Starting phenix.real_space_refine on Fri Jul 3 06:58:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t3w_41015/07_2026/8t3w_41015.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3w_41015/07_2026/8t3w_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8t3w_41015/07_2026/8t3w_41015.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t3w_41015/07_2026/8t3w_41015.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t3w_41015/07_2026/8t3w_41015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3w_41015/07_2026/8t3w_41015.map" model { file = "/net/cci-nas-00/data/ceres_data/8t3w_41015/07_2026/8t3w_41015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3w_41015/07_2026/8t3w_41015.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 2.29, per 1000 atoms: 0.18 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: 0.81 Conformation dependent library (CDL) restraints added in 361.3 milliseconds 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: 1.60 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: 2.43 Time building geometry restraints manager: 1.15 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=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DT I 104 " pdb=" C2' DT I 104 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DC I 95 " pdb=" C2' DC I 95 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.99e+00 bond pdb=" C3' DC I 96 " pdb=" C2' DC I 96 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.37e+00 bond pdb=" C3' DT J 140 " pdb=" C2' DT J 140 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.77e+00 ... (remaining 13816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 18836 1.69 - 3.37: 1028 3.37 - 5.06: 44 5.06 - 6.74: 9 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=" O4' DG J 56 " pdb=" C4' DG J 56 " pdb=" C3' DG J 56 " ideal model delta sigma weight residual 106.00 103.19 2.81 6.00e-01 2.78e+00 2.19e+01 angle pdb=" N3 DT J 13 " pdb=" C4 DT J 13 " pdb=" O4 DT J 13 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+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: 1759 0.051 - 0.102: 447 0.102 - 0.153: 55 0.153 - 0.204: 5 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: 3.760 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.480 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 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 : 0.009 0.628 13837 Z= 0.570 Angle : 0.845 44.084 19936 Z= 0.673 Chirality : 0.047 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG E 129 TYR 0.009 0.001 TYR F 51 PHE 0.021 0.001 PHE L 690 TRP 0.003 0.001 TRP K 655 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.50 (13821) covalent geometry : angle 0.77399 / 0.67 (19918) hydrogen bonds : bond 0.18345 / 12.09 ( 679) hydrogen bonds : angle 4.69384 / 3.43 ( 1674) metal coordination : bond 0.21951 / 19.90 ( 16) metal coordination : angle 11.33294 / 7.24 ( 18) *********************** 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 : 0.234 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: 0.1568 time to fit residues: 52.1235 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 : 0.262 ------------------------------------------------------------------------------- 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 108 optimal weight: 50.0000 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN G 104 GLN L 670 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.089523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.059214 restraints weight = 29400.638| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.81 r_work: 0.2638 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.237 13837 Z= 0.216 Angle : 0.695 23.865 19936 Z= 0.395 Chirality : 0.048 0.337 2274 Planarity : 0.004 0.041 1507 Dihedral : 29.736 172.379 4180 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.22 % Allowed : 10.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.29), residues: 866 helix: 0.52 (0.23), residues: 562 sheet: -1.48 (1.17), residues: 20 loop : -1.94 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 35 TYR 0.009 0.001 TYR L 647 PHE 0.012 0.001 PHE H 65 TRP 0.002 0.000 TRP L 655 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.21 (13821) covalent geometry : angle 0.66149 / 0.39 (19918) hydrogen bonds : bond 0.06849 / 4.47 ( 679) hydrogen bonds : angle 3.20408 / 2.29 ( 1674) metal coordination : bond 0.06206 / 5.44 ( 16) metal coordination : angle 7.08622 / 2.85 ( 18) *********************** 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: 24 poor density : 193 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 107 THR cc_start: 0.9466 (t) cc_final: 0.9176 (p) REVERT: A 120 MET cc_start: 0.8195 (mmm) cc_final: 0.7716 (mtt) REVERT: C 73 ASN cc_start: 0.8860 (t0) cc_final: 0.8484 (t0) REVERT: D 47 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8883 (mt0) REVERT: E 73 GLU cc_start: 0.8729 (tt0) cc_final: 0.8254 (tt0) REVERT: F 25 ASN cc_start: 0.8988 (m110) cc_final: 0.8639 (m110) REVERT: K 647 TYR cc_start: 0.7071 (m-10) cc_final: 0.6731 (m-80) REVERT: K 669 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7968 (tm-30) REVERT: L 667 PHE cc_start: 0.6442 (m-80) cc_final: 0.6188 (m-80) REVERT: L 675 ARG cc_start: 0.6925 (mtt180) cc_final: 0.6339 (mtp-110) outliers start: 24 outliers final: 18 residues processed: 201 average time/residue: 0.1432 time to fit residues: 37.7387 Evaluate side-chains 202 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 74 GLU 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 113 GLU 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 K residue 692 SER 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 102 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 108 optimal weight: 40.0000 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN K 699 HIS ** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 670 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.090780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.060717 restraints weight = 29592.701| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.81 r_work: 0.2678 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 13837 Z= 0.147 Angle : 0.599 12.161 19936 Z= 0.350 Chirality : 0.043 0.322 2274 Planarity : 0.004 0.040 1507 Dihedral : 29.841 175.508 4174 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.95 % Allowed : 10.86 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.29), residues: 866 helix: 0.91 (0.23), residues: 560 sheet: -1.45 (1.30), residues: 20 loop : -1.84 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 35 TYR 0.014 0.001 TYR L 647 PHE 0.011 0.001 PHE L 690 TRP 0.001 0.000 TRP K 655 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.15 (13821) covalent geometry : angle 0.58072 / 0.35 (19918) hydrogen bonds : bond 0.05339 / 3.50 ( 679) hydrogen bonds : angle 2.87349 / 2.02 ( 1674) metal coordination : bond 0.03067 / 2.62 ( 16) metal coordination : angle 4.95075 / 2.33 ( 18) *********************** 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 205 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.9449 (t) cc_final: 0.9124 (p) REVERT: A 120 MET cc_start: 0.8179 (mmm) cc_final: 0.7593 (mtt) REVERT: C 73 ASN cc_start: 0.8910 (t0) cc_final: 0.8508 (t0) REVERT: K 657 ASN cc_start: 0.9051 (t0) cc_final: 0.8774 (m-40) REVERT: K 658 MET cc_start: 0.9052 (tpp) cc_final: 0.8702 (tpp) REVERT: K 661 LYS cc_start: 0.8843 (ptpt) cc_final: 0.8516 (ptpp) REVERT: K 675 ARG cc_start: 0.8977 (mmm-85) cc_final: 0.8503 (ttt180) REVERT: L 667 PHE cc_start: 0.6451 (m-80) cc_final: 0.6159 (m-80) REVERT: L 675 ARG cc_start: 0.7031 (mtt180) cc_final: 0.6653 (mtp-110) outliers start: 22 outliers final: 16 residues processed: 192 average time/residue: 0.1365 time to fit residues: 34.1873 Evaluate side-chains 195 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 113 SER Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain F residue 60 VAL 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 K residue 652 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 80 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 108 optimal weight: 0.2980 chunk 35 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN D 47 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.090765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.060612 restraints weight = 29765.749| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.84 r_work: 0.2676 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 13837 Z= 0.143 Angle : 0.585 8.949 19936 Z= 0.343 Chirality : 0.043 0.323 2274 Planarity : 0.004 0.035 1507 Dihedral : 29.875 174.921 4174 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.08 % Allowed : 12.60 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.29), residues: 866 helix: 1.18 (0.23), residues: 560 sheet: -1.45 (1.29), residues: 20 loop : -1.73 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 681 TYR 0.006 0.001 TYR F 51 PHE 0.013 0.001 PHE L 690 TRP 0.005 0.001 TRP L 655 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (13821) covalent geometry : angle 0.57210 / 0.34 (19918) hydrogen bonds : bond 0.05015 / 3.28 ( 679) hydrogen bonds : angle 2.77577 / 1.95 ( 1674) metal coordination : bond 0.02062 / 1.69 ( 16) metal coordination : angle 4.13395 / 2.06 ( 18) *********************** 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 210 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.9408 (t) cc_final: 0.9072 (p) REVERT: A 120 MET cc_start: 0.8137 (mmm) cc_final: 0.7796 (mtt) REVERT: K 658 MET cc_start: 0.9088 (tpp) cc_final: 0.8736 (tpp) REVERT: K 661 LYS cc_start: 0.8907 (ptpt) cc_final: 0.8628 (ptpp) REVERT: K 675 ARG cc_start: 0.8981 (mmm-85) cc_final: 0.8566 (ttt180) REVERT: K 682 LYS cc_start: 0.8414 (mmmt) cc_final: 0.8206 (mmmt) REVERT: L 667 PHE cc_start: 0.6498 (m-80) cc_final: 0.6197 (m-80) REVERT: L 675 ARG cc_start: 0.7355 (mtt180) cc_final: 0.6813 (mtp-110) outliers start: 23 outliers final: 17 residues processed: 199 average time/residue: 0.1459 time to fit residues: 37.9626 Evaluate side-chains 197 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 114 VAL 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 G residue 90 ASP Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 113 GLU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 14 optimal weight: 0.5980 chunk 30 optimal weight: 0.2980 chunk 110 optimal weight: 20.0000 chunk 2 optimal weight: 0.0030 chunk 109 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN D 47 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS G 104 GLN ** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.091097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.061063 restraints weight = 29736.841| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.82 r_work: 0.2688 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13837 Z= 0.133 Angle : 0.564 7.479 19936 Z= 0.334 Chirality : 0.042 0.317 2274 Planarity : 0.003 0.038 1507 Dihedral : 29.883 175.722 4174 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.14 % Allowed : 14.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.29), residues: 866 helix: 1.39 (0.23), residues: 560 sheet: -1.51 (1.26), residues: 20 loop : -1.71 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.006 0.001 TYR F 51 PHE 0.011 0.001 PHE L 690 TRP 0.006 0.001 TRP L 655 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.13 (13821) covalent geometry : angle 0.55473 / 0.33 (19918) hydrogen bonds : bond 0.04639 / 3.04 ( 679) hydrogen bonds : angle 2.66213 / 1.88 ( 1674) metal coordination : bond 0.01249 / 0.92 ( 16) metal coordination : angle 3.49744 / 1.81 ( 18) *********************** 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 200 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.9387 (t) cc_final: 0.9022 (p) REVERT: A 120 MET cc_start: 0.8035 (mmm) cc_final: 0.7689 (mtt) REVERT: K 658 MET cc_start: 0.8958 (tpp) cc_final: 0.8751 (tpp) REVERT: K 674 GLU cc_start: 0.9218 (pp20) cc_final: 0.8970 (pp20) REVERT: K 675 ARG cc_start: 0.8978 (mmm-85) cc_final: 0.8520 (ttt180) REVERT: K 682 LYS cc_start: 0.8328 (mmmt) cc_final: 0.8087 (mmmt) REVERT: L 667 PHE cc_start: 0.6422 (m-80) cc_final: 0.6159 (m-80) outliers start: 16 outliers final: 12 residues processed: 189 average time/residue: 0.1453 time to fit residues: 35.7555 Evaluate side-chains 189 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 G residue 110 ASN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain K residue 660 ILE Chi-restraints excluded: chain K residue 676 LEU 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 85 optimal weight: 30.0000 chunk 9 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN D 84 ASN G 104 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 = 0.3441 r_free = 0.3441 target = 0.088953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.058533 restraints weight = 29326.214| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 1.83 r_work: 0.2619 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13837 Z= 0.176 Angle : 0.606 7.372 19936 Z= 0.350 Chirality : 0.044 0.339 2274 Planarity : 0.004 0.033 1507 Dihedral : 29.997 173.734 4170 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.82 % Allowed : 14.34 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.30), residues: 866 helix: 1.49 (0.23), residues: 561 sheet: -1.48 (1.27), residues: 20 loop : -1.74 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 675 TYR 0.009 0.001 TYR L 647 PHE 0.016 0.001 PHE H 65 TRP 0.006 0.001 TRP L 655 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 (13821) covalent geometry : angle 0.59703 / 0.35 (19918) hydrogen bonds : bond 0.05671 / 3.70 ( 679) hydrogen bonds : angle 2.79102 / 1.97 ( 1674) metal coordination : bond 0.01019 / 0.76 ( 16) metal coordination : angle 3.54091 / 2.03 ( 18) *********************** 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 202 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8219 (mmm) cc_final: 0.7814 (mtt) REVERT: G 74 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8876 (mttp) REVERT: K 658 MET cc_start: 0.9034 (tpp) cc_final: 0.8785 (tpp) REVERT: K 661 LYS cc_start: 0.8948 (ptmt) cc_final: 0.8639 (ptpp) REVERT: K 674 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.9001 (pp20) REVERT: K 675 ARG cc_start: 0.9006 (mmm-85) cc_final: 0.8571 (ttt180) REVERT: K 682 LYS cc_start: 0.8330 (mmmt) cc_final: 0.8124 (mmmt) outliers start: 21 outliers final: 18 residues processed: 190 average time/residue: 0.1386 time to fit residues: 34.2379 Evaluate side-chains 192 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 114 VAL 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 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 660 ILE Chi-restraints excluded: chain K residue 674 GLU Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain K residue 692 SER Chi-restraints excluded: chain L residue 663 CYS Chi-restraints excluded: chain L residue 697 THR Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 99 optimal weight: 40.0000 chunk 19 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN 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 = 0.3421 r_free = 0.3421 target = 0.087895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.057457 restraints weight = 29486.931| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 1.82 r_work: 0.2592 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9187 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13837 Z= 0.198 Angle : 0.628 8.753 19936 Z= 0.357 Chirality : 0.046 0.348 2274 Planarity : 0.004 0.041 1507 Dihedral : 30.085 174.559 4170 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.49 % Allowed : 15.55 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.29), residues: 866 helix: 1.46 (0.23), residues: 561 sheet: -1.62 (1.21), residues: 20 loop : -1.92 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 675 TYR 0.009 0.001 TYR F 51 PHE 0.016 0.002 PHE L 667 TRP 0.006 0.001 TRP L 655 HIS 0.008 0.001 HIS K 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 (13821) covalent geometry : angle 0.61802 / 0.36 (19918) hydrogen bonds : bond 0.05866 / 3.83 ( 679) hydrogen bonds : angle 2.86163 / 2.03 ( 1674) metal coordination : bond 0.01416 / 0.82 ( 16) metal coordination : angle 3.78216 / 1.93 ( 18) *********************** 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 205 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8319 (mmm) cc_final: 0.7812 (mtt) REVERT: D 85 LYS cc_start: 0.9491 (mmtm) cc_final: 0.9248 (mttp) REVERT: E 73 GLU cc_start: 0.9030 (tt0) cc_final: 0.8428 (tt0) REVERT: F 25 ASN cc_start: 0.8938 (m-40) cc_final: 0.8450 (m110) REVERT: G 74 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.9008 (mttp) REVERT: K 658 MET cc_start: 0.9112 (tpp) cc_final: 0.8849 (tpp) REVERT: K 661 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8669 (ptpp) REVERT: K 675 ARG cc_start: 0.9029 (mmm-85) cc_final: 0.8680 (ttt180) REVERT: K 697 THR cc_start: 0.8699 (p) cc_final: 0.8486 (t) outliers start: 26 outliers final: 20 residues processed: 190 average time/residue: 0.1365 time to fit residues: 34.1394 Evaluate side-chains 195 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 122 THR 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 39 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 660 ILE Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain K residue 670 ASN Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain K residue 691 SER Chi-restraints excluded: chain K residue 692 SER 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 95 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN G 104 GLN G 112 GLN H 109 HIS ** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.088988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.058694 restraints weight = 29016.724| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.81 r_work: 0.2624 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9163 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 13837 Z= 0.138 Angle : 0.610 9.004 19936 Z= 0.350 Chirality : 0.044 0.336 2274 Planarity : 0.004 0.057 1507 Dihedral : 30.050 175.618 4170 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.55 % Allowed : 17.29 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.29), residues: 866 helix: 1.61 (0.23), residues: 560 sheet: -1.47 (1.25), residues: 20 loop : -1.85 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG L 675 TYR 0.008 0.001 TYR F 51 PHE 0.012 0.001 PHE H 65 TRP 0.006 0.001 TRP L 655 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (13821) covalent geometry : angle 0.60098 / 0.35 (19918) hydrogen bonds : bond 0.05199 / 3.39 ( 679) hydrogen bonds : angle 2.73778 / 1.93 ( 1674) metal coordination : bond 0.01855 / 1.03 ( 16) metal coordination : angle 3.58649 / 1.85 ( 18) *********************** 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 198 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8168 (mmm) cc_final: 0.7806 (mtt) REVERT: D 85 LYS cc_start: 0.9497 (mmtm) cc_final: 0.9244 (mttp) REVERT: F 25 ASN cc_start: 0.8866 (m-40) cc_final: 0.8414 (m110) REVERT: G 74 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8985 (mttp) REVERT: K 658 MET cc_start: 0.9166 (tpp) cc_final: 0.8874 (tpp) REVERT: K 661 LYS cc_start: 0.8939 (ptmt) cc_final: 0.8648 (ptpp) REVERT: K 675 ARG cc_start: 0.8975 (mmm-85) cc_final: 0.8617 (ttt180) REVERT: K 682 LYS cc_start: 0.8480 (mmmt) cc_final: 0.8258 (mmmt) REVERT: K 697 THR cc_start: 0.8700 (p) cc_final: 0.8498 (t) outliers start: 19 outliers final: 17 residues processed: 187 average time/residue: 0.1273 time to fit residues: 31.2894 Evaluate side-chains 190 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 39 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 113 GLU 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 122 THR Chi-restraints excluded: chain K residue 652 SER Chi-restraints excluded: chain K residue 676 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 8 optimal weight: 0.0370 chunk 81 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 95 GLN 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 = 0.3393 r_free = 0.3393 target = 0.086547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.055984 restraints weight = 29406.988| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 1.83 r_work: 0.2549 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2410 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9221 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13837 Z= 0.258 Angle : 0.697 9.623 19936 Z= 0.387 Chirality : 0.049 0.367 2274 Planarity : 0.005 0.045 1507 Dihedral : 30.144 172.772 4170 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.08 % Allowed : 16.62 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.29), residues: 866 helix: 1.40 (0.23), residues: 559 sheet: -1.54 (1.18), residues: 20 loop : -1.95 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 675 TYR 0.012 0.002 TYR A 54 PHE 0.018 0.002 PHE H 65 TRP 0.007 0.001 TRP K 655 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.26 (13821) covalent geometry : angle 0.68631 / 0.39 (19918) hydrogen bonds : bond 0.07019 / 4.59 ( 679) hydrogen bonds : angle 3.04095 / 2.16 ( 1674) metal coordination : bond 0.00957 / 0.59 ( 16) metal coordination : angle 4.08748 / 2.29 ( 18) *********************** 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 202 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: D 85 LYS cc_start: 0.9499 (mmtm) cc_final: 0.9269 (mttp) REVERT: F 25 ASN cc_start: 0.8975 (m-40) cc_final: 0.8373 (m110) REVERT: H 102 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9248 (mp) REVERT: K 658 MET cc_start: 0.9219 (tpp) cc_final: 0.8927 (tpp) REVERT: K 661 LYS cc_start: 0.8857 (ptmt) cc_final: 0.8617 (ptpt) REVERT: K 682 LYS cc_start: 0.8444 (mmmt) cc_final: 0.8133 (mmmt) REVERT: K 688 LYS cc_start: 0.9062 (ttpp) cc_final: 0.8719 (ttpt) outliers start: 23 outliers final: 17 residues processed: 189 average time/residue: 0.1510 time to fit residues: 37.5283 Evaluate side-chains 194 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 50 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 102 LEU 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 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 21 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 30.0000 chunk 100 optimal weight: 40.0000 chunk 42 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN G 112 GLN ** 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 = 0.3405 r_free = 0.3405 target = 0.087090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.056834 restraints weight = 29386.887| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 1.81 r_work: 0.2570 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2430 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9207 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13837 Z= 0.179 Angle : 0.668 9.312 19936 Z= 0.376 Chirality : 0.047 0.357 2274 Planarity : 0.004 0.034 1507 Dihedral : 30.142 174.043 4170 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.41 % Allowed : 17.96 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.29), residues: 866 helix: 1.48 (0.23), residues: 559 sheet: -1.80 (1.09), residues: 20 loop : -1.88 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 675 TYR 0.011 0.001 TYR F 51 PHE 0.016 0.001 PHE H 65 TRP 0.006 0.001 TRP K 655 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (13821) covalent geometry : angle 0.65741 / 0.38 (19918) hydrogen bonds : bond 0.06184 / 4.05 ( 679) hydrogen bonds : angle 2.93418 / 2.07 ( 1674) metal coordination : bond 0.01213 / 0.73 ( 16) metal coordination : angle 3.96462 / 2.32 ( 18) ********************** 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 196 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 85 LYS cc_start: 0.9505 (mmtm) cc_final: 0.9273 (mttp) REVERT: F 25 ASN cc_start: 0.8899 (m-40) cc_final: 0.8378 (m110) REVERT: G 92 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8756 (mp0) REVERT: H 102 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9200 (mp) REVERT: K 658 MET cc_start: 0.9208 (tpp) cc_final: 0.8890 (tpp) REVERT: K 661 LYS cc_start: 0.8902 (ptmt) cc_final: 0.8619 (ptpt) REVERT: K 675 ARG cc_start: 0.8985 (mmm-85) cc_final: 0.8667 (ttt180) REVERT: K 682 LYS cc_start: 0.8351 (mmmt) cc_final: 0.8096 (mmmt) REVERT: K 688 LYS cc_start: 0.9059 (ttpp) cc_final: 0.8679 (ttpt) outliers start: 18 outliers final: 17 residues processed: 185 average time/residue: 0.1433 time to fit residues: 34.5789 Evaluate side-chains 192 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 652 SER Chi-restraints excluded: chain K residue 670 ASN Chi-restraints excluded: chain K residue 676 LEU 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 12 optimal weight: 0.8980 chunk 66 optimal weight: 0.0170 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN G 112 GLN ** 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 = 0.3415 r_free = 0.3415 target = 0.087584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.057388 restraints weight = 29123.633| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 1.80 r_work: 0.2587 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2448 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9195 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13837 Z= 0.147 Angle : 0.645 10.270 19936 Z= 0.364 Chirality : 0.046 0.349 2274 Planarity : 0.004 0.035 1507 Dihedral : 30.119 174.653 4170 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.68 % Allowed : 17.29 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.29), residues: 866 helix: 1.58 (0.23), residues: 559 sheet: -1.88 (1.08), residues: 20 loop : -1.79 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 675 TYR 0.010 0.001 TYR F 51 PHE 0.013 0.001 PHE H 65 TRP 0.005 0.001 TRP K 655 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 (13821) covalent geometry : angle 0.63397 / 0.36 (19918) hydrogen bonds : bond 0.05770 / 3.78 ( 679) hydrogen bonds : angle 2.86977 / 2.02 ( 1674) metal coordination : bond 0.01252 / 0.74 ( 16) metal coordination : angle 3.99391 / 2.34 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2955.50 seconds wall clock time: 51 minutes 0.77 seconds (3060.77 seconds total)