821 Z= 0.178 Angle : 0.571 14.200 19918 Z= 0.333 Chirality : 0.034 0.164 2274 Planarity : 0.004 0.055 1507 Dihedral : 29.347 173.144 4170 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.28 % Allowed : 17.29 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.29), residues: 866 helix: 1.59 (0.22), residues: 571 sheet: -1.79 (1.13), residues: 20 loop : -1.69 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 655 HIS 0.005 0.001 HIS B 75 PHE 0.023 0.001 PHE L 642 TYR 0.019 0.001 TYR L 647 ARG 0.010 0.000 ARG L 643 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 GLU cc_start: 0.8021 (tt0) cc_final: 0.7664 (tt0) REVERT: F 25 ASN cc_start: 0.8905 (m110) cc_final: 0.8396 (m110) REVERT: K 642 PHE cc_start: 0.7248 (m-80) cc_final: 0.6884 (m-80) outliers start: 17 outliers final: 16 residues processed: 177 average time/residue: 0.3244 time to fit residues: 76.2334 Evaluate side-chains 178 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 647 TYR Chi-restraints excluded: chain L residue 654 ASN Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.6919 > 50: distance: 39 - 58: 19.957 distance: 44 - 65: 15.106 distance: 48 - 77: 4.372 distance: 53 - 58: 21.731 distance: 54 - 86: 14.180 distance: 58 - 59: 12.355 distance: 59 - 60: 7.381 distance: 59 - 62: 13.994 distance: 60 - 61: 18.673 distance: 60 - 65: 10.046 distance: 61 - 93: 31.144 distance: 62 - 63: 13.162 distance: 62 - 64: 19.693 distance: 65 - 66: 6.825 distance: 66 - 67: 11.904 distance: 66 - 69: 12.058 distance: 67 - 68: 26.975 distance: 67 - 77: 5.574 distance: 68 - 101: 37.491 distance: 69 - 70: 10.718 distance: 70 - 71: 9.234 distance: 70 - 72: 3.574 distance: 71 - 73: 15.496 distance: 72 - 74: 13.060 distance: 73 - 75: 7.429 distance: 74 - 75: 11.385 distance: 77 - 78: 4.668 distance: 78 - 79: 12.377 distance: 78 - 81: 9.845 distance: 79 - 80: 12.349 distance: 79 - 86: 8.411 distance: 81 - 82: 15.006 distance: 82 - 83: 10.663 distance: 83 - 84: 13.447 distance: 84 - 85: 27.494 distance: 86 - 87: 12.023 distance: 87 - 88: 10.358 distance: 87 - 90: 15.599 distance: 88 - 89: 16.093 distance: 88 - 93: 15.967 distance: 90 - 91: 13.571 distance: 90 - 92: 9.742 distance: 93 - 94: 17.413 distance: 94 - 95: 9.224 distance: 94 - 97: 11.474 distance: 95 - 96: 7.845 distance: 95 - 101: 22.526 distance: 96 - 126: 24.909 distance: 97 - 98: 19.926 distance: 98 - 99: 35.140 distance: 98 - 100: 30.085 distance: 101 - 102: 22.775 distance: 102 - 103: 29.128 distance: 102 - 105: 25.300 distance: 103 - 104: 7.793 distance: 103 - 110: 35.217 distance: 105 - 106: 38.048 distance: 106 - 107: 37.379 distance: 107 - 108: 21.539 distance: 108 - 109: 51.586 distance: 110 - 111: 24.928 distance: 111 - 112: 33.113 distance: 111 - 114: 13.215 distance: 112 - 113: 14.857 distance: 112 - 119: 50.195 distance: 114 - 115: 55.937 distance: 115 - 116: 44.122 distance: 116 - 117: 9.793 distance: 116 - 118: 47.790 distance: 119 - 120: 30.535 distance: 120 - 121: 4.373 distance: 120 - 123: 16.306 distance: 121 - 122: 19.875 distance: 121 - 126: 10.179 distance: 123 - 124: 16.107 distance: 123 - 125: 15.102 distance: 126 - 127: 15.252 distance: 127 - 128: 7.607 distance: 127 - 130: 5.938 distance: 128 - 129: 23.585 distance: 128 - 136: 13.314 distance: 131 - 132: 14.536 distance: 131 - 133: 4.189 distance: 132 - 134: 9.041 distance: 133 - 135: 3.406 distance: 134 - 135: 7.784 distance: 136 - 137: 5.282 distance: 136 - 142: 9.801 distance: 137 - 138: 16.019 distance: 137 - 140: 20.839 distance: 138 - 139: 11.319 distance: 138 - 143: 10.376 distance: 140 - 141: 8.656 distance: 141 - 142: 19.377