Starting phenix.real_space_refine on Sat Aug 23 14:35:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t3y_41016/08_2025/8t3y_41016.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3y_41016/08_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_41016/08_2025/8t3y_41016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3y_41016/08_2025/8t3y_41016.map" model { file = "/net/cci-nas-00/data/ceres_data/8t3y_41016/08_2025/8t3y_41016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3y_41016/08_2025/8t3y_41016.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 292 5.49 5 S 32 5.16 5 C 7249 2.51 5 N 2425 2.21 5 O 2999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13001 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 543 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "L" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 543 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12166 SG CYS K 663 94.355 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: 2.49, per 1000 atoms: 0.19 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: 1.10 Conformation dependent library (CDL) restraints added in 328.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.97 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: 2.25 Time building geometry restraints manager: 1.40 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: 2.990 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.520 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.830 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.28), residues: 866 helix: -0.07 (0.23), residues: 539 sheet: -1.72 (0.98), residues: 30 loop : -2.10 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 129 TYR 0.009 0.001 TYR A 54 PHE 0.020 0.002 PHE L 690 TRP 0.003 0.001 TRP K 655 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00374 (13821) covalent geometry : angle 0.64191 (19918) hydrogen bonds : bond 0.18344 ( 679) hydrogen bonds : angle 4.69391 ( 1674) metal coordination : bond 0.21940 ( 16) metal coordination : angle 11.33189 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 249 time to evaluate : 0.281 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: 0.1640 time to fit residues: 53.8195 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 : 0.304 ------------------------------------------------------------------------------- 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 108 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.0050 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 104 GLN E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 654 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.084814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.056096 restraints weight = 33708.902| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.04 r_work: 0.2581 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13837 Z= 0.191 Angle : 0.597 12.222 19936 Z= 0.345 Chirality : 0.036 0.131 2274 Planarity : 0.004 0.041 1507 Dihedral : 29.346 172.427 4184 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.68 % Allowed : 8.98 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.29), residues: 866 helix: 0.61 (0.23), residues: 562 sheet: -1.91 (1.02), residues: 20 loop : -1.89 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 86 TYR 0.019 0.001 TYR K 647 PHE 0.014 0.002 PHE L 690 TRP 0.006 0.001 TRP L 655 HIS 0.006 0.001 HIS L 699 Details of bonding type rmsd covalent geometry : bond 0.00418 (13821) covalent geometry : angle 0.58155 (19918) hydrogen bonds : bond 0.05293 ( 679) hydrogen bonds : angle 2.91570 ( 1674) metal coordination : bond 0.01603 ( 16) metal coordination : angle 4.49199 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8755 (mmm) cc_final: 0.8439 (mtp) REVERT: B 84 MET cc_start: 0.9016 (mmt) cc_final: 0.8736 (mmt) REVERT: C 91 GLU cc_start: 0.7925 (pm20) cc_final: 0.7366 (pm20) REVERT: C 92 GLU cc_start: 0.8729 (mp0) cc_final: 0.7840 (mp0) REVERT: D 34 LYS cc_start: 0.9168 (mtmm) cc_final: 0.8915 (mtpt) REVERT: E 73 GLU cc_start: 0.8761 (tt0) cc_final: 0.8423 (tt0) REVERT: F 25 ASN cc_start: 0.9301 (m110) cc_final: 0.8784 (m110) REVERT: F 74 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8483 (tp30) REVERT: G 90 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8182 (p0) REVERT: K 647 TYR cc_start: 0.7909 (m-10) cc_final: 0.7646 (m-80) REVERT: K 658 MET cc_start: 0.8756 (tpp) cc_final: 0.8370 (tpp) REVERT: K 688 LYS cc_start: 0.9062 (mmmm) cc_final: 0.8534 (mppt) REVERT: L 693 ASN cc_start: 0.7965 (OUTLIER) cc_final: 0.7141 (p0) outliers start: 20 outliers final: 11 residues processed: 184 average time/residue: 0.1625 time to fit residues: 39.0423 Evaluate side-chains 177 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 66 ILE 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 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 102 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 108 optimal weight: 9.9990 chunk 14 optimal weight: 0.4980 chunk 57 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 31 HIS 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 = 0.085487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.056804 restraints weight = 34304.256| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.04 r_work: 0.2600 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2181 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= 0.155 Angle : 0.563 12.614 19936 Z= 0.326 Chirality : 0.034 0.154 2274 Planarity : 0.004 0.050 1507 Dihedral : 29.270 173.236 4176 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.28 % Allowed : 11.53 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.29), residues: 866 helix: 0.97 (0.23), residues: 565 sheet: -1.12 (1.16), residues: 20 loop : -1.84 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 99 TYR 0.016 0.001 TYR K 647 PHE 0.010 0.001 PHE L 690 TRP 0.007 0.001 TRP L 655 HIS 0.011 0.001 HIS L 699 Details of bonding type rmsd covalent geometry : bond 0.00333 (13821) covalent geometry : angle 0.54565 (19918) hydrogen bonds : bond 0.04425 ( 679) hydrogen bonds : angle 2.72593 ( 1674) metal coordination : bond 0.00825 ( 16) metal coordination : angle 4.59934 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8669 (mmm) cc_final: 0.8274 (mtp) REVERT: B 84 MET cc_start: 0.9009 (mmt) cc_final: 0.8800 (mmt) REVERT: D 34 LYS cc_start: 0.9169 (mtmm) cc_final: 0.8961 (mtpt) REVERT: D 35 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7984 (mm-30) REVERT: E 73 GLU cc_start: 0.8768 (tt0) cc_final: 0.8369 (tt0) REVERT: F 25 ASN cc_start: 0.9268 (m110) cc_final: 0.8826 (m110) REVERT: F 74 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8520 (tp30) REVERT: K 658 MET cc_start: 0.8802 (tpp) cc_final: 0.8517 (tpp) REVERT: K 688 LYS cc_start: 0.9070 (mmmm) cc_final: 0.8533 (mptt) REVERT: L 655 TRP cc_start: 0.8910 (m100) cc_final: 0.8665 (m100) REVERT: L 700 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.8749 (tp) outliers start: 17 outliers final: 14 residues processed: 186 average time/residue: 0.1718 time to fit residues: 41.6453 Evaluate side-chains 183 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 43 VAL 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 657 ASN Chi-restraints excluded: chain L residue 700 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 104 GLN G 84 GLN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.083260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.054159 restraints weight = 34340.090| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 2.06 r_work: 0.2528 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13837 Z= 0.215 Angle : 0.602 12.181 19936 Z= 0.348 Chirality : 0.037 0.157 2274 Planarity : 0.005 0.079 1507 Dihedral : 29.399 171.536 4172 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.22 % Allowed : 12.73 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.29), residues: 866 helix: 1.14 (0.23), residues: 563 sheet: -1.55 (1.09), residues: 20 loop : -1.80 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG K 643 TYR 0.017 0.001 TYR K 647 PHE 0.045 0.002 PHE L 642 TRP 0.005 0.001 TRP L 655 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00488 (13821) covalent geometry : angle 0.58691 (19918) hydrogen bonds : bond 0.05403 ( 679) hydrogen bonds : angle 2.86725 ( 1674) metal coordination : bond 0.00786 ( 16) metal coordination : angle 4.51823 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8831 (mmm) cc_final: 0.8266 (mtt) REVERT: C 91 GLU cc_start: 0.7794 (pm20) cc_final: 0.7158 (pm20) REVERT: C 92 GLU cc_start: 0.8641 (mp0) cc_final: 0.7950 (mp0) REVERT: D 34 LYS cc_start: 0.9244 (mtmm) cc_final: 0.8941 (mtpt) REVERT: F 25 ASN cc_start: 0.9236 (m110) cc_final: 0.8704 (m110) REVERT: F 74 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8655 (tp30) REVERT: G 90 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8307 (p0) REVERT: K 642 PHE cc_start: 0.7858 (m-80) cc_final: 0.7169 (m-80) REVERT: K 643 ARG cc_start: 0.7381 (mmm160) cc_final: 0.6769 (mmm160) REVERT: K 645 LEU cc_start: 0.9027 (mt) cc_final: 0.8810 (tp) REVERT: K 658 MET cc_start: 0.8920 (tpp) cc_final: 0.8553 (tpp) REVERT: L 655 TRP cc_start: 0.8943 (m100) cc_final: 0.8419 (m100) outliers start: 24 outliers final: 19 residues processed: 178 average time/residue: 0.1617 time to fit residues: 37.8202 Evaluate side-chains 182 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 657 ASN Chi-restraints excluded: chain L residue 662 THR Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 110 optimal weight: 30.0000 chunk 2 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.083835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.054816 restraints weight = 34351.083| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 2.06 r_work: 0.2541 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2660 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= 0.182 Angle : 0.580 11.004 19936 Z= 0.337 Chirality : 0.035 0.172 2274 Planarity : 0.004 0.096 1507 Dihedral : 29.378 172.173 4172 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.95 % Allowed : 13.67 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.29), residues: 866 helix: 1.27 (0.23), residues: 562 sheet: -1.68 (1.06), residues: 20 loop : -1.74 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 643 TYR 0.008 0.001 TYR B 51 PHE 0.029 0.002 PHE L 642 TRP 0.003 0.001 TRP L 655 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00405 (13821) covalent geometry : angle 0.56519 (19918) hydrogen bonds : bond 0.04972 ( 679) hydrogen bonds : angle 2.80360 ( 1674) metal coordination : bond 0.00671 ( 16) metal coordination : angle 4.32471 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8809 (mmm) cc_final: 0.8196 (mtt) REVERT: C 91 GLU cc_start: 0.7806 (pm20) cc_final: 0.7296 (pm20) REVERT: C 92 GLU cc_start: 0.8631 (mp0) cc_final: 0.7918 (mp0) REVERT: D 34 LYS cc_start: 0.9168 (mtmm) cc_final: 0.8950 (mtpt) REVERT: E 73 GLU cc_start: 0.8901 (tt0) cc_final: 0.8307 (tt0) REVERT: F 25 ASN cc_start: 0.9178 (m110) cc_final: 0.8645 (m110) REVERT: F 74 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8633 (tp30) REVERT: K 642 PHE cc_start: 0.7869 (m-80) cc_final: 0.7251 (m-80) REVERT: K 645 LEU cc_start: 0.9006 (mt) cc_final: 0.8755 (tp) REVERT: K 658 MET cc_start: 0.8923 (tpp) cc_final: 0.8495 (tpp) REVERT: L 647 TYR cc_start: 0.8942 (m-80) cc_final: 0.8397 (m-80) REVERT: L 655 TRP cc_start: 0.8923 (m100) cc_final: 0.8404 (m100) outliers start: 22 outliers final: 21 residues processed: 177 average time/residue: 0.1615 time to fit residues: 37.4591 Evaluate side-chains 182 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU 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 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 85 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.084311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.055488 restraints weight = 33976.572| |-----------------------------------------------------------------------------| 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: 0.2761 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= 0.164 Angle : 0.561 10.921 19936 Z= 0.327 Chirality : 0.034 0.168 2274 Planarity : 0.004 0.089 1507 Dihedral : 29.339 172.715 4170 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.29), residues: 866 helix: 1.48 (0.23), residues: 563 sheet: -1.81 (1.06), residues: 20 loop : -1.67 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 99 TYR 0.006 0.001 TYR F 51 PHE 0.038 0.002 PHE L 642 TRP 0.002 0.000 TRP L 655 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00362 (13821) covalent geometry : angle 0.54748 (19918) hydrogen bonds : bond 0.04511 ( 679) hydrogen bonds : angle 2.65366 ( 1674) metal coordination : bond 0.00680 ( 16) metal coordination : angle 4.10306 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8735 (mmm) cc_final: 0.8249 (mtt) REVERT: C 91 GLU cc_start: 0.7813 (pm20) cc_final: 0.7351 (pm20) REVERT: C 92 GLU cc_start: 0.8639 (mp0) cc_final: 0.7888 (mp0) REVERT: D 34 LYS cc_start: 0.9179 (mtmm) cc_final: 0.8961 (mtpt) REVERT: E 73 GLU cc_start: 0.8857 (tt0) cc_final: 0.8228 (tt0) REVERT: F 25 ASN cc_start: 0.9112 (m110) cc_final: 0.8506 (m-40) REVERT: K 642 PHE cc_start: 0.7849 (m-80) cc_final: 0.7072 (m-80) REVERT: K 645 LEU cc_start: 0.9018 (mt) cc_final: 0.8812 (tp) REVERT: K 655 TRP cc_start: 0.8299 (m-10) cc_final: 0.8085 (m-10) REVERT: K 658 MET cc_start: 0.8977 (tpp) cc_final: 0.8575 (tpp) REVERT: K 699 HIS cc_start: 0.7575 (m90) cc_final: 0.7189 (m-70) REVERT: L 654 ASN cc_start: 0.7135 (m110) cc_final: 0.6117 (t0) outliers start: 23 outliers final: 19 residues processed: 175 average time/residue: 0.1505 time to fit residues: 34.5826 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 : 0.353 ------------------------------------------------------------------------------- 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 43 VAL Chi-restraints excluded: chain F residue 49 LEU 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 657 ASN Chi-restraints excluded: chain L residue 662 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN F 75 HIS L 654 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.082905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.054026 restraints weight = 34153.008| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 2.05 r_work: 0.2520 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13837 Z= 0.208 Angle : 0.590 10.812 19936 Z= 0.343 Chirality : 0.036 0.177 2274 Planarity : 0.004 0.058 1507 Dihedral : 29.410 171.569 4170 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.35 % Allowed : 15.01 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.29), residues: 866 helix: 1.51 (0.23), residues: 568 sheet: -1.83 (1.10), residues: 20 loop : -1.69 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 99 TYR 0.009 0.001 TYR F 72 PHE 0.024 0.002 PHE L 642 TRP 0.011 0.002 TRP L 655 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00471 (13821) covalent geometry : angle 0.57675 (19918) hydrogen bonds : bond 0.05191 ( 679) hydrogen bonds : angle 2.78365 ( 1674) metal coordination : bond 0.00729 ( 16) metal coordination : angle 4.25494 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8837 (mmm) cc_final: 0.8278 (mtt) REVERT: D 34 LYS cc_start: 0.9206 (mtmm) cc_final: 0.8996 (mtpt) REVERT: E 73 GLU cc_start: 0.8893 (tt0) cc_final: 0.8361 (tt0) REVERT: F 25 ASN cc_start: 0.9103 (m110) cc_final: 0.8544 (m-40) REVERT: K 642 PHE cc_start: 0.7797 (m-80) cc_final: 0.7026 (m-80) REVERT: K 645 LEU cc_start: 0.9065 (mt) cc_final: 0.8829 (tp) REVERT: K 658 MET cc_start: 0.9010 (tpp) cc_final: 0.8697 (tpp) REVERT: K 688 LYS cc_start: 0.9246 (mmmm) cc_final: 0.8926 (mmmm) REVERT: K 699 HIS cc_start: 0.7771 (m90) cc_final: 0.7361 (m-70) REVERT: L 647 TYR cc_start: 0.8883 (m-80) cc_final: 0.8668 (t80) REVERT: L 654 ASN cc_start: 0.7209 (OUTLIER) cc_final: 0.6152 (t0) REVERT: L 661 LYS cc_start: 0.9129 (ttmt) cc_final: 0.8884 (mttp) REVERT: L 688 LYS cc_start: 0.9343 (mttt) cc_final: 0.8709 (tptp) outliers start: 25 outliers final: 20 residues processed: 176 average time/residue: 0.1576 time to fit residues: 36.6138 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 : 0.428 ------------------------------------------------------------------------------- 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 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 K residue 676 LEU Chi-restraints excluded: chain L residue 654 ASN Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 51 optimal weight: 0.0270 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN H 84 ASN L 654 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.083892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.055153 restraints weight = 33626.413| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.05 r_work: 0.2551 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13837 Z= 0.156 Angle : 0.578 10.364 19936 Z= 0.335 Chirality : 0.034 0.156 2274 Planarity : 0.004 0.044 1507 Dihedral : 29.374 172.712 4170 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.35 % Allowed : 15.01 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.29), residues: 866 helix: 1.54 (0.22), residues: 571 sheet: -1.65 (1.10), residues: 20 loop : -1.65 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG L 643 TYR 0.007 0.001 TYR F 51 PHE 0.051 0.002 PHE L 642 TRP 0.008 0.001 TRP K 655 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00339 (13821) covalent geometry : angle 0.56205 (19918) hydrogen bonds : bond 0.04527 ( 679) hydrogen bonds : angle 2.66954 ( 1674) metal coordination : bond 0.00827 ( 16) metal coordination : angle 4.46120 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8768 (mmm) cc_final: 0.8376 (mtt) REVERT: C 91 GLU cc_start: 0.7769 (pm20) cc_final: 0.7099 (pm20) REVERT: C 92 GLU cc_start: 0.8650 (mp0) cc_final: 0.8151 (mp0) REVERT: F 25 ASN cc_start: 0.9087 (m110) cc_final: 0.8553 (m110) REVERT: K 642 PHE cc_start: 0.7846 (m-80) cc_final: 0.7210 (m-80) REVERT: K 645 LEU cc_start: 0.8975 (mt) cc_final: 0.8763 (tp) REVERT: K 658 MET cc_start: 0.9004 (tpp) cc_final: 0.8781 (tpp) REVERT: K 699 HIS cc_start: 0.7741 (m90) cc_final: 0.7356 (m-70) REVERT: L 647 TYR cc_start: 0.8856 (m-80) cc_final: 0.8567 (t80) REVERT: L 661 LYS cc_start: 0.9128 (ttmt) cc_final: 0.8876 (mttp) REVERT: L 688 LYS cc_start: 0.9313 (mttt) cc_final: 0.8681 (tptp) outliers start: 25 outliers final: 24 residues processed: 177 average time/residue: 0.1469 time to fit residues: 34.6375 Evaluate side-chains 185 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 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 657 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 25 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN F 25 ASN L 654 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.081287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.052255 restraints weight = 34085.610| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 2.07 r_work: 0.2469 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.3255 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= 0.316 Angle : 0.661 10.198 19936 Z= 0.379 Chirality : 0.040 0.170 2274 Planarity : 0.005 0.072 1507 Dihedral : 29.515 170.020 4170 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.22 % Allowed : 15.55 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.29), residues: 866 helix: 1.39 (0.22), residues: 565 sheet: -1.60 (1.17), residues: 20 loop : -1.77 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 643 TYR 0.012 0.001 TYR F 72 PHE 0.028 0.002 PHE L 642 TRP 0.010 0.002 TRP L 655 HIS 0.005 0.001 HIS K 699 Details of bonding type rmsd covalent geometry : bond 0.00731 (13821) covalent geometry : angle 0.64734 (19918) hydrogen bonds : bond 0.06377 ( 679) hydrogen bonds : angle 3.04689 ( 1674) metal coordination : bond 0.01118 ( 16) metal coordination : angle 4.49294 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8903 (mmm) cc_final: 0.8400 (mtt) REVERT: C 73 ASN cc_start: 0.8998 (t0) cc_final: 0.8611 (t0) REVERT: K 642 PHE cc_start: 0.7848 (m-80) cc_final: 0.7310 (m-80) REVERT: K 645 LEU cc_start: 0.9015 (mt) cc_final: 0.8789 (tp) REVERT: K 658 MET cc_start: 0.9045 (tpp) cc_final: 0.8687 (tpp) REVERT: K 687 ASN cc_start: 0.9201 (t0) cc_final: 0.8979 (t0) REVERT: K 688 LYS cc_start: 0.9287 (mmmm) cc_final: 0.9041 (mmmm) REVERT: K 699 HIS cc_start: 0.7854 (m90) cc_final: 0.7478 (m-70) REVERT: L 647 TYR cc_start: 0.8761 (m-80) cc_final: 0.8507 (t80) REVERT: L 654 ASN cc_start: 0.6782 (OUTLIER) cc_final: 0.5993 (m-40) REVERT: L 688 LYS cc_start: 0.9358 (mttt) cc_final: 0.8654 (tptp) outliers start: 24 outliers final: 22 residues processed: 175 average time/residue: 0.1694 time to fit residues: 38.7811 Evaluate side-chains 182 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.081138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.052258 restraints weight = 34395.653| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 2.08 r_work: 0.2472 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 13837 Z= 0.289 Angle : 0.656 12.298 19936 Z= 0.376 Chirality : 0.039 0.167 2274 Planarity : 0.005 0.082 1507 Dihedral : 29.500 171.036 4170 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.08 % Allowed : 16.09 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.29), residues: 866 helix: 1.30 (0.22), residues: 565 sheet: -1.90 (1.18), residues: 20 loop : -1.84 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 643 TYR 0.009 0.001 TYR F 72 PHE 0.022 0.002 PHE L 642 TRP 0.005 0.001 TRP L 655 HIS 0.005 0.001 HIS K 699 Details of bonding type rmsd covalent geometry : bond 0.00667 (13821) covalent geometry : angle 0.63827 (19918) hydrogen bonds : bond 0.05964 ( 679) hydrogen bonds : angle 2.97390 ( 1674) metal coordination : bond 0.00956 ( 16) metal coordination : angle 5.09118 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8865 (mmm) cc_final: 0.8339 (mtt) REVERT: C 73 ASN cc_start: 0.9001 (t0) cc_final: 0.8619 (t0) REVERT: E 73 GLU cc_start: 0.8965 (tt0) cc_final: 0.8510 (tt0) REVERT: F 25 ASN cc_start: 0.9206 (m-40) cc_final: 0.8556 (m110) REVERT: K 642 PHE cc_start: 0.7873 (m-80) cc_final: 0.7259 (m-80) REVERT: K 645 LEU cc_start: 0.8949 (mt) cc_final: 0.8719 (tp) REVERT: K 655 TRP cc_start: 0.8202 (m-10) cc_final: 0.7051 (m100) REVERT: K 658 MET cc_start: 0.9086 (tpp) cc_final: 0.8781 (tpp) REVERT: K 687 ASN cc_start: 0.9213 (t0) cc_final: 0.8928 (t0) REVERT: K 688 LYS cc_start: 0.9315 (mmmm) cc_final: 0.9065 (mmmm) REVERT: K 699 HIS cc_start: 0.7949 (m90) cc_final: 0.7613 (m-70) REVERT: L 647 TYR cc_start: 0.8745 (m-80) cc_final: 0.8518 (t80) REVERT: L 654 ASN cc_start: 0.7041 (OUTLIER) cc_final: 0.6188 (m-40) REVERT: L 688 LYS cc_start: 0.9314 (mttt) cc_final: 0.8617 (tptp) outliers start: 23 outliers final: 22 residues processed: 170 average time/residue: 0.1629 time to fit residues: 36.7084 Evaluate side-chains 178 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 12 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.082746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.054105 restraints weight = 33864.369| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.04 r_work: 0.2526 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13837 Z= 0.163 Angle : 0.606 11.699 19936 Z= 0.348 Chirality : 0.035 0.166 2274 Planarity : 0.004 0.069 1507 Dihedral : 29.419 173.197 4170 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.35 % Allowed : 16.09 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.29), residues: 866 helix: 1.52 (0.22), residues: 568 sheet: -1.97 (1.16), residues: 20 loop : -1.77 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 643 TYR 0.007 0.001 TYR L 647 PHE 0.024 0.002 PHE L 642 TRP 0.011 0.001 TRP L 655 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00357 (13821) covalent geometry : angle 0.58684 (19918) hydrogen bonds : bond 0.04668 ( 679) hydrogen bonds : angle 2.71726 ( 1674) metal coordination : bond 0.00880 ( 16) metal coordination : angle 5.12771 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2735.26 seconds wall clock time: 47 minutes 29.00 seconds (2849.00 seconds total)