Starting phenix.real_space_refine on Thu May 15 05:04:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t3y_41016/05_2025/8t3y_41016.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3y_41016/05_2025/8t3y_41016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t3y_41016/05_2025/8t3y_41016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3y_41016/05_2025/8t3y_41016.map" model { file = "/net/cci-nas-00/data/ceres_data/8t3y_41016/05_2025/8t3y_41016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3y_41016/05_2025/8t3y_41016.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 292 5.49 5 S 32 5.16 5 C 7249 2.51 5 N 2425 2.21 5 O 2999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13001 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 543 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "L" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 543 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12166 SG CYS K 663 94.355 72.816 65.837 1.00139.73 S ATOM 12325 SG CYS K 683 93.142 74.641 62.690 1.00119.37 S ATOM 12345 SG CYS K 686 96.345 72.628 62.545 1.00125.56 S ATOM 12049 SG CYS K 648 85.738 81.611 66.914 1.00162.60 S ATOM 12069 SG CYS K 651 83.084 84.229 67.970 1.00163.36 S ATOM 12204 SG CYS K 668 82.674 80.608 68.908 1.00143.24 S ATOM 12227 SG CYS K 671 81.963 81.360 65.671 1.00136.31 S ATOM 12709 SG CYS L 663 91.116 70.796 85.897 1.00172.78 S ATOM 12868 SG CYS L 683 92.443 70.565 89.900 1.00186.18 S ATOM 12888 SG CYS L 686 89.213 70.114 89.733 1.00190.44 S ATOM 12592 SG CYS L 648 100.439 80.745 85.760 1.00189.02 S ATOM 12612 SG CYS L 651 103.664 82.864 85.645 1.00190.09 S ATOM 12747 SG CYS L 668 103.350 79.634 83.727 1.00189.67 S ATOM 12770 SG CYS L 671 103.665 79.459 87.442 1.00190.98 S Time building chain proxies: 7.93, per 1000 atoms: 0.61 Number of scatterers: 13001 At special positions: 0 Unit cell: (127.395, 115.425, 117.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 32 16.00 P 292 15.00 O 2999 8.00 N 2425 7.00 C 7249 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 801 " pdb="ZN ZN K 801 " - pdb=" ND1 HIS K 665 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 683 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 686 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 663 " pdb=" ZN K 802 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 668 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 671 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 651 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 648 " pdb=" ZN L 801 " pdb="ZN ZN L 801 " - pdb=" ND1 HIS L 665 " pdb="ZN ZN L 801 " - pdb=" SG CYS L 663 " pdb="ZN ZN L 801 " - pdb=" SG CYS L 683 " pdb="ZN ZN L 801 " - pdb=" SG CYS L 686 " pdb=" ZN L 802 " pdb="ZN ZN L 802 " - pdb=" SG CYS L 668 " pdb="ZN ZN L 802 " - pdb=" SG CYS L 648 " pdb="ZN ZN L 802 " - pdb=" SG CYS L 671 " pdb="ZN ZN L 802 " - pdb=" SG CYS L 651 " Number of angles added : 18 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1672 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 10 sheets defined 65.7% alpha, 3.4% beta 134 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 6.34 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.713A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.544A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.759A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.505A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.701A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.527A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.562A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 35 removed outlier: 3.665A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.585A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.866A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.604A pdb=" N LEU C 116 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.719A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.716A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 100 removed outlier: 3.689A pdb=" N ARG D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.647A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 removed outlier: 3.788A pdb=" N ILE E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.562A pdb=" N ALA E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER E 96 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN E 108 " --> pdb=" O PHE E 104 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.988A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.885A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.516A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.009A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL F 57 " --> pdb=" O GLU F 53 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE F 66 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 4.137A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.851A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 73 removed outlier: 3.978A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 85 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.873A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.686A pdb=" N VAL H 66 " --> pdb=" O MET H 62 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU H 80 " --> pdb=" O GLU H 76 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.858A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 123 removed outlier: 4.318A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 633 through 647 removed outlier: 3.758A pdb=" N LEU K 645 " --> pdb=" O ASN K 641 " (cutoff:3.500A) Processing helix chain 'K' and resid 668 through 677 removed outlier: 3.699A pdb=" N GLU K 674 " --> pdb=" O ASN K 670 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG K 675 " --> pdb=" O CYS K 671 " (cutoff:3.500A) Processing helix chain 'K' and resid 691 through 693 No H-bonds generated for 'chain 'K' and resid 691 through 693' Processing helix chain 'L' and resid 633 through 647 removed outlier: 4.039A pdb=" N GLU L 638 " --> pdb=" O ALA L 634 " (cutoff:3.500A) Processing helix chain 'L' and resid 669 through 678 removed outlier: 3.732A pdb=" N LYS L 673 " --> pdb=" O GLU L 669 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU L 674 " --> pdb=" O ASN L 670 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG L 675 " --> pdb=" O CYS L 671 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU L 676 " --> pdb=" O CYS L 672 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA L 678 " --> pdb=" O GLU L 674 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.587A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 7.073A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.521A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.715A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.852A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.561A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.455A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 666 through 667 Processing sheet with id=AB1, first strand: chain 'L' and resid 666 through 667 331 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 696 hydrogen bond angles 0 basepair planarities 134 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1728 1.32 - 1.45: 5025 1.45 - 1.57: 6440 1.57 - 1.70: 582 1.70 - 1.82: 46 Bond restraints: 13821 Sorted by residual: bond pdb=" CA ARG A 53 " pdb=" C ARG A 53 " ideal model delta sigma weight residual 1.524 1.489 0.035 1.29e-02 6.01e+03 7.38e+00 bond pdb=" C TYR A 54 " pdb=" O TYR A 54 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.31e-02 5.83e+03 7.26e+00 bond pdb=" O3' DT J 140 " pdb=" P DT J 141 " ideal model delta sigma weight residual 1.607 1.644 -0.037 1.50e-02 4.44e+03 6.24e+00 bond pdb=" C ARG A 53 " pdb=" O ARG A 53 " ideal model delta sigma weight residual 1.236 1.207 0.029 1.19e-02 7.06e+03 5.92e+00 bond pdb=" C LYS H 120 " pdb=" O LYS H 120 " ideal model delta sigma weight residual 1.237 1.208 0.028 1.19e-02 7.06e+03 5.61e+00 ... (remaining 13816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 19334 1.69 - 3.38: 535 3.38 - 5.06: 37 5.06 - 6.75: 11 6.75 - 8.44: 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 111.36 117.42 -6.06 1.09e+00 8.42e-01 3.09e+01 angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.71 108.49 5.22 9.50e-01 1.11e+00 3.02e+01 angle pdb=" O3' DC I 78 " pdb=" C3' DC I 78 " pdb=" C2' DC I 78 " ideal model delta sigma weight residual 111.50 105.07 6.43 1.50e+00 4.44e-01 1.84e+01 angle pdb=" N GLY E 132 " pdb=" CA GLY E 132 " pdb=" C GLY E 132 " ideal model delta sigma weight residual 113.18 121.62 -8.44 2.37e+00 1.78e-01 1.27e+01 angle pdb=" O3' DT J 99 " pdb=" C3' DT J 99 " pdb=" C2' DT J 99 " ideal model delta sigma weight residual 111.50 106.43 5.07 1.50e+00 4.44e-01 1.14e+01 ... (remaining 19913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 6216 34.73 - 69.47: 1341 69.47 - 104.20: 13 104.20 - 138.94: 0 138.94 - 173.67: 3 Dihedral angle restraints: 7573 sinusoidal: 4993 harmonic: 2580 Sorted by residual: dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 46.33 173.67 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual -140.00 31.72 -171.72 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 69.93 150.07 1 3.50e+01 8.16e-04 1.46e+01 ... (remaining 7570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1973 0.052 - 0.104: 258 0.104 - 0.157: 32 0.157 - 0.209: 5 0.209 - 0.261: 6 Chirality restraints: 2274 Sorted by residual: chirality pdb=" CA ARG E 131 " pdb=" N ARG E 131 " pdb=" C ARG E 131 " pdb=" CB ARG E 131 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ASN L 687 " pdb=" N ASN L 687 " pdb=" C ASN L 687 " pdb=" CB ASN L 687 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA THR A 58 " pdb=" N THR A 58 " pdb=" C THR A 58 " pdb=" CB THR A 58 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2271 not shown) Planarity restraints: 1507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO E 43 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 100 " 0.020 2.00e-02 2.50e+03 8.26e-03 2.05e+00 pdb=" N9 DG I 100 " -0.018 2.00e-02 2.50e+03 pdb=" C8 DG I 100 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 100 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 100 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 100 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 100 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 100 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 100 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 100 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 100 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 100 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " 0.019 2.00e-02 2.50e+03 8.62e-03 2.04e+00 pdb=" N9 DA I 20 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " -0.002 2.00e-02 2.50e+03 ... (remaining 1504 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2801 2.81 - 3.33: 10764 3.33 - 3.85: 22906 3.85 - 4.38: 27619 4.38 - 4.90: 39610 Nonbonded interactions: 103700 Sorted by model distance: nonbonded pdb=" N THR L 662 " pdb=" OD2 ASP L 694 " model vdw 2.284 3.120 nonbonded pdb=" OE2 GLU A 50 " pdb=" NE ARG B 39 " model vdw 2.320 3.120 nonbonded pdb=" N CYS L 683 " pdb=" O LYS L 688 " model vdw 2.320 3.120 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.342 3.040 nonbonded pdb=" O TYR K 647 " pdb=" NZ LYS K 656 " model vdw 2.370 3.120 ... (remaining 103695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 32 through 124) } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 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: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 38.280 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 44.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.628 13837 Z= 0.335 Angle : 0.726 44.076 19936 Z= 0.423 Chirality : 0.039 0.261 2274 Planarity : 0.003 0.045 1507 Dihedral : 26.537 173.671 5901 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.74 % Allowed : 1.21 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.28), residues: 866 helix: -0.07 (0.23), residues: 539 sheet: -1.72 (0.98), residues: 30 loop : -2.10 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 655 HIS 0.003 0.001 HIS A 113 PHE 0.020 0.002 PHE L 690 TYR 0.009 0.001 TYR A 54 ARG 0.003 0.001 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.18344 ( 679) hydrogen bonds : angle 4.69391 ( 1674) metal coordination : bond 0.21940 ( 16) metal coordination : angle 11.33189 ( 18) covalent geometry : bond 0.00374 (13821) covalent geometry : angle 0.64191 (19918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 249 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8419 (mmm) cc_final: 0.7945 (mtt) REVERT: B 59 LYS cc_start: 0.9028 (tttm) cc_final: 0.8814 (ttpp) REVERT: E 73 GLU cc_start: 0.7972 (tt0) cc_final: 0.7669 (tt0) REVERT: F 25 ASN cc_start: 0.9112 (m110) cc_final: 0.8673 (m110) REVERT: H 113 GLU cc_start: 0.8196 (tp30) cc_final: 0.7984 (tp30) REVERT: K 647 TYR cc_start: 0.8040 (m-10) cc_final: 0.6852 (m-80) REVERT: K 658 MET cc_start: 0.8527 (tpp) cc_final: 0.8304 (tpp) REVERT: K 693 ASN cc_start: 0.9276 (p0) cc_final: 0.9039 (p0) REVERT: L 693 ASN cc_start: 0.7363 (OUTLIER) cc_final: 0.6977 (m-40) REVERT: L 694 ASP cc_start: 0.6627 (OUTLIER) cc_final: 0.6113 (m-30) outliers start: 13 outliers final: 5 residues processed: 257 average time/residue: 0.3801 time to fit residues: 124.0579 Evaluate side-chains 177 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 170 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain L residue 693 ASN Chi-restraints excluded: chain L residue 694 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS B 93 GLN C 104 GLN E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN K 654 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.083574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.054739 restraints weight = 33935.600| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.02 r_work: 0.2541 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13837 Z= 0.239 Angle : 0.626 11.840 19936 Z= 0.361 Chirality : 0.037 0.129 2274 Planarity : 0.005 0.043 1507 Dihedral : 29.417 172.262 4184 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.68 % Allowed : 8.85 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.29), residues: 866 helix: 0.54 (0.23), residues: 563 sheet: -1.91 (1.02), residues: 20 loop : -1.94 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 655 HIS 0.006 0.001 HIS C 31 PHE 0.015 0.002 PHE L 690 TYR 0.019 0.001 TYR K 647 ARG 0.004 0.001 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.05922 ( 679) hydrogen bonds : angle 3.05993 ( 1674) metal coordination : bond 0.01702 ( 16) metal coordination : angle 4.51156 ( 18) covalent geometry : bond 0.00546 (13821) covalent geometry : angle 0.61155 (19918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8790 (mmm) cc_final: 0.8413 (mtt) REVERT: B 84 MET cc_start: 0.9054 (mmt) cc_final: 0.8767 (mmt) REVERT: C 91 GLU cc_start: 0.7882 (pm20) cc_final: 0.7526 (pm20) REVERT: C 92 GLU cc_start: 0.8726 (mp0) cc_final: 0.8276 (mp0) REVERT: D 34 LYS cc_start: 0.9203 (mtmm) cc_final: 0.8931 (mtpt) REVERT: E 73 GLU cc_start: 0.8771 (tt0) cc_final: 0.8453 (tt0) REVERT: F 25 ASN cc_start: 0.9303 (m110) cc_final: 0.8771 (m110) REVERT: F 74 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8555 (tp30) REVERT: G 90 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8159 (p0) REVERT: K 647 TYR cc_start: 0.7945 (m-10) cc_final: 0.7680 (m-80) REVERT: K 658 MET cc_start: 0.8761 (tpp) cc_final: 0.8464 (tpp) REVERT: K 688 LYS cc_start: 0.9088 (mmmm) cc_final: 0.8526 (mptt) REVERT: L 655 TRP cc_start: 0.8761 (m100) cc_final: 0.8535 (m100) REVERT: L 693 ASN cc_start: 0.7984 (OUTLIER) cc_final: 0.7157 (p0) outliers start: 20 outliers final: 12 residues processed: 186 average time/residue: 0.3429 time to fit residues: 83.9063 Evaluate side-chains 178 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain L residue 657 ASN Chi-restraints excluded: chain L residue 693 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 654 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.084409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.055570 restraints weight = 34085.652| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.05 r_work: 0.2562 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13837 Z= 0.177 Angle : 0.572 11.796 19936 Z= 0.334 Chirality : 0.035 0.157 2274 Planarity : 0.004 0.083 1507 Dihedral : 29.339 172.599 4176 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.08 % Allowed : 11.39 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.29), residues: 866 helix: 0.88 (0.23), residues: 561 sheet: -1.41 (1.12), residues: 20 loop : -1.91 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 655 HIS 0.008 0.001 HIS L 699 PHE 0.012 0.001 PHE K 642 TYR 0.017 0.001 TYR K 647 ARG 0.008 0.001 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.04805 ( 679) hydrogen bonds : angle 2.81970 ( 1674) metal coordination : bond 0.00662 ( 16) metal coordination : angle 4.22370 ( 18) covalent geometry : bond 0.00392 (13821) covalent geometry : angle 0.55797 (19918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8751 (mmm) cc_final: 0.8321 (mtt) REVERT: C 35 ARG cc_start: 0.8857 (ttp80) cc_final: 0.8657 (ttp80) REVERT: D 34 LYS cc_start: 0.9189 (mtmm) cc_final: 0.8933 (mtpt) REVERT: E 73 GLU cc_start: 0.8789 (tt0) cc_final: 0.8445 (tt0) REVERT: F 25 ASN cc_start: 0.9302 (m110) cc_final: 0.8852 (m110) REVERT: F 74 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8615 (tp30) REVERT: K 658 MET cc_start: 0.8850 (tpp) cc_final: 0.8478 (tpp) REVERT: K 688 LYS cc_start: 0.9130 (mmmm) cc_final: 0.8586 (mptt) REVERT: L 647 TYR cc_start: 0.8872 (m-80) cc_final: 0.8278 (m-80) REVERT: L 655 TRP cc_start: 0.8936 (m100) cc_final: 0.8511 (m100) outliers start: 23 outliers final: 19 residues processed: 179 average time/residue: 0.3432 time to fit residues: 80.4921 Evaluate side-chains 182 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 654 ASN Chi-restraints excluded: chain L residue 657 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.0980 chunk 53 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN F 27 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN L 654 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.084730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.056028 restraints weight = 33914.844| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 2.04 r_work: 0.2577 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13837 Z= 0.160 Angle : 0.565 12.068 19936 Z= 0.329 Chirality : 0.034 0.157 2274 Planarity : 0.004 0.050 1507 Dihedral : 29.321 172.839 4172 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.08 % Allowed : 12.47 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.29), residues: 866 helix: 1.12 (0.23), residues: 566 sheet: -1.48 (1.12), residues: 20 loop : -1.78 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 655 HIS 0.007 0.001 HIS B 75 PHE 0.048 0.002 PHE L 642 TYR 0.021 0.001 TYR K 647 ARG 0.021 0.000 ARG K 643 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 679) hydrogen bonds : angle 2.66873 ( 1674) metal coordination : bond 0.00744 ( 16) metal coordination : angle 4.61533 ( 18) covalent geometry : bond 0.00349 (13821) covalent geometry : angle 0.54802 (19918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8728 (mmm) cc_final: 0.8403 (mtp) REVERT: C 91 GLU cc_start: 0.7763 (pm20) cc_final: 0.7203 (pm20) REVERT: C 92 GLU cc_start: 0.8650 (mp0) cc_final: 0.7968 (mp0) REVERT: D 34 LYS cc_start: 0.9172 (mtmm) cc_final: 0.8945 (mtpt) REVERT: E 73 GLU cc_start: 0.8804 (tt0) cc_final: 0.8574 (tt0) REVERT: F 25 ASN cc_start: 0.9209 (m110) cc_final: 0.8713 (m110) REVERT: F 74 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8653 (tp30) REVERT: G 90 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8263 (p0) REVERT: K 642 PHE cc_start: 0.7644 (m-80) cc_final: 0.7006 (m-80) REVERT: K 643 ARG cc_start: 0.7287 (mmm160) cc_final: 0.6892 (mmm160) REVERT: K 647 TYR cc_start: 0.8463 (m-80) cc_final: 0.8127 (m-80) REVERT: K 658 MET cc_start: 0.8928 (tpp) cc_final: 0.8550 (tpp) REVERT: L 647 TYR cc_start: 0.8832 (m-80) cc_final: 0.8405 (m-80) REVERT: L 655 TRP cc_start: 0.8966 (m100) cc_final: 0.8702 (m100) outliers start: 23 outliers final: 17 residues processed: 181 average time/residue: 0.3466 time to fit residues: 81.9506 Evaluate side-chains 181 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 654 ASN Chi-restraints excluded: chain L residue 657 ASN Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9980 chunk 9 optimal weight: 0.0770 chunk 51 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS L 654 ASN L 670 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.085284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.056569 restraints weight = 33958.007| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.03 r_work: 0.2594 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13837 Z= 0.152 Angle : 0.555 11.218 19936 Z= 0.322 Chirality : 0.034 0.159 2274 Planarity : 0.003 0.038 1507 Dihedral : 29.289 173.097 4172 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.82 % Allowed : 13.67 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.29), residues: 866 helix: 1.36 (0.23), residues: 566 sheet: -1.53 (1.13), residues: 20 loop : -1.66 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 655 HIS 0.007 0.001 HIS L 699 PHE 0.031 0.002 PHE L 642 TYR 0.018 0.001 TYR K 647 ARG 0.012 0.000 ARG L 643 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 679) hydrogen bonds : angle 2.58047 ( 1674) metal coordination : bond 0.00742 ( 16) metal coordination : angle 4.54834 ( 18) covalent geometry : bond 0.00330 (13821) covalent geometry : angle 0.53851 (19918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8677 (mmm) cc_final: 0.8343 (mtp) REVERT: C 91 GLU cc_start: 0.7792 (pm20) cc_final: 0.7269 (pm20) REVERT: C 92 GLU cc_start: 0.8655 (mp0) cc_final: 0.7891 (mp0) REVERT: D 34 LYS cc_start: 0.9142 (mtmm) cc_final: 0.8929 (mtpt) REVERT: E 73 GLU cc_start: 0.8806 (tt0) cc_final: 0.8589 (tt0) REVERT: F 25 ASN cc_start: 0.9191 (m110) cc_final: 0.8745 (m110) REVERT: F 74 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8672 (tp30) REVERT: K 642 PHE cc_start: 0.7793 (m-80) cc_final: 0.7509 (m-80) REVERT: K 647 TYR cc_start: 0.8424 (m-80) cc_final: 0.8121 (m-80) REVERT: K 658 MET cc_start: 0.8965 (tpp) cc_final: 0.8574 (tpp) REVERT: L 647 TYR cc_start: 0.8797 (m-80) cc_final: 0.8390 (m-80) REVERT: L 655 TRP cc_start: 0.8978 (m100) cc_final: 0.8737 (m100) outliers start: 21 outliers final: 20 residues processed: 187 average time/residue: 0.3345 time to fit residues: 82.3981 Evaluate side-chains 186 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 654 ASN Chi-restraints excluded: chain L residue 657 ASN Chi-restraints excluded: chain L residue 662 THR Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 106 optimal weight: 20.0000 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN L 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.085416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.056712 restraints weight = 34601.351| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.10 r_work: 0.2598 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13837 Z= 0.149 Angle : 0.551 10.941 19936 Z= 0.319 Chirality : 0.033 0.165 2274 Planarity : 0.003 0.036 1507 Dihedral : 29.270 173.336 4170 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.08 % Allowed : 13.94 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.29), residues: 866 helix: 1.55 (0.23), residues: 566 sheet: -1.39 (1.16), residues: 20 loop : -1.57 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 655 HIS 0.005 0.001 HIS B 75 PHE 0.045 0.002 PHE L 642 TYR 0.017 0.001 TYR K 647 ARG 0.012 0.000 ARG L 643 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 679) hydrogen bonds : angle 2.50097 ( 1674) metal coordination : bond 0.00679 ( 16) metal coordination : angle 4.56327 ( 18) covalent geometry : bond 0.00324 (13821) covalent geometry : angle 0.53393 (19918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8656 (mmm) cc_final: 0.8339 (mtp) REVERT: C 92 GLU cc_start: 0.8702 (mp0) cc_final: 0.8468 (mp0) REVERT: E 73 GLU cc_start: 0.8812 (tt0) cc_final: 0.8527 (tt0) REVERT: F 25 ASN cc_start: 0.9177 (m110) cc_final: 0.8741 (m110) REVERT: K 642 PHE cc_start: 0.7821 (m-80) cc_final: 0.7328 (m-80) REVERT: K 645 LEU cc_start: 0.8973 (mt) cc_final: 0.8734 (tp) REVERT: K 647 TYR cc_start: 0.8295 (m-80) cc_final: 0.7981 (m-80) REVERT: K 658 MET cc_start: 0.8966 (tpp) cc_final: 0.8572 (tpp) REVERT: K 699 HIS cc_start: 0.7563 (m90) cc_final: 0.7247 (m-70) REVERT: L 647 TYR cc_start: 0.8845 (m-80) cc_final: 0.8542 (m-80) REVERT: L 655 TRP cc_start: 0.8977 (m100) cc_final: 0.8758 (m100) REVERT: L 661 LYS cc_start: 0.9106 (ttmt) cc_final: 0.8880 (mttp) REVERT: L 688 LYS cc_start: 0.9315 (mttt) cc_final: 0.8788 (tptp) outliers start: 23 outliers final: 19 residues processed: 190 average time/residue: 0.3420 time to fit residues: 85.4805 Evaluate side-chains 189 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 654 ASN Chi-restraints excluded: chain L residue 670 ASN Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN E 68 GLN L 654 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.083137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.054276 restraints weight = 34242.053| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.05 r_work: 0.2528 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13837 Z= 0.214 Angle : 0.598 10.111 19936 Z= 0.344 Chirality : 0.036 0.173 2274 Planarity : 0.004 0.058 1507 Dihedral : 29.382 171.640 4170 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.22 % Allowed : 14.34 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.29), residues: 866 helix: 1.50 (0.22), residues: 569 sheet: -1.38 (1.19), residues: 20 loop : -1.63 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 655 HIS 0.006 0.001 HIS L 699 PHE 0.032 0.002 PHE L 642 TYR 0.012 0.001 TYR K 647 ARG 0.013 0.001 ARG L 643 Details of bonding type rmsd hydrogen bonds : bond 0.05256 ( 679) hydrogen bonds : angle 2.74467 ( 1674) metal coordination : bond 0.00683 ( 16) metal coordination : angle 4.69275 ( 18) covalent geometry : bond 0.00489 (13821) covalent geometry : angle 0.58124 (19918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8846 (mmm) cc_final: 0.8258 (mtt) REVERT: B 84 MET cc_start: 0.9150 (mmm) cc_final: 0.8930 (mmt) REVERT: C 91 GLU cc_start: 0.7855 (pm20) cc_final: 0.7137 (pm20) REVERT: C 92 GLU cc_start: 0.8597 (mp0) cc_final: 0.8021 (mp0) REVERT: F 25 ASN cc_start: 0.9190 (m110) cc_final: 0.8734 (m110) REVERT: K 642 PHE cc_start: 0.7829 (m-80) cc_final: 0.7296 (m-80) REVERT: K 645 LEU cc_start: 0.8988 (mt) cc_final: 0.8718 (tp) REVERT: K 647 TYR cc_start: 0.8371 (m-80) cc_final: 0.8023 (m-80) REVERT: K 658 MET cc_start: 0.8991 (tpp) cc_final: 0.8756 (tpp) REVERT: K 688 LYS cc_start: 0.9222 (mmmm) cc_final: 0.8672 (mptt) REVERT: K 699 HIS cc_start: 0.7781 (m90) cc_final: 0.7349 (m-70) REVERT: L 647 TYR cc_start: 0.8832 (m-80) cc_final: 0.8348 (m-80) REVERT: L 661 LYS cc_start: 0.9119 (ttmt) cc_final: 0.8871 (mttp) REVERT: L 688 LYS cc_start: 0.9371 (mttt) cc_final: 0.8786 (tptp) outliers start: 24 outliers final: 22 residues processed: 183 average time/residue: 0.3342 time to fit residues: 80.5008 Evaluate side-chains 187 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 654 ASN Chi-restraints excluded: chain L residue 670 ASN Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 102 optimal weight: 40.0000 chunk 25 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN L 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.083891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.055226 restraints weight = 34123.838| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.06 r_work: 0.2554 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13837 Z= 0.172 Angle : 0.579 9.890 19936 Z= 0.333 Chirality : 0.034 0.161 2274 Planarity : 0.004 0.038 1507 Dihedral : 29.327 172.833 4170 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.95 % Allowed : 15.15 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.29), residues: 866 helix: 1.57 (0.22), residues: 572 sheet: -1.46 (1.17), residues: 20 loop : -1.61 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 655 HIS 0.006 0.001 HIS L 699 PHE 0.044 0.002 PHE L 642 TYR 0.018 0.001 TYR L 647 ARG 0.012 0.000 ARG L 643 Details of bonding type rmsd hydrogen bonds : bond 0.04567 ( 679) hydrogen bonds : angle 2.61799 ( 1674) metal coordination : bond 0.00639 ( 16) metal coordination : angle 4.77345 ( 18) covalent geometry : bond 0.00383 (13821) covalent geometry : angle 0.56082 (19918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8756 (mmm) cc_final: 0.8352 (mtt) REVERT: C 91 GLU cc_start: 0.7823 (pm20) cc_final: 0.7189 (pm20) REVERT: C 92 GLU cc_start: 0.8589 (mp0) cc_final: 0.8021 (mp0) REVERT: F 25 ASN cc_start: 0.9091 (m110) cc_final: 0.8529 (m-40) REVERT: K 642 PHE cc_start: 0.7696 (m-80) cc_final: 0.7213 (m-80) REVERT: K 645 LEU cc_start: 0.8914 (mt) cc_final: 0.8619 (tp) REVERT: K 647 TYR cc_start: 0.8265 (m-80) cc_final: 0.7917 (m-80) REVERT: K 658 MET cc_start: 0.9013 (tpp) cc_final: 0.8780 (tpp) REVERT: K 688 LYS cc_start: 0.9235 (mmmm) cc_final: 0.8700 (mptt) REVERT: K 699 HIS cc_start: 0.7778 (m90) cc_final: 0.7378 (m-70) REVERT: L 647 TYR cc_start: 0.8728 (m-80) cc_final: 0.8347 (m-80) REVERT: L 661 LYS cc_start: 0.9093 (ttmt) cc_final: 0.8866 (mttp) REVERT: L 688 LYS cc_start: 0.9313 (mttt) cc_final: 0.8635 (tptp) outliers start: 22 outliers final: 21 residues processed: 178 average time/residue: 0.3180 time to fit residues: 75.0907 Evaluate side-chains 187 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 654 ASN Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 83 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN L 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.084753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.056301 restraints weight = 34113.419| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.05 r_work: 0.2587 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13837 Z= 0.147 Angle : 0.569 9.563 19936 Z= 0.327 Chirality : 0.033 0.199 2274 Planarity : 0.004 0.037 1507 Dihedral : 29.271 173.663 4170 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.82 % Allowed : 15.68 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.29), residues: 866 helix: 1.70 (0.22), residues: 571 sheet: -1.53 (1.14), residues: 20 loop : -1.52 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 655 HIS 0.005 0.001 HIS L 699 PHE 0.036 0.001 PHE L 642 TYR 0.015 0.001 TYR K 647 ARG 0.009 0.000 ARG L 643 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 679) hydrogen bonds : angle 2.49461 ( 1674) metal coordination : bond 0.00653 ( 16) metal coordination : angle 4.71784 ( 18) covalent geometry : bond 0.00319 (13821) covalent geometry : angle 0.55115 (19918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8663 (mmm) cc_final: 0.8338 (mtp) REVERT: C 91 GLU cc_start: 0.7839 (pm20) cc_final: 0.7204 (pm20) REVERT: C 92 GLU cc_start: 0.8588 (mp0) cc_final: 0.8004 (mp0) REVERT: F 25 ASN cc_start: 0.9013 (m110) cc_final: 0.8478 (m-40) REVERT: K 642 PHE cc_start: 0.7672 (m-80) cc_final: 0.7161 (m-80) REVERT: K 645 LEU cc_start: 0.8837 (mt) cc_final: 0.8533 (tp) REVERT: K 647 TYR cc_start: 0.8217 (m-80) cc_final: 0.7870 (m-80) REVERT: K 658 MET cc_start: 0.9026 (tpp) cc_final: 0.8781 (tpp) REVERT: K 699 HIS cc_start: 0.7792 (m90) cc_final: 0.7474 (m-70) REVERT: L 647 TYR cc_start: 0.8773 (m-80) cc_final: 0.8399 (m-80) REVERT: L 688 LYS cc_start: 0.9290 (mttt) cc_final: 0.8600 (tptp) outliers start: 21 outliers final: 17 residues processed: 183 average time/residue: 0.3323 time to fit residues: 80.5530 Evaluate side-chains 186 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain L residue 654 ASN Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 18 optimal weight: 0.0570 overall best weight: 3.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN L 654 ASN L 670 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.081973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.053127 restraints weight = 33991.204| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 2.05 r_work: 0.2494 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13837 Z= 0.275 Angle : 0.642 11.005 19936 Z= 0.366 Chirality : 0.039 0.169 2274 Planarity : 0.005 0.046 1507 Dihedral : 29.397 170.848 4170 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.82 % Allowed : 15.68 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.29), residues: 866 helix: 1.52 (0.22), residues: 569 sheet: -1.52 (1.17), residues: 20 loop : -1.61 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 655 HIS 0.005 0.001 HIS L 699 PHE 0.030 0.002 PHE L 642 TYR 0.012 0.001 TYR K 647 ARG 0.012 0.001 ARG L 643 Details of bonding type rmsd hydrogen bonds : bond 0.05903 ( 679) hydrogen bonds : angle 2.89573 ( 1674) metal coordination : bond 0.00971 ( 16) metal coordination : angle 4.87344 ( 18) covalent geometry : bond 0.00633 (13821) covalent geometry : angle 0.62534 (19918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8885 (mmm) cc_final: 0.8581 (mtp) REVERT: B 84 MET cc_start: 0.9174 (mmm) cc_final: 0.8932 (mmt) REVERT: C 91 GLU cc_start: 0.7924 (pm20) cc_final: 0.7334 (pm20) REVERT: C 92 GLU cc_start: 0.8616 (mp0) cc_final: 0.8042 (mp0) REVERT: F 25 ASN cc_start: 0.9103 (m110) cc_final: 0.8566 (m-40) REVERT: K 642 PHE cc_start: 0.7728 (m-80) cc_final: 0.7248 (m-80) REVERT: K 645 LEU cc_start: 0.8945 (mt) cc_final: 0.8628 (tp) REVERT: K 647 TYR cc_start: 0.8327 (m-80) cc_final: 0.8092 (m-80) REVERT: K 658 MET cc_start: 0.9021 (tpp) cc_final: 0.8675 (tpp) REVERT: K 687 ASN cc_start: 0.9153 (t0) cc_final: 0.8929 (t0) REVERT: K 688 LYS cc_start: 0.9262 (mmmm) cc_final: 0.9016 (mmmm) REVERT: K 699 HIS cc_start: 0.7819 (m90) cc_final: 0.7420 (m-70) REVERT: L 647 TYR cc_start: 0.8736 (m-80) cc_final: 0.8286 (m-80) REVERT: L 688 LYS cc_start: 0.9327 (mttt) cc_final: 0.8631 (tptp) outliers start: 21 outliers final: 19 residues processed: 175 average time/residue: 0.3276 time to fit residues: 75.3530 Evaluate side-chains 178 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 666 VAL Chi-restraints excluded: chain L residue 654 ASN Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN E 68 GLN L 654 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.081601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.052673 restraints weight = 34031.743| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 2.05 r_work: 0.2483 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 13837 Z= 0.282 Angle : 0.658 14.110 19936 Z= 0.371 Chirality : 0.039 0.167 2274 Planarity : 0.004 0.043 1507 Dihedral : 29.423 171.230 4170 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.68 % Allowed : 15.28 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.29), residues: 866 helix: 1.42 (0.22), residues: 566 sheet: -1.66 (1.16), residues: 20 loop : -1.71 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 655 HIS 0.004 0.001 HIS L 699 PHE 0.026 0.002 PHE L 642 TYR 0.012 0.001 TYR K 647 ARG 0.011 0.001 ARG L 643 Details of bonding type rmsd hydrogen bonds : bond 0.05905 ( 679) hydrogen bonds : angle 2.92113 ( 1674) metal coordination : bond 0.01089 ( 16) metal coordination : angle 6.19021 ( 18) covalent geometry : bond 0.00650 (13821) covalent geometry : angle 0.63154 (19918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5732.77 seconds wall clock time: 99 minutes 48.97 seconds (5988.97 seconds total)