Starting phenix.real_space_refine on Wed Jul 30 20:09:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t3w_41015/07_2025/8t3w_41015.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3w_41015/07_2025/8t3w_41015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t3w_41015/07_2025/8t3w_41015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3w_41015/07_2025/8t3w_41015.map" model { file = "/net/cci-nas-00/data/ceres_data/8t3w_41015/07_2025/8t3w_41015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3w_41015/07_2025/8t3w_41015.cif" } resolution = 3.25 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. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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 94.558 74.806 62.875 1.00139.73 S ATOM 12325 SG CYS K 683 92.501 76.362 60.038 1.00119.37 S ATOM 12345 SG CYS K 686 95.897 74.876 59.264 1.00125.56 S ATOM 12049 SG CYS K 648 85.019 82.149 65.675 1.00162.60 S ATOM 12069 SG CYS K 651 82.233 84.334 67.247 1.00163.36 S ATOM 12204 SG CYS K 668 82.584 80.711 68.198 1.00143.24 S ATOM 12227 SG CYS K 671 81.166 81.285 65.164 1.00136.31 S ATOM 12709 SG CYS L 663 95.523 72.650 83.157 1.00172.78 S ATOM 12868 SG CYS L 683 97.601 72.700 86.835 1.00186.18 S ATOM 12888 SG CYS L 686 94.510 71.743 87.275 1.00190.44 S ATOM 12592 SG CYS L 648 102.961 83.940 81.389 1.00189.02 S ATOM 12612 SG CYS L 651 105.730 86.538 80.694 1.00190.09 S ATOM 12747 SG CYS L 668 105.574 83.267 78.829 1.00189.67 S ATOM 12770 SG CYS L 671 106.608 83.208 82.415 1.00190.98 S Time building chain proxies: 8.98, per 1000 atoms: 0.69 Number of scatterers: 13001 At special positions: 0 Unit cell: (127.395, 117.99, 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 - 3.00 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=0, symmetry=0 Time building additional restraints: 3.43 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 663 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 686 " pdb=" ZN K 802 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 668 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 651 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 671 " 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: 6.17 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.712A 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: 3.543A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.503A 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: 3.758A 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: 3.700A 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: 3.843A 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: 3.526A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.564A 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: 3.666A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.586A 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: 3.867A 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: 4.173A pdb=" N GLU D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 3.817A 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: 4.089A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 100 removed outlier: 3.690A pdb=" N ARG D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.648A 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: 3.554A 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: 3.789A pdb=" N ILE E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) removed outlier: 4.075A 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: 3.561A 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: 3.988A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.737A 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: 3.592A pdb=" N ALA E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.989A 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: 3.581A 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: 3.609A 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: 4.067A 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: 3.764A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE F 66 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 3.677A 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: 3.623A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.583A 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: 3.511A pdb=" N THR G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) removed outlier: 3.671A 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: 4.035A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.545A 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: 3.874A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.685A 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: 3.950A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.595A 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: 4.317A 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: 3.606A pdb=" N LYS H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.684A 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: 4.038A 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: 4.225A 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: 6.586A 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: 7.074A 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: 6.853A 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: 7.456A 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: 5.44 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1754 1.33 - 1.45: 5009 1.45 - 1.57: 6430 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 1.488 0.036 1.29e-02 6.01e+03 7.82e+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 6.98e+00 bond pdb=" O3' DT J 140 " pdb=" P DT J 141 " ideal model delta sigma weight residual 1.607 1.645 -0.038 1.50e-02 4.44e+03 6.42e+00 bond pdb=" C ARG A 53 " pdb=" O ARG A 53 " ideal model delta sigma weight residual 1.236 1.207 0.028 1.19e-02 7.06e+03 5.70e+00 bond pdb=" C LYS H 120 " pdb=" O LYS H 120 " ideal model delta sigma weight residual 1.237 1.209 0.028 1.19e-02 7.06e+03 5.47e+00 ... (remaining 13816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 19326 1.69 - 3.37: 543 3.37 - 5.06: 37 5.06 - 6.74: 11 6.74 - 8.43: 1 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 111.36 117.44 -6.08 1.09e+00 8.42e-01 3.11e+01 angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.71 108.47 5.24 9.50e-01 1.11e+00 3.05e+01 angle pdb=" O3' DC I 78 " pdb=" C3' DC I 78 " pdb=" C2' DC I 78 " ideal model delta sigma weight residual 111.50 105.03 6.47 1.50e+00 4.44e-01 1.86e+01 angle pdb=" N GLY E 132 " pdb=" CA GLY E 132 " pdb=" C GLY E 132 " ideal model delta sigma weight residual 113.18 121.61 -8.43 2.37e+00 1.78e-01 1.26e+01 angle pdb=" O3' DT J 99 " pdb=" C3' DT J 99 " pdb=" C2' DT J 99 " ideal model delta sigma weight residual 111.50 106.41 5.09 1.50e+00 4.44e-01 1.15e+01 ... (remaining 19913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 6218 34.73 - 69.47: 1339 69.47 - 104.20: 13 104.20 - 138.93: 0 138.93 - 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 31.77 -171.77 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 69.84 150.16 1 3.50e+01 8.16e-04 1.46e+01 ... (remaining 7570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1971 0.051 - 0.102: 259 0.102 - 0.153: 33 0.153 - 0.204: 3 0.204 - 0.255: 8 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 2.26 0.26 2.00e-01 2.50e+01 1.63e+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 2.26 0.25 2.00e-01 2.50e+01 1.51e+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 1.40e+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 4.47e-02 3.20e+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 8.27e-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 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 100 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 100 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 100 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 100 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 100 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 100 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 91 " 0.019 2.00e-02 2.50e+03 8.54e-03 2.00e+00 pdb=" N9 DA I 91 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DA I 91 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 91 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 91 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 91 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 91 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 91 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 91 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 91 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 91 " -0.001 2.00e-02 2.50e+03 ... (remaining 1504 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2808 2.81 - 3.33: 10768 3.33 - 3.85: 22906 3.85 - 4.38: 27597 4.38 - 4.90: 39616 Nonbonded interactions: 103695 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 2.322 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 2.369 3.120 ... (remaining 103690 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: 67.440 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 43.380 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.628 13837 Z= 0.336 Angle : 0.726 44.084 19936 Z= 0.423 Chirality : 0.039 0.255 2274 Planarity : 0.003 0.045 1507 Dihedral : 26.528 173.667 5901 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.74 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 : -2.09 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 655 HIS 0.004 0.001 HIS A 113 PHE 0.021 0.001 PHE L 690 TYR 0.009 0.001 TYR F 51 ARG 0.003 0.000 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.18345 ( 679) hydrogen bonds : angle 4.69384 ( 1674) metal coordination : bond 0.21951 ( 16) metal coordination : angle 11.33294 ( 18) covalent geometry : bond 0.00374 (13821) covalent geometry : angle 0.64171 (19918) *********************** 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 265 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 252 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.9382 (t) cc_final: 0.9127 (p) REVERT: A 120 MET cc_start: 0.7849 (mmm) cc_final: 0.7572 (mtt) REVERT: B 59 LYS cc_start: 0.9045 (tttm) cc_final: 0.8801 (ttmm) REVERT: C 73 ASN cc_start: 0.8698 (t0) cc_final: 0.8307 (t0) REVERT: D 99 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.8171 (mtm-85) REVERT: E 73 GLU cc_start: 0.8130 (tt0) cc_final: 0.7725 (tt0) REVERT: F 25 ASN cc_start: 0.8842 (m110) cc_final: 0.8523 (m110) REVERT: F 67 ARG cc_start: 0.8497 (ttp-110) cc_final: 0.8297 (ttp-110) REVERT: H 71 GLU cc_start: 0.7694 (tp30) cc_final: 0.7443 (tp30) outliers start: 13 outliers final: 5 residues processed: 260 average time/residue: 0.4113 time to fit residues: 135.1757 Evaluate side-chains 197 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 192 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 56 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS D 47 GLN E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN G 104 GLN ** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 670 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.088677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.058765 restraints weight = 29863.276| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.82 r_work: 0.2635 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 13837 Z= 0.216 Angle : 0.609 13.575 19936 Z= 0.350 Chirality : 0.037 0.129 2274 Planarity : 0.004 0.042 1507 Dihedral : 29.474 172.172 4180 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.82 % Allowed : 10.59 % Favored : 86.60 % 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: -0.38 (0.29), residues: 866 helix: 0.64 (0.23), residues: 561 sheet: -1.65 (1.18), residues: 20 loop : -1.93 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 655 HIS 0.005 0.002 HIS L 699 PHE 0.019 0.002 PHE H 65 TYR 0.011 0.001 TYR F 51 ARG 0.005 0.001 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.05640 ( 679) hydrogen bonds : angle 2.94637 ( 1674) metal coordination : bond 0.02748 ( 16) metal coordination : angle 5.57607 ( 18) covalent geometry : bond 0.00487 (13821) covalent geometry : angle 0.58567 (19918) *********************** 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 217 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.9478 (t) cc_final: 0.9151 (p) REVERT: A 120 MET cc_start: 0.8221 (mmm) cc_final: 0.7802 (mtt) REVERT: C 73 ASN cc_start: 0.8979 (t0) cc_final: 0.8587 (t0) REVERT: D 85 LYS cc_start: 0.9512 (mmtm) cc_final: 0.9285 (mttp) REVERT: G 74 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8941 (mttp) REVERT: K 675 ARG cc_start: 0.8959 (mmm-85) cc_final: 0.8560 (ttt180) REVERT: L 675 ARG cc_start: 0.7072 (mtt180) cc_final: 0.6453 (mtp-110) outliers start: 21 outliers final: 15 residues processed: 202 average time/residue: 0.3925 time to fit residues: 101.4481 Evaluate side-chains 203 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 105 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 660 ILE Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 697 THR Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 0.2980 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS ** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 670 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.088165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.058200 restraints weight = 29392.103| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 1.77 r_work: 0.2626 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 13837 Z= 0.202 Angle : 0.576 10.635 19936 Z= 0.336 Chirality : 0.036 0.137 2274 Planarity : 0.004 0.041 1507 Dihedral : 29.483 173.494 4174 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.95 % Allowed : 12.87 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.29), residues: 866 helix: 0.98 (0.23), residues: 560 sheet: -1.66 (1.17), residues: 20 loop : -1.92 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 655 HIS 0.005 0.001 HIS L 665 PHE 0.014 0.001 PHE H 65 TYR 0.009 0.001 TYR F 51 ARG 0.004 0.000 ARG K 679 Details of bonding type rmsd hydrogen bonds : bond 0.05263 ( 679) hydrogen bonds : angle 2.77716 ( 1674) metal coordination : bond 0.02601 ( 16) metal coordination : angle 4.69822 ( 18) covalent geometry : bond 0.00454 (13821) covalent geometry : angle 0.55838 (19918) *********************** 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 210 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8897 (mttp) cc_final: 0.8683 (mttp) REVERT: A 120 MET cc_start: 0.8236 (mmm) cc_final: 0.7882 (mtt) REVERT: D 85 LYS cc_start: 0.9481 (mmtm) cc_final: 0.9269 (mttp) REVERT: G 74 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.9003 (mttp) REVERT: K 658 MET cc_start: 0.9088 (tpp) cc_final: 0.8640 (tpp) REVERT: K 661 LYS cc_start: 0.8917 (ptpt) cc_final: 0.8636 (ptpp) REVERT: K 675 ARG cc_start: 0.8998 (mmm-85) cc_final: 0.8623 (ttt180) REVERT: K 697 THR cc_start: 0.8683 (p) cc_final: 0.8389 (t) REVERT: L 675 ARG cc_start: 0.6984 (mtt180) cc_final: 0.6612 (mtp-110) outliers start: 22 outliers final: 17 residues processed: 196 average time/residue: 0.3756 time to fit residues: 94.5893 Evaluate side-chains 200 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 649 SER Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain K residue 691 SER Chi-restraints excluded: chain L residue 697 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 55 optimal weight: 0.0980 chunk 4 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 102 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.088723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.058900 restraints weight = 29100.305| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.77 r_work: 0.2646 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13837 Z= 0.155 Angle : 0.556 8.907 19936 Z= 0.326 Chirality : 0.035 0.134 2274 Planarity : 0.003 0.038 1507 Dihedral : 29.483 174.447 4170 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.01 % Allowed : 14.21 % Favored : 83.78 % 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: 0.24 (0.29), residues: 866 helix: 1.22 (0.23), residues: 560 sheet: -1.67 (1.16), residues: 20 loop : -1.87 (0.33), residues: 286 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 0.010 0.001 PHE L 690 TYR 0.008 0.001 TYR F 51 ARG 0.005 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.04649 ( 679) hydrogen bonds : angle 2.68850 ( 1674) metal coordination : bond 0.01776 ( 16) metal coordination : angle 4.11858 ( 18) covalent geometry : bond 0.00334 (13821) covalent geometry : angle 0.54281 (19918) *********************** 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 201 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8187 (mmm) cc_final: 0.7797 (mtt) REVERT: G 74 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8970 (mttp) REVERT: K 658 MET cc_start: 0.8998 (tpp) cc_final: 0.8683 (tpp) REVERT: K 661 LYS cc_start: 0.8911 (ptpt) cc_final: 0.8627 (ptpp) REVERT: K 674 GLU cc_start: 0.9197 (pp20) cc_final: 0.8930 (pp20) REVERT: K 675 ARG cc_start: 0.9002 (mmm-85) cc_final: 0.8556 (ttt180) REVERT: K 697 THR cc_start: 0.8688 (p) cc_final: 0.8467 (t) REVERT: L 675 ARG cc_start: 0.7407 (mtt180) cc_final: 0.6906 (mtp-110) outliers start: 15 outliers final: 12 residues processed: 192 average time/residue: 0.4143 time to fit residues: 102.4531 Evaluate side-chains 193 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 697 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 108 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 112 GLN ** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.089330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.059602 restraints weight = 29490.399| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.78 r_work: 0.2665 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13837 Z= 0.147 Angle : 0.542 7.933 19936 Z= 0.319 Chirality : 0.034 0.130 2274 Planarity : 0.003 0.038 1507 Dihedral : 29.448 175.190 4170 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.82 % Allowed : 14.75 % Favored : 82.44 % 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: 0.45 (0.29), residues: 866 helix: 1.40 (0.23), residues: 559 sheet: -1.52 (1.16), residues: 20 loop : -1.82 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 655 HIS 0.005 0.001 HIS B 75 PHE 0.012 0.001 PHE L 690 TYR 0.007 0.001 TYR F 51 ARG 0.004 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 679) hydrogen bonds : angle 2.58831 ( 1674) metal coordination : bond 0.01518 ( 16) metal coordination : angle 3.83865 ( 18) covalent geometry : bond 0.00313 (13821) covalent geometry : angle 0.52964 (19918) *********************** 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 212 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8076 (mmm) cc_final: 0.7615 (mtt) REVERT: F 25 ASN cc_start: 0.8936 (m-40) cc_final: 0.8577 (m110) REVERT: G 74 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8975 (mttp) REVERT: K 658 MET cc_start: 0.9038 (tpp) cc_final: 0.8708 (tpp) REVERT: K 661 LYS cc_start: 0.8919 (ptpt) cc_final: 0.8631 (ptpp) REVERT: K 674 GLU cc_start: 0.9205 (pp20) cc_final: 0.8920 (pp20) REVERT: K 675 ARG cc_start: 0.9008 (mmm-85) cc_final: 0.8567 (ttt180) REVERT: K 697 THR cc_start: 0.8708 (p) cc_final: 0.8505 (t) outliers start: 21 outliers final: 15 residues processed: 200 average time/residue: 0.3788 time to fit residues: 97.2729 Evaluate side-chains 197 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 80 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain K residue 692 SER Chi-restraints excluded: chain L residue 697 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 112 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.089218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.059394 restraints weight = 29817.108| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.80 r_work: 0.2656 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13837 Z= 0.163 Angle : 0.544 7.716 19936 Z= 0.319 Chirality : 0.034 0.134 2274 Planarity : 0.003 0.037 1507 Dihedral : 29.424 175.179 4170 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.08 % Allowed : 15.82 % Favored : 81.10 % 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: 0.65 (0.29), residues: 866 helix: 1.58 (0.23), residues: 561 sheet: -1.47 (1.12), residues: 20 loop : -1.81 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 655 HIS 0.008 0.001 HIS B 75 PHE 0.014 0.001 PHE K 690 TYR 0.017 0.001 TYR L 647 ARG 0.006 0.000 ARG L 675 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 679) hydrogen bonds : angle 2.56924 ( 1674) metal coordination : bond 0.01262 ( 16) metal coordination : angle 3.58105 ( 18) covalent geometry : bond 0.00359 (13821) covalent geometry : angle 0.53371 (19918) *********************** 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 210 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8134 (mmm) cc_final: 0.7677 (mtt) REVERT: D 85 LYS cc_start: 0.9510 (mmtm) cc_final: 0.9267 (mttp) REVERT: F 25 ASN cc_start: 0.8962 (m-40) cc_final: 0.8523 (m110) REVERT: G 74 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.9004 (mttp) REVERT: K 658 MET cc_start: 0.9158 (tpp) cc_final: 0.8849 (tpp) REVERT: K 674 GLU cc_start: 0.9228 (pp20) cc_final: 0.8913 (pp20) REVERT: K 675 ARG cc_start: 0.9013 (mmm-85) cc_final: 0.8641 (ttt180) REVERT: K 697 THR cc_start: 0.8825 (p) cc_final: 0.8612 (t) outliers start: 23 outliers final: 18 residues processed: 196 average time/residue: 0.4136 time to fit residues: 104.2970 Evaluate side-chains 198 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 105 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 670 ASN Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 697 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 67 optimal weight: 0.3980 chunk 87 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 699 HIS ** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.087840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.057962 restraints weight = 29734.075| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.80 r_work: 0.2618 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13837 Z= 0.195 Angle : 0.564 7.032 19936 Z= 0.331 Chirality : 0.035 0.141 2274 Planarity : 0.004 0.038 1507 Dihedral : 29.439 174.949 4170 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.62 % Allowed : 15.15 % Favored : 81.23 % 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: 0.72 (0.29), residues: 866 helix: 1.58 (0.23), residues: 567 sheet: -2.34 (1.70), residues: 10 loop : -1.71 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 655 HIS 0.009 0.001 HIS B 75 PHE 0.013 0.001 PHE K 690 TYR 0.009 0.001 TYR F 51 ARG 0.003 0.000 ARG F 23 Details of bonding type rmsd hydrogen bonds : bond 0.04943 ( 679) hydrogen bonds : angle 2.65756 ( 1674) metal coordination : bond 0.01162 ( 16) metal coordination : angle 3.47758 ( 18) covalent geometry : bond 0.00439 (13821) covalent geometry : angle 0.55495 (19918) *********************** 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 214 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8265 (mmm) cc_final: 0.7948 (mtt) REVERT: D 85 LYS cc_start: 0.9524 (mmtm) cc_final: 0.9292 (mttp) REVERT: F 25 ASN cc_start: 0.8930 (m-40) cc_final: 0.8486 (m110) REVERT: K 658 MET cc_start: 0.9158 (tpp) cc_final: 0.8843 (tpp) REVERT: K 675 ARG cc_start: 0.8989 (mmm-85) cc_final: 0.8711 (ttt180) outliers start: 27 outliers final: 23 residues processed: 198 average time/residue: 0.4753 time to fit residues: 122.7733 Evaluate side-chains 202 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 2.146 ------------------------------------------------------------------------------- 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 80 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 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 F residue 50 ILE Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 113 SER 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 K residue 692 SER Chi-restraints excluded: chain K residue 695 LEU Chi-restraints excluded: chain L residue 655 TRP Chi-restraints excluded: chain L residue 663 CYS Chi-restraints excluded: chain L residue 697 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 107 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 105 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.088825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.058973 restraints weight = 29543.161| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.78 r_work: 0.2643 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13837 Z= 0.145 Angle : 0.558 8.114 19936 Z= 0.327 Chirality : 0.034 0.153 2274 Planarity : 0.003 0.037 1507 Dihedral : 29.435 175.685 4170 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.35 % Allowed : 15.55 % Favored : 81.10 % 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: 0.91 (0.29), residues: 866 helix: 1.73 (0.23), residues: 566 sheet: -2.24 (1.70), residues: 10 loop : -1.65 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 655 HIS 0.009 0.001 HIS B 75 PHE 0.012 0.001 PHE K 690 TYR 0.008 0.001 TYR F 51 ARG 0.009 0.000 ARG L 675 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 679) hydrogen bonds : angle 2.59427 ( 1674) metal coordination : bond 0.01140 ( 16) metal coordination : angle 3.39250 ( 18) covalent geometry : bond 0.00306 (13821) covalent geometry : angle 0.54842 (19918) *********************** 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 207 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8154 (mmm) cc_final: 0.7784 (mtt) REVERT: D 85 LYS cc_start: 0.9513 (mmtm) cc_final: 0.9274 (mttp) REVERT: F 25 ASN cc_start: 0.8888 (m-40) cc_final: 0.8471 (m110) REVERT: K 658 MET cc_start: 0.9142 (tpp) cc_final: 0.8809 (tpp) REVERT: K 675 ARG cc_start: 0.8970 (mmm-85) cc_final: 0.8692 (ttt180) REVERT: K 688 LYS cc_start: 0.8950 (ttpp) cc_final: 0.8450 (pttp) outliers start: 25 outliers final: 20 residues processed: 191 average time/residue: 0.7288 time to fit residues: 188.9998 Evaluate side-chains 197 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 80 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 36 SER 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 K residue 695 LEU Chi-restraints excluded: chain L residue 663 CYS Chi-restraints excluded: chain L residue 697 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.089115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.059205 restraints weight = 29686.129| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.81 r_work: 0.2656 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13837 Z= 0.149 Angle : 0.554 8.995 19936 Z= 0.323 Chirality : 0.034 0.158 2274 Planarity : 0.004 0.038 1507 Dihedral : 29.386 176.519 4170 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.08 % Allowed : 15.82 % Favored : 81.10 % 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: 0.99 (0.30), residues: 866 helix: 1.78 (0.23), residues: 566 sheet: -2.11 (1.60), residues: 10 loop : -1.58 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 655 HIS 0.008 0.001 HIS B 75 PHE 0.016 0.001 PHE K 690 TYR 0.010 0.001 TYR K 647 ARG 0.006 0.000 ARG L 675 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 679) hydrogen bonds : angle 2.54036 ( 1674) metal coordination : bond 0.01031 ( 16) metal coordination : angle 3.22574 ( 18) covalent geometry : bond 0.00320 (13821) covalent geometry : angle 0.54589 (19918) *********************** 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 200 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8091 (mmm) cc_final: 0.7676 (mtt) REVERT: D 85 LYS cc_start: 0.9504 (mmtm) cc_final: 0.9300 (mttp) REVERT: F 25 ASN cc_start: 0.8886 (m-40) cc_final: 0.8481 (m110) REVERT: G 92 GLU cc_start: 0.8908 (mp0) cc_final: 0.8555 (mp0) REVERT: K 658 MET cc_start: 0.9143 (tpp) cc_final: 0.8817 (tpp) REVERT: K 675 ARG cc_start: 0.8975 (mmm-85) cc_final: 0.8709 (ttt180) REVERT: K 688 LYS cc_start: 0.8969 (ttpp) cc_final: 0.8462 (pttp) outliers start: 23 outliers final: 19 residues processed: 185 average time/residue: 0.3578 time to fit residues: 86.3385 Evaluate side-chains 195 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 80 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 663 CYS Chi-restraints excluded: chain L residue 697 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.084711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.054933 restraints weight = 29468.827| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 1.79 r_work: 0.2531 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2396 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 13837 Z= 0.358 Angle : 0.688 10.776 19936 Z= 0.394 Chirality : 0.043 0.157 2274 Planarity : 0.005 0.040 1507 Dihedral : 29.604 172.266 4170 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.49 % Allowed : 15.42 % Favored : 81.10 % 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: 0.52 (0.29), residues: 866 helix: 1.42 (0.23), residues: 564 sheet: -1.71 (1.45), residues: 10 loop : -1.79 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP K 655 HIS 0.008 0.002 HIS A 113 PHE 0.020 0.002 PHE H 65 TYR 0.011 0.002 TYR F 51 ARG 0.007 0.001 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.07204 ( 679) hydrogen bonds : angle 3.08096 ( 1674) metal coordination : bond 0.00783 ( 16) metal coordination : angle 4.02886 ( 18) covalent geometry : bond 0.00831 (13821) covalent geometry : angle 0.67787 (19918) ********************** 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 204 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 85 LYS cc_start: 0.9555 (mmtm) cc_final: 0.9344 (mttp) REVERT: F 25 ASN cc_start: 0.9004 (m-40) cc_final: 0.8406 (m110) REVERT: G 92 GLU cc_start: 0.8986 (mp0) cc_final: 0.8659 (mp0) REVERT: K 658 MET cc_start: 0.9143 (tpp) cc_final: 0.8814 (tpp) REVERT: K 675 ARG cc_start: 0.8974 (mmm-85) cc_final: 0.8718 (ttt180) REVERT: K 688 LYS cc_start: 0.9020 (ttpp) cc_final: 0.8448 (pttp) outliers start: 26 outliers final: 24 residues processed: 189 average time/residue: 0.3634 time to fit residues: 89.2777 Evaluate side-chains 197 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 105 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 670 ASN Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain K residue 692 SER Chi-restraints excluded: chain L residue 647 TYR Chi-restraints excluded: chain L residue 663 CYS Chi-restraints excluded: chain L residue 697 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.086100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.056199 restraints weight = 29446.547| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 1.79 r_work: 0.2569 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13837 Z= 0.185 Angle : 0.620 10.127 19936 Z= 0.361 Chirality : 0.037 0.145 2274 Planarity : 0.004 0.041 1507 Dihedral : 29.566 174.270 4170 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.08 % Allowed : 16.49 % 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: 0.64 (0.29), residues: 866 helix: 1.51 (0.23), residues: 564 sheet: -1.28 (1.55), residues: 10 loop : -1.73 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP K 655 HIS 0.004 0.001 HIS A 113 PHE 0.014 0.002 PHE H 65 TYR 0.011 0.001 TYR F 51 ARG 0.007 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.05818 ( 679) hydrogen bonds : angle 2.86915 ( 1674) metal coordination : bond 0.01008 ( 16) metal coordination : angle 3.69268 ( 18) covalent geometry : bond 0.00409 (13821) covalent geometry : angle 0.61072 (19918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8773.94 seconds wall clock time: 157 minutes 52.31 seconds (9472.31 seconds total)