Starting phenix.real_space_refine on Thu Aug 6 01:14:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t3y_41016/08_2026/8t3y_41016.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3y_41016/08_2026/8t3y_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 { model { file = "/net/cci-nas-00/data/ceres_data/8t3y_41016/08_2026/8t3y_41016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3y_41016/08_2026/8t3y_41016.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8t3y_41016/08_2026/8t3y_41016.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t3y_41016/08_2026/8t3y_41016.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t3y_41016/08_2026/8t3y_41016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3y_41016/08_2026/8t3y_41016.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13001 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 543 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "L" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 543 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12166 SG CYS K 663 94.355 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: 2.62, per 1000 atoms: 0.20 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: 1.03 Conformation dependent library (CDL) restraints added in 340.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 801 " pdb="ZN ZN K 801 " - pdb=" ND1 HIS K 665 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 683 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 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: 1.48 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: 2.05 Time building geometry restraints manager: 1.39 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=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DT I 104 " pdb=" C2' DT I 104 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" O3' DT J 140 " pdb=" P DT J 141 " ideal model delta sigma weight residual 1.607 1.644 -0.037 1.20e-02 6.94e+03 9.74e+00 bond pdb=" C3' DT J 140 " pdb=" C2' DT J 140 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.60e+00 bond pdb=" C3' DC I 96 " pdb=" C2' DC I 96 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.46e+00 ... (remaining 13816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 18833 1.69 - 3.38: 1030 3.38 - 5.06: 45 5.06 - 6.75: 9 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=" O4' DG J 56 " pdb=" C4' DG J 56 " pdb=" C3' DG J 56 " ideal model delta sigma weight residual 106.00 103.19 2.81 6.00e-01 2.78e+00 2.20e+01 angle pdb=" N3 DT I 57 " pdb=" C4 DT I 57 " pdb=" O4 DT I 57 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" O4' DT I 89 " pdb=" C4' DT I 89 " pdb=" C3' DT I 89 " ideal model delta sigma weight residual 106.00 103.35 2.65 6.00e-01 2.78e+00 1.95e+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: 1776 0.052 - 0.104: 439 0.104 - 0.157: 46 0.157 - 0.209: 7 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: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.380 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.628 13837 Z= 0.570 Angle : 0.851 44.076 19936 Z= 0.678 Chirality : 0.047 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 are not related in a simple way. whole: -1.27 (0.28), residues: 866 helix: -0.07 (0.23), residues: 539 sheet: -1.72 (0.98), residues: 30 loop : -2.10 (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/Z covalent geometry : bond 0.00557 / 0.50 (13821) covalent geometry : angle 0.78033 / 0.67 (19918) hydrogen bonds : bond 0.18344 / 12.09 ( 679) hydrogen bonds : angle 4.69391 / 3.44 ( 1674) metal coordination : bond 0.21940 / 19.89 ( 16) metal coordination : angle 11.33189 / 7.31 ( 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 : 0.343 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: 0.9040 (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: 0.6111 (m-30) outliers start: 13 outliers final: 5 residues processed: 257 average time/residue: 0.1606 time to fit residues: 52.9960 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 : 0.292 ------------------------------------------------------------------------------- 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: 1.9990 chunk 97 optimal weight: 11.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS C 104 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 654 ASN L 657 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.085480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.056856 restraints weight = 33927.017| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.04 r_work: 0.2602 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 13837 Z= 0.173 Angle : 0.663 9.648 19936 Z= 0.387 Chirality : 0.047 0.349 2274 Planarity : 0.004 0.047 1507 Dihedral : 29.622 172.485 4184 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.55 % Allowed : 8.85 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.29), residues: 866 helix: 0.51 (0.23), residues: 562 sheet: -1.88 (1.03), residues: 20 loop : -1.90 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 643 TYR 0.021 0.001 TYR K 647 PHE 0.013 0.001 PHE A 104 TRP 0.006 0.001 TRP L 655 HIS 0.004 0.001 HIS L 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.17 (13821) covalent geometry : angle 0.65261 / 0.39 (19918) hydrogen bonds : bond 0.06198 / 4.04 ( 679) hydrogen bonds : angle 3.17400 / 2.26 ( 1674) metal coordination : bond 0.02400 / 2.06 ( 16) metal coordination : angle 3.87070 / 2.27 ( 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 189 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8697 (mmm) cc_final: 0.8345 (mtp) REVERT: B 84 MET cc_start: 0.8971 (mmt) cc_final: 0.8635 (mmt) REVERT: C 91 GLU cc_start: 0.7890 (pm20) cc_final: 0.7397 (pm20) REVERT: C 92 GLU cc_start: 0.8703 (mp0) cc_final: 0.7994 (mp0) REVERT: D 34 LYS cc_start: 0.9153 (mtmm) cc_final: 0.8910 (mtpt) REVERT: E 73 GLU cc_start: 0.8720 (tt0) cc_final: 0.8308 (tt0) REVERT: F 25 ASN cc_start: 0.9235 (m110) cc_final: 0.8800 (m110) REVERT: F 74 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8380 (tp30) REVERT: G 64 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8711 (tm-30) REVERT: G 90 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8114 (p0) REVERT: K 658 MET cc_start: 0.8751 (tpp) cc_final: 0.8469 (tpp) REVERT: L 693 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7267 (p0) outliers start: 19 outliers final: 13 residues processed: 182 average time/residue: 0.1347 time to fit residues: 32.5257 Evaluate side-chains 177 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 90 ASP 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 693 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN E 68 GLN F 75 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.086198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.057643 restraints weight = 34480.921| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.08 r_work: 0.2620 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 13837 Z= 0.143 Angle : 0.596 9.421 19936 Z= 0.353 Chirality : 0.043 0.341 2274 Planarity : 0.004 0.037 1507 Dihedral : 29.694 173.452 4176 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.55 % Allowed : 9.65 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.29), residues: 866 helix: 0.86 (0.23), residues: 563 sheet: -2.02 (1.04), residues: 20 loop : -1.82 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.005 0.001 TYR H 37 PHE 0.015 0.001 PHE K 667 TRP 0.008 0.002 TRP L 655 HIS 0.011 0.001 HIS L 699 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.14 (13821) covalent geometry : angle 0.58664 / 0.35 (19918) hydrogen bonds : bond 0.05183 / 3.39 ( 679) hydrogen bonds : angle 2.87836 / 2.04 ( 1674) metal coordination : bond 0.01378 / 1.18 ( 16) metal coordination : angle 3.53265 / 1.94 ( 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 194 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8627 (mmm) cc_final: 0.8173 (mtp) REVERT: B 84 MET cc_start: 0.8970 (mmt) cc_final: 0.8739 (mmt) REVERT: D 34 LYS cc_start: 0.9160 (mtmm) cc_final: 0.8946 (mtpt) REVERT: E 73 GLU cc_start: 0.8767 (tt0) cc_final: 0.8374 (tt0) REVERT: F 25 ASN cc_start: 0.9239 (m110) cc_final: 0.8787 (m110) REVERT: F 74 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8404 (tp30) REVERT: G 64 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8742 (tm-30) REVERT: G 90 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8204 (p0) REVERT: K 643 ARG cc_start: 0.8524 (tpp80) cc_final: 0.8257 (mmm160) REVERT: K 658 MET cc_start: 0.8796 (tpp) cc_final: 0.8460 (tpp) REVERT: L 647 TYR cc_start: 0.8682 (m-80) cc_final: 0.8408 (m-80) REVERT: L 661 LYS cc_start: 0.9137 (ttmm) cc_final: 0.8670 (mtpp) REVERT: L 693 ASN cc_start: 0.7960 (OUTLIER) cc_final: 0.7063 (p0) outliers start: 19 outliers final: 11 residues processed: 186 average time/residue: 0.1644 time to fit residues: 40.3110 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 : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU 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 91 SER Chi-restraints excluded: chain E residue 129 ARG 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 L residue 660 ILE Chi-restraints excluded: chain L residue 693 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 104 GLN E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN H 63 ASN L 654 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.083543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.054475 restraints weight = 34050.985| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.05 r_work: 0.2528 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13837 Z= 0.228 Angle : 0.668 9.866 19936 Z= 0.378 Chirality : 0.047 0.363 2274 Planarity : 0.005 0.044 1507 Dihedral : 29.871 170.973 4176 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.08 % Allowed : 11.53 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.29), residues: 866 helix: 0.93 (0.23), residues: 565 sheet: -1.75 (1.08), residues: 20 loop : -1.86 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 35 TYR 0.017 0.001 TYR L 647 PHE 0.014 0.002 PHE H 65 TRP 0.012 0.003 TRP L 655 HIS 0.009 0.002 HIS L 699 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.23 (13821) covalent geometry : angle 0.65843 / 0.38 (19918) hydrogen bonds : bond 0.06369 / 4.19 ( 679) hydrogen bonds : angle 3.04505 / 2.17 ( 1674) metal coordination : bond 0.00781 / 0.47 ( 16) metal coordination : angle 3.81608 / 2.13 ( 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 183 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8880 (mmm) cc_final: 0.8291 (mtt) REVERT: B 84 MET cc_start: 0.9108 (mmt) cc_final: 0.8848 (mmt) REVERT: C 91 GLU cc_start: 0.7934 (pm20) cc_final: 0.7692 (pm20) REVERT: C 92 GLU cc_start: 0.8807 (mp0) cc_final: 0.8489 (mp0) REVERT: E 73 GLU cc_start: 0.8833 (tt0) cc_final: 0.8459 (tt0) REVERT: F 25 ASN cc_start: 0.9220 (m-40) cc_final: 0.8626 (m110) REVERT: F 74 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8567 (tp30) REVERT: G 64 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8734 (tm-30) REVERT: K 643 ARG cc_start: 0.8600 (tpp80) cc_final: 0.8128 (tpp80) REVERT: K 647 TYR cc_start: 0.7583 (m-10) cc_final: 0.7292 (m-10) REVERT: K 658 MET cc_start: 0.8829 (tpp) cc_final: 0.8592 (tpp) REVERT: L 658 MET cc_start: 0.8510 (tpp) cc_final: 0.8303 (tpp) outliers start: 23 outliers final: 18 residues processed: 173 average time/residue: 0.1644 time to fit residues: 37.4996 Evaluate side-chains 175 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 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 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 L residue 654 ASN Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.084592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.055545 restraints weight = 34369.413| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.08 r_work: 0.2565 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13837 Z= 0.146 Angle : 0.606 9.022 19936 Z= 0.351 Chirality : 0.044 0.345 2274 Planarity : 0.005 0.115 1507 Dihedral : 29.865 172.416 4174 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.28 % Allowed : 13.54 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.29), residues: 866 helix: 1.10 (0.23), residues: 566 sheet: -1.53 (1.15), residues: 20 loop : -1.74 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 35 TYR 0.007 0.001 TYR F 51 PHE 0.020 0.002 PHE K 642 TRP 0.008 0.002 TRP L 655 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.15 (13821) covalent geometry : angle 0.59683 / 0.35 (19918) hydrogen bonds : bond 0.05207 / 3.41 ( 679) hydrogen bonds : angle 2.81136 / 1.99 ( 1674) metal coordination : bond 0.00806 / 0.63 ( 16) metal coordination : angle 3.60054 / 2.02 ( 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 183 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8759 (mmm) cc_final: 0.8303 (mtt) REVERT: B 84 MET cc_start: 0.9035 (mmt) cc_final: 0.8804 (mmt) REVERT: F 25 ASN cc_start: 0.9185 (m-40) cc_final: 0.8569 (m110) REVERT: F 74 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8603 (tp30) REVERT: G 64 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8694 (tm-30) REVERT: K 658 MET cc_start: 0.8898 (tpp) cc_final: 0.8588 (tpp) REVERT: L 647 TYR cc_start: 0.8735 (m-80) cc_final: 0.8368 (t80) outliers start: 17 outliers final: 13 residues processed: 176 average time/residue: 0.1576 time to fit residues: 36.6703 Evaluate side-chains 176 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 56 GLU 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 698 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 30.0000 chunk 9 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.083591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.054616 restraints weight = 33920.277| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.05 r_work: 0.2533 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13837 Z= 0.187 Angle : 0.639 8.688 19936 Z= 0.363 Chirality : 0.046 0.352 2274 Planarity : 0.005 0.075 1507 Dihedral : 29.899 171.048 4172 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.35 % Allowed : 13.67 % 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 are not related in a simple way. whole: 0.32 (0.29), residues: 866 helix: 1.22 (0.23), residues: 565 sheet: -1.81 (1.12), residues: 20 loop : -1.73 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 79 TYR 0.010 0.001 TYR F 72 PHE 0.012 0.002 PHE K 642 TRP 0.012 0.002 TRP L 655 HIS 0.006 0.001 HIS L 699 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.19 (13821) covalent geometry : angle 0.63039 / 0.36 (19918) hydrogen bonds : bond 0.05819 / 3.82 ( 679) hydrogen bonds : angle 2.89918 / 2.06 ( 1674) metal coordination : bond 0.00570 / 0.37 ( 16) metal coordination : angle 3.50334 / 2.04 ( 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 186 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8807 (mmm) cc_final: 0.8208 (mtt) REVERT: C 91 GLU cc_start: 0.7840 (pm20) cc_final: 0.6913 (pm20) REVERT: C 92 GLU cc_start: 0.8718 (mp0) cc_final: 0.8088 (mp0) REVERT: E 73 GLU cc_start: 0.8900 (tt0) cc_final: 0.8288 (tt0) REVERT: F 25 ASN cc_start: 0.9182 (m-40) cc_final: 0.8500 (m110) REVERT: F 74 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8651 (tp30) REVERT: G 90 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8076 (p0) REVERT: K 658 MET cc_start: 0.8934 (tpp) cc_final: 0.8574 (tpp) REVERT: L 661 LYS cc_start: 0.9136 (ttmm) cc_final: 0.8708 (mtpp) outliers start: 25 outliers final: 22 residues processed: 174 average time/residue: 0.1580 time to fit residues: 36.1627 Evaluate side-chains 183 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 666 VAL Chi-restraints excluded: chain K residue 696 LEU Chi-restraints excluded: chain L residue 654 ASN Chi-restraints excluded: chain L residue 657 ASN Chi-restraints excluded: chain L residue 660 ILE Chi-restraints excluded: chain L residue 698 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 73 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 654 ASN L 657 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.083006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.053931 restraints weight = 34202.260| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 2.06 r_work: 0.2514 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13837 Z= 0.226 Angle : 0.665 7.935 19936 Z= 0.374 Chirality : 0.047 0.356 2274 Planarity : 0.004 0.062 1507 Dihedral : 29.933 170.661 4172 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.08 % Allowed : 15.55 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.29), residues: 866 helix: 1.20 (0.22), residues: 570 sheet: -1.78 (1.13), residues: 20 loop : -1.74 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.013 0.001 TYR L 647 PHE 0.013 0.002 PHE H 65 TRP 0.018 0.004 TRP L 655 HIS 0.005 0.001 HIS L 699 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.23 (13821) covalent geometry : angle 0.65440 / 0.37 (19918) hydrogen bonds : bond 0.06069 / 3.98 ( 679) hydrogen bonds : angle 2.96269 / 2.10 ( 1674) metal coordination : bond 0.00918 / 0.67 ( 16) metal coordination : angle 4.01184 / 2.40 ( 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 185 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8812 (mmm) cc_final: 0.8240 (mtt) REVERT: C 91 GLU cc_start: 0.7841 (pm20) cc_final: 0.7081 (pm20) REVERT: C 92 GLU cc_start: 0.8648 (mp0) cc_final: 0.8024 (mp0) REVERT: E 73 GLU cc_start: 0.8932 (tt0) cc_final: 0.8339 (tt0) REVERT: F 25 ASN cc_start: 0.9163 (m-40) cc_final: 0.8480 (m110) REVERT: F 74 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8661 (tp30) REVERT: K 647 TYR cc_start: 0.7537 (m-10) cc_final: 0.7160 (m-80) REVERT: K 658 MET cc_start: 0.8968 (tpp) cc_final: 0.8562 (tpp) REVERT: K 688 LYS cc_start: 0.9184 (mmmm) cc_final: 0.8869 (mmmm) REVERT: L 647 TYR cc_start: 0.8762 (m-80) cc_final: 0.8415 (t80) REVERT: L 661 LYS cc_start: 0.9149 (ttmm) cc_final: 0.8787 (mttp) outliers start: 23 outliers final: 21 residues processed: 176 average time/residue: 0.1568 time to fit residues: 36.5654 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 : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 56 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 0.0170 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.083641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.054675 restraints weight = 33391.246| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.03 r_work: 0.2540 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13837 Z= 0.161 Angle : 0.634 9.581 19936 Z= 0.359 Chirality : 0.045 0.347 2274 Planarity : 0.004 0.078 1507 Dihedral : 29.906 171.370 4170 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.95 % Allowed : 16.22 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.29), residues: 866 helix: 1.36 (0.22), residues: 568 sheet: -1.86 (1.12), residues: 20 loop : -1.68 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.007 0.001 TYR L 647 PHE 0.010 0.001 PHE H 65 TRP 0.013 0.003 TRP L 655 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (13821) covalent geometry : angle 0.62031 / 0.36 (19918) hydrogen bonds : bond 0.05402 / 3.53 ( 679) hydrogen bonds : angle 2.82316 / 2.00 ( 1674) metal coordination : bond 0.00614 / 0.43 ( 16) metal coordination : angle 4.43382 / 2.77 ( 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 187 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 GLU cc_start: 0.8921 (tt0) cc_final: 0.8478 (tt0) REVERT: F 25 ASN cc_start: 0.9120 (m-40) cc_final: 0.8411 (m110) REVERT: F 74 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8638 (tp30) REVERT: K 658 MET cc_start: 0.8995 (tpp) cc_final: 0.8591 (tpp) REVERT: L 643 ARG cc_start: 0.7485 (mmp80) cc_final: 0.6926 (mmp80) REVERT: L 647 TYR cc_start: 0.8663 (m-80) cc_final: 0.8277 (t80) REVERT: L 661 LYS cc_start: 0.9132 (ttmm) cc_final: 0.8784 (mttp) outliers start: 22 outliers final: 17 residues processed: 178 average time/residue: 0.1516 time to fit residues: 35.9122 Evaluate side-chains 178 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 666 VAL Chi-restraints excluded: chain K residue 676 LEU 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: 0.9980 chunk 31 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 100 optimal weight: 0.0370 chunk 103 optimal weight: 0.9980 overall best weight: 1.3460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 654 ASN L 657 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.083926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.055202 restraints weight = 34064.788| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.04 r_work: 0.2552 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13837 Z= 0.155 Angle : 0.628 9.568 19936 Z= 0.358 Chirality : 0.044 0.342 2274 Planarity : 0.005 0.140 1507 Dihedral : 29.887 171.615 4170 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.82 % Allowed : 16.35 % 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 are not related in a simple way. whole: 0.61 (0.29), residues: 866 helix: 1.45 (0.22), residues: 569 sheet: -1.85 (1.12), residues: 20 loop : -1.65 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG K 643 TYR 0.019 0.001 TYR K 647 PHE 0.034 0.002 PHE L 642 TRP 0.009 0.001 TRP L 655 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (13821) covalent geometry : angle 0.61685 / 0.36 (19918) hydrogen bonds : bond 0.05163 / 3.38 ( 679) hydrogen bonds : angle 2.78728 / 1.95 ( 1674) metal coordination : bond 0.00656 / 0.48 ( 16) metal coordination : angle 3.89806 / 2.33 ( 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 183 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.7698 (pm20) cc_final: 0.6890 (pm20) REVERT: C 92 GLU cc_start: 0.8570 (mp0) cc_final: 0.8074 (mp0) REVERT: E 73 GLU cc_start: 0.8893 (tt0) cc_final: 0.8464 (tt0) REVERT: F 25 ASN cc_start: 0.9099 (m-40) cc_final: 0.8406 (m110) REVERT: F 74 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8639 (tp30) REVERT: K 658 MET cc_start: 0.9043 (tpp) cc_final: 0.8631 (tpp) REVERT: K 699 HIS cc_start: 0.7598 (m90) cc_final: 0.7167 (m-70) REVERT: L 643 ARG cc_start: 0.7542 (mmp80) cc_final: 0.7164 (mmp80) REVERT: L 647 TYR cc_start: 0.8777 (m-80) cc_final: 0.8364 (t80) REVERT: L 661 LYS cc_start: 0.9137 (ttmm) cc_final: 0.8731 (mtpp) outliers start: 21 outliers final: 21 residues processed: 173 average time/residue: 0.1569 time to fit residues: 36.0296 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 : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 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 E residue 59 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 666 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 100 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 52 optimal weight: 0.0370 chunk 103 optimal weight: 3.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.083942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.055007 restraints weight = 33972.997| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.04 r_work: 0.2552 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.196 13837 Z= 0.239 Angle : 0.985 59.200 19936 Z= 0.594 Chirality : 0.045 0.431 2274 Planarity : 0.005 0.126 1507 Dihedral : 29.890 171.622 4170 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.82 % Allowed : 15.95 % Favored : 81.23 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.29), residues: 866 helix: 1.46 (0.22), residues: 569 sheet: -1.72 (1.11), residues: 20 loop : -1.65 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG K 643 TYR 0.014 0.001 TYR K 647 PHE 0.028 0.001 PHE L 642 TRP 0.010 0.002 TRP L 655 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.24 (13821) covalent geometry : angle 0.97850 / 0.59 (19918) hydrogen bonds : bond 0.05125 / 3.35 ( 679) hydrogen bonds : angle 2.78406 / 1.95 ( 1674) metal coordination : bond 0.00723 / 0.54 ( 16) metal coordination : angle 3.90446 / 2.32 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 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 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.7702 (pm20) cc_final: 0.6902 (pm20) REVERT: C 92 GLU cc_start: 0.8571 (mp0) cc_final: 0.8078 (mp0) REVERT: E 73 GLU cc_start: 0.8893 (tt0) cc_final: 0.8460 (tt0) REVERT: F 25 ASN cc_start: 0.9099 (m-40) cc_final: 0.8393 (m110) REVERT: F 74 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8636 (tp30) REVERT: K 658 MET cc_start: 0.9043 (tpp) cc_final: 0.8626 (tpp) REVERT: K 699 HIS cc_start: 0.7591 (m90) cc_final: 0.7166 (m-70) REVERT: L 643 ARG cc_start: 0.7542 (mmp80) cc_final: 0.7167 (mmp80) REVERT: L 647 TYR cc_start: 0.8792 (m-80) cc_final: 0.8379 (t80) REVERT: L 657 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7705 (p0) REVERT: L 661 LYS cc_start: 0.9137 (ttmm) cc_final: 0.8736 (mtpp) outliers start: 21 outliers final: 20 residues processed: 171 average time/residue: 0.1635 time to fit residues: 36.9856 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 : 0.350 ------------------------------------------------------------------------------- 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 59 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 666 VAL Chi-restraints excluded: chain K residue 676 LEU Chi-restraints excluded: chain L residue 657 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: 0.9980 chunk 66 optimal weight: 3.9990 chunk 20 optimal weight: 0.0010 chunk 30 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.083888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.055069 restraints weight = 33899.369| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.05 r_work: 0.2552 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.196 13837 Z= 0.239 Angle : 0.985 59.200 19936 Z= 0.594 Chirality : 0.045 0.431 2274 Planarity : 0.005 0.126 1507 Dihedral : 29.890 171.622 4170 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.82 % Allowed : 15.95 % Favored : 81.23 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.29), residues: 866 helix: 1.46 (0.22), residues: 569 sheet: -1.72 (1.11), residues: 20 loop : -1.65 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG K 643 TYR 0.014 0.001 TYR K 647 PHE 0.028 0.001 PHE L 642 TRP 0.010 0.002 TRP L 655 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.24 (13821) covalent geometry : angle 0.97850 / 0.59 (19918) hydrogen bonds : bond 0.05125 / 3.35 ( 679) hydrogen bonds : angle 2.78406 / 1.95 ( 1674) metal coordination : bond 0.00723 / 0.54 ( 16) metal coordination : angle 3.90446 / 2.32 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2701.84 seconds wall clock time: 46 minutes 52.50 seconds (2812.50 seconds total)