Starting phenix.real_space_refine on Sun Sep 29 14:26:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v96_31810/09_2024/7v96_31810.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v96_31810/09_2024/7v96_31810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v96_31810/09_2024/7v96_31810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v96_31810/09_2024/7v96_31810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v96_31810/09_2024/7v96_31810.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v96_31810/09_2024/7v96_31810.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 549 5.49 5 S 28 5.16 5 C 13350 2.51 5 N 4535 2.21 5 O 5506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23968 Number of models: 1 Model: "" Number of chains: 18 Chain: "I" Number of atoms: 5818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 5818 Classifications: {'DNA': 275} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 274} Chain: "J" Number of atoms: 5454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 5454 Classifications: {'DNA': 275} Link IDs: {'rna3p': 274} Chain: "A" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 826 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "B" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "E" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 927 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "H" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 773 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "K" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "L" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "M" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "O" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "P" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "Q" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "R" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 773 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Time building chain proxies: 13.11, per 1000 atoms: 0.55 Number of scatterers: 23968 At special positions: 0 Unit cell: (136.422, 141.57, 120.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 549 15.00 O 5506 8.00 N 4535 7.00 C 13350 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: 5.70 Conformation dependent library (CDL) restraints added in 1.9 seconds 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2974 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 13 sheets defined 58.9% alpha, 1.6% beta 188 base pairs and 478 stacking pairs defined. Time for finding SS restraints: 9.41 Creating SS restraints... Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 99 through 103 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.906A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 27 Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'B' and resid 49 through 57 removed outlier: 3.842A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 69 through 76 removed outlier: 3.524A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.757A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.300A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 58 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.554A 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 'D' and resid 34 through 46 removed outlier: 3.822A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 82 removed outlier: 3.541A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 99 removed outlier: 3.858A pdb=" N VAL D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.927A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.761A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.518A pdb=" N ARG E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.764A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.921A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 28 removed outlier: 3.987A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 36 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.869A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 58 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.719A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR F 88 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 31 through 36 Processing helix chain 'G' and resid 46 through 61 removed outlier: 3.841A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU G 61 " --> pdb=" O TYR G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 72 removed outlier: 3.817A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.675A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA G 86 " --> pdb=" O HIS G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.540A pdb=" N LEU G 115 " --> pdb=" O GLN G 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 46 removed outlier: 3.522A pdb=" N TYR H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.986A pdb=" N PHE H 62 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.527A pdb=" N ALA H 94 " --> pdb=" O GLU H 90 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL H 95 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.913A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.840A pdb=" N ARG K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 79 removed outlier: 3.559A pdb=" N ARG K 69 " --> pdb=" O LEU K 65 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 removed outlier: 3.758A pdb=" N VAL K 89 " --> pdb=" O GLN K 85 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS K 113 " --> pdb=" O LEU K 109 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA K 114 " --> pdb=" O CYS K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 131 removed outlier: 3.875A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN K 125 " --> pdb=" O PRO K 121 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 42 removed outlier: 4.160A pdb=" N ARG L 39 " --> pdb=" O ARG L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 77 removed outlier: 3.809A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU L 58 " --> pdb=" O THR L 54 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS L 59 " --> pdb=" O ARG L 55 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN L 64 " --> pdb=" O VAL L 60 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 94 removed outlier: 3.646A pdb=" N VAL L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG L 92 " --> pdb=" O TYR L 88 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN L 93 " --> pdb=" O ALA L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 21 removed outlier: 3.753A pdb=" N ALA M 21 " --> pdb=" O ARG M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 36 removed outlier: 3.551A pdb=" N ARG M 32 " --> pdb=" O GLY M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 51 removed outlier: 3.806A pdb=" N TYR M 50 " --> pdb=" O GLY M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 66 removed outlier: 3.557A pdb=" N LEU M 63 " --> pdb=" O THR M 59 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU M 64 " --> pdb=" O ALA M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 72 removed outlier: 3.821A pdb=" N ASP M 72 " --> pdb=" O ASN M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 88 removed outlier: 3.680A pdb=" N LEU M 83 " --> pdb=" O ILE M 79 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN M 84 " --> pdb=" O PRO M 80 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA M 86 " --> pdb=" O HIS M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 116 removed outlier: 3.546A pdb=" N LEU M 115 " --> pdb=" O GLN M 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 46 removed outlier: 3.724A pdb=" N VAL N 45 " --> pdb=" O VAL N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 64 removed outlier: 4.221A pdb=" N PHE N 62 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN N 64 " --> pdb=" O ASN N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 81 Processing helix chain 'N' and resid 87 through 99 removed outlier: 3.993A pdb=" N VAL N 95 " --> pdb=" O ILE N 91 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU N 99 " --> pdb=" O VAL N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 121 removed outlier: 3.938A pdb=" N SER N 109 " --> pdb=" O LYS N 105 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU N 110 " --> pdb=" O HIS N 106 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR N 118 " --> pdb=" O ALA N 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 55 Processing helix chain 'O' and resid 64 through 68 Processing helix chain 'O' and resid 70 through 74 removed outlier: 3.581A pdb=" N ILE O 74 " --> pdb=" O VAL O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 112 removed outlier: 4.388A pdb=" N GLU O 105 " --> pdb=" O VAL O 101 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP O 106 " --> pdb=" O GLY O 102 " (cutoff:3.500A) Processing helix chain 'O' and resid 120 through 132 removed outlier: 3.860A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN O 125 " --> pdb=" O PRO O 121 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU O 126 " --> pdb=" O LYS O 122 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG O 129 " --> pdb=" O GLN O 125 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 28 Processing helix chain 'P' and resid 31 through 34 Processing helix chain 'P' and resid 35 through 40 Processing helix chain 'P' and resid 49 through 76 removed outlier: 3.876A pdb=" N ARG P 55 " --> pdb=" O TYR P 51 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY P 56 " --> pdb=" O GLU P 52 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU P 58 " --> pdb=" O THR P 54 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP P 68 " --> pdb=" O ASN P 64 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS P 75 " --> pdb=" O THR P 71 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA P 76 " --> pdb=" O TYR P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 removed outlier: 3.755A pdb=" N VAL P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS P 91 " --> pdb=" O VAL P 87 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG P 92 " --> pdb=" O TYR P 88 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 22 Processing helix chain 'Q' and resid 28 through 37 Processing helix chain 'Q' and resid 45 through 74 removed outlier: 4.326A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR Q 50 " --> pdb=" O GLY Q 46 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU Q 58 " --> pdb=" O VAL Q 54 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA Q 69 " --> pdb=" O LEU Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 88 removed outlier: 3.553A pdb=" N LEU Q 83 " --> pdb=" O ILE Q 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 95 Processing helix chain 'R' and resid 34 through 46 removed outlier: 3.820A pdb=" N VAL R 38 " --> pdb=" O TYR R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 64 Processing helix chain 'R' and resid 68 through 82 removed outlier: 3.758A pdb=" N ALA R 74 " --> pdb=" O ILE R 70 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 92 Processing helix chain 'R' and resid 101 through 121 removed outlier: 3.883A pdb=" N LYS R 105 " --> pdb=" O GLY R 101 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS R 106 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA R 107 " --> pdb=" O LEU R 103 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU R 110 " --> pdb=" O HIS R 106 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS R 113 " --> pdb=" O SER R 109 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA R 114 " --> pdb=" O GLU R 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.444A 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 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.597A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.089A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (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: 7.781A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'K' and resid 83 through 84 removed outlier: 7.234A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'L' and resid 97 through 98 removed outlier: 3.668A pdb=" N TYR L 98 " --> pdb=" O THR Q 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'M' and resid 101 through 102 removed outlier: 6.431A pdb=" N THR M 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'O' and resid 83 through 84 removed outlier: 7.460A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AB4, first strand: chain 'Q' and resid 77 through 78 506 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 451 hydrogen bonds 856 hydrogen bond angles 0 basepair planarities 188 basepair parallelities 478 stacking parallelities Total time for adding SS restraints: 8.16 Time building geometry restraints manager: 6.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2681 1.31 - 1.43: 8755 1.43 - 1.56: 12926 1.56 - 1.68: 1097 1.68 - 1.81: 48 Bond restraints: 25507 Sorted by residual: bond pdb=" N MET O 120 " pdb=" CA MET O 120 " ideal model delta sigma weight residual 1.453 1.492 -0.039 8.30e-03 1.45e+04 2.25e+01 bond pdb=" N MET A 120 " pdb=" CA MET A 120 " ideal model delta sigma weight residual 1.453 1.492 -0.039 8.30e-03 1.45e+04 2.24e+01 bond pdb=" CA SER H 35 " pdb=" CB SER H 35 " ideal model delta sigma weight residual 1.536 1.471 0.064 1.42e-02 4.96e+03 2.06e+01 bond pdb=" CA SER H 84 " pdb=" CB SER H 84 " ideal model delta sigma weight residual 1.536 1.465 0.071 1.58e-02 4.01e+03 2.02e+01 bond pdb=" CA SER H 61 " pdb=" CB SER H 61 " ideal model delta sigma weight residual 1.528 1.460 0.069 1.56e-02 4.11e+03 1.93e+01 ... (remaining 25502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 34340 3.13 - 6.25: 2258 6.25 - 9.38: 144 9.38 - 12.51: 12 12.51 - 15.63: 3 Bond angle restraints: 36757 Sorted by residual: angle pdb=" O3' DC J 213 " pdb=" C3' DC J 213 " pdb=" C2' DC J 213 " ideal model delta sigma weight residual 111.50 127.13 -15.63 1.50e+00 4.44e-01 1.09e+02 angle pdb=" N VAL O 89 " pdb=" CA VAL O 89 " pdb=" C VAL O 89 " ideal model delta sigma weight residual 112.90 104.09 8.81 9.60e-01 1.09e+00 8.42e+01 angle pdb=" O3' DA J 242 " pdb=" C3' DA J 242 " pdb=" C2' DA J 242 " ideal model delta sigma weight residual 111.50 125.11 -13.61 1.50e+00 4.44e-01 8.24e+01 angle pdb=" O3' DT J 102 " pdb=" C3' DT J 102 " pdb=" C2' DT J 102 " ideal model delta sigma weight residual 111.50 124.97 -13.47 1.50e+00 4.44e-01 8.07e+01 angle pdb=" N VAL A 89 " pdb=" CA VAL A 89 " pdb=" C VAL A 89 " ideal model delta sigma weight residual 112.17 103.71 8.46 9.50e-01 1.11e+00 7.93e+01 ... (remaining 36752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 10735 35.66 - 71.33: 3252 71.33 - 106.99: 74 106.99 - 142.66: 8 142.66 - 178.32: 8 Dihedral angle restraints: 14077 sinusoidal: 9466 harmonic: 4611 Sorted by residual: dihedral pdb=" C ARG E 128 " pdb=" N ARG E 128 " pdb=" CA ARG E 128 " pdb=" CB ARG E 128 " ideal model delta harmonic sigma weight residual -122.60 -137.84 15.24 0 2.50e+00 1.60e-01 3.71e+01 dihedral pdb=" C HIS H 79 " pdb=" N HIS H 79 " pdb=" CA HIS H 79 " pdb=" CB HIS H 79 " ideal model delta harmonic sigma weight residual -122.60 -137.11 14.51 0 2.50e+00 1.60e-01 3.37e+01 dihedral pdb=" C ASN L 64 " pdb=" N ASN L 64 " pdb=" CA ASN L 64 " pdb=" CB ASN L 64 " ideal model delta harmonic sigma weight residual -122.60 -136.89 14.29 0 2.50e+00 1.60e-01 3.27e+01 ... (remaining 14074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.240: 4001 0.240 - 0.480: 150 0.480 - 0.719: 7 0.719 - 0.959: 2 0.959 - 1.199: 1 Chirality restraints: 4161 Sorted by residual: chirality pdb=" C3' DC J 213 " pdb=" C4' DC J 213 " pdb=" O3' DC J 213 " pdb=" C2' DC J 213 " both_signs ideal model delta sigma weight residual False -2.66 -1.46 -1.20 2.00e-01 2.50e+01 3.59e+01 chirality pdb=" C3' DT J 102 " pdb=" C4' DT J 102 " pdb=" O3' DT J 102 " pdb=" C2' DT J 102 " both_signs ideal model delta sigma weight residual False -2.66 -1.70 -0.96 2.00e-01 2.50e+01 2.29e+01 chirality pdb=" C3' DA J 242 " pdb=" C4' DA J 242 " pdb=" O3' DA J 242 " pdb=" C2' DA J 242 " both_signs ideal model delta sigma weight residual False -2.66 -1.71 -0.95 2.00e-01 2.50e+01 2.25e+01 ... (remaining 4158 not shown) Planarity restraints: 2744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 10 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C ALA Q 10 " -0.052 2.00e-02 2.50e+03 pdb=" O ALA Q 10 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG Q 11 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 80 " 0.010 2.00e-02 2.50e+03 1.73e-02 8.18e+00 pdb=" N9 DA J 80 " -0.036 2.00e-02 2.50e+03 pdb=" C8 DA J 80 " 0.012 2.00e-02 2.50e+03 pdb=" N7 DA J 80 " 0.016 2.00e-02 2.50e+03 pdb=" C5 DA J 80 " -0.019 2.00e-02 2.50e+03 pdb=" C6 DA J 80 " -0.010 2.00e-02 2.50e+03 pdb=" N6 DA J 80 " 0.014 2.00e-02 2.50e+03 pdb=" N1 DA J 80 " -0.017 2.00e-02 2.50e+03 pdb=" C2 DA J 80 " 0.014 2.00e-02 2.50e+03 pdb=" N3 DA J 80 " 0.017 2.00e-02 2.50e+03 pdb=" C4 DA J 80 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 242 " 0.036 2.00e-02 2.50e+03 1.70e-02 7.96e+00 pdb=" N9 DA J 242 " -0.040 2.00e-02 2.50e+03 pdb=" C8 DA J 242 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA J 242 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA J 242 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA J 242 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA J 242 " 0.012 2.00e-02 2.50e+03 pdb=" N1 DA J 242 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA J 242 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA J 242 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DA J 242 " -0.008 2.00e-02 2.50e+03 ... (remaining 2741 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 25 2.49 - 3.09: 14461 3.09 - 3.70: 37263 3.70 - 4.30: 59383 4.30 - 4.90: 83199 Nonbonded interactions: 194331 Sorted by model distance: nonbonded pdb=" O4' DC J 173 " pdb=" OP1 DT J 174 " model vdw 1.891 3.040 nonbonded pdb=" OP1 DC J 173 " pdb=" O4' DC J 173 " model vdw 2.099 3.040 nonbonded pdb=" O ASN M 73 " pdb=" OD1 ASN M 73 " model vdw 2.113 3.040 nonbonded pdb=" C4 DC J 173 " pdb=" O4 DT J 174 " model vdw 2.295 3.260 nonbonded pdb=" C1' DC J 173 " pdb=" OP1 DT J 174 " model vdw 2.329 3.470 ... (remaining 194326 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' and resid 36 through 134) selection = (chain 'E' and resid 36 through 134) selection = chain 'K' selection = (chain 'O' and resid 36 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 19 through 102) selection = (chain 'L' and resid 19 through 102) selection = chain 'P' } ncs_group { reference = (chain 'C' and ((resid 11 and (name N or name CA or name C or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 12 through \ 118)) selection = (chain 'G' and ((resid 11 and (name N or name CA or name C or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 12 through \ 118)) selection = (chain 'M' and resid 11 through 118) selection = (chain 'Q' and ((resid 11 and (name N or name CA or name C or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 12 through \ 118)) } ncs_group { reference = (chain 'D' and resid 24 through 121) selection = chain 'H' selection = (chain 'N' and resid 24 through 121) selection = chain 'R' } 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 group one per residue 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: 1.070 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: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 55.000 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 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 : 0.011 0.071 25507 Z= 0.679 Angle : 1.593 15.632 36757 Z= 1.150 Chirality : 0.111 1.199 4161 Planarity : 0.007 0.030 2744 Dihedral : 30.755 178.319 11103 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.77 % Allowed : 4.74 % Favored : 94.49 % Rotamer: Outliers : 15.66 % Allowed : 16.04 % Favored : 68.30 % Cbeta Deviations : 2.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.20), residues: 1561 helix: -0.33 (0.16), residues: 957 sheet: None (None), residues: 0 loop : -1.79 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS O 113 PHE 0.022 0.003 PHE K 78 TYR 0.029 0.003 TYR N 34 ARG 0.007 0.001 ARG R 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 256 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. REVERT: B 27 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7099 (mp10) REVERT: B 79 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8332 (mttp) REVERT: B 88 TYR cc_start: 0.8358 (m-10) cc_final: 0.8100 (m-10) REVERT: B 92 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.7948 (ttp80) REVERT: B 95 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7979 (ttp-110) REVERT: C 13 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6634 (tptt) REVERT: C 74 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.7959 (mtpt) REVERT: D 30 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7328 (mtp-110) REVERT: D 56 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7751 (tpt) REVERT: E 42 ARG cc_start: 0.7665 (mtp85) cc_final: 0.7448 (mtm-85) REVERT: E 50 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: E 70 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8620 (tt) REVERT: G 24 GLN cc_start: 0.7607 (mm110) cc_final: 0.7202 (mp10) REVERT: G 73 ASN cc_start: 0.8012 (m-40) cc_final: 0.7806 (t0) REVERT: G 78 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8579 (mm) REVERT: G 94 ASN cc_start: 0.9311 (t0) cc_final: 0.8772 (t0) REVERT: G 99 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6613 (mmt180) REVERT: G 110 ASN cc_start: 0.8227 (t0) cc_final: 0.7302 (p0) REVERT: H 90 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7597 (mm-30) REVERT: H 103 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8902 (mt) REVERT: K 36 LYS cc_start: -0.0587 (OUTLIER) cc_final: -0.2574 (mmtt) REVERT: L 44 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8204 (tttt) REVERT: L 95 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8207 (mtp85) REVERT: M 13 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.6148 (ptmm) REVERT: M 24 GLN cc_start: 0.7485 (mm-40) cc_final: 0.7222 (mp10) REVERT: M 29 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8239 (mmm160) REVERT: M 34 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8735 (mp) REVERT: M 110 ASN cc_start: 0.8484 (t0) cc_final: 0.7443 (p0) REVERT: N 66 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9099 (mt) REVERT: N 76 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7800 (mtt90) REVERT: O 37 LYS cc_start: 0.5090 (OUTLIER) cc_final: 0.3972 (ttmt) REVERT: O 123 ASP cc_start: 0.9039 (m-30) cc_final: 0.8511 (m-30) REVERT: P 29 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8778 (mt) REVERT: P 53 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: P 88 TYR cc_start: 0.8519 (m-10) cc_final: 0.8115 (m-10) REVERT: P 92 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.7953 (ttp80) REVERT: R 81 ASN cc_start: 0.8392 (m-40) cc_final: 0.8069 (m-40) outliers start: 208 outliers final: 59 residues processed: 416 average time/residue: 0.4628 time to fit residues: 269.8487 Evaluate side-chains 277 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 192 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 36 LYS Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 76 GLN Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 98 TYR Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 76 ARG Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 37 LYS Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 43 PRO Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 84 GLN Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 89 ARG Chi-restraints excluded: chain R residue 102 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 25 ASN B 64 ASN B 75 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 60 ASN D 81 ASN F 27 GLN F 75 HIS F 93 GLN G 84 GLN G 104 GLN G 110 ASN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN K 125 GLN M 84 GLN M 110 ASN ** M 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25507 Z= 0.221 Angle : 0.661 7.724 36757 Z= 0.394 Chirality : 0.038 0.159 4161 Planarity : 0.005 0.042 2744 Dihedral : 32.617 177.124 8090 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.69 % Favored : 97.05 % Rotamer: Outliers : 6.33 % Allowed : 20.33 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.21), residues: 1561 helix: -0.06 (0.17), residues: 993 sheet: None (None), residues: 0 loop : -1.63 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.015 0.001 PHE D 67 TYR 0.018 0.001 TYR R 80 ARG 0.008 0.000 ARG F 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 180 time to evaluate : 1.920 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. REVERT: A 122 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8145 (mtmm) REVERT: B 27 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7750 (mp10) REVERT: B 75 HIS cc_start: 0.9151 (t70) cc_final: 0.8912 (t-90) REVERT: B 79 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8404 (mtmp) REVERT: B 88 TYR cc_start: 0.8403 (m-10) cc_final: 0.7025 (m-10) REVERT: C 13 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.6700 (tptt) REVERT: C 74 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.7582 (tmtt) REVERT: D 30 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7079 (mtp-110) REVERT: E 122 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7742 (mtmt) REVERT: E 129 ARG cc_start: 0.7217 (tmt170) cc_final: 0.7010 (tpt170) REVERT: F 77 LYS cc_start: 0.8950 (mtmm) cc_final: 0.8709 (ttpp) REVERT: H 113 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7049 (ttpt) REVERT: K 122 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7552 (mtmt) REVERT: K 129 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7368 (ttm-80) REVERT: M 13 LYS cc_start: 0.6749 (OUTLIER) cc_final: 0.6371 (ptmt) REVERT: M 34 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8967 (mp) REVERT: M 118 LYS cc_start: 0.6159 (OUTLIER) cc_final: 0.5621 (tppt) REVERT: N 90 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: N 116 THR cc_start: 0.7936 (m) cc_final: 0.7720 (p) REVERT: O 37 LYS cc_start: 0.5600 (OUTLIER) cc_final: 0.4746 (tttt) REVERT: O 122 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8106 (mtmm) REVERT: O 123 ASP cc_start: 0.8758 (m-30) cc_final: 0.8537 (m-30) REVERT: P 29 ILE cc_start: 0.9257 (mm) cc_final: 0.8938 (mt) REVERT: R 110 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: R 117 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7496 (mtmt) outliers start: 84 outliers final: 33 residues processed: 247 average time/residue: 0.4170 time to fit residues: 150.4745 Evaluate side-chains 203 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 153 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain O residue 37 LYS Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 122 LYS Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain Q residue 118 LYS Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 110 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 186 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 108 ASN G 104 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 84 GLN Q 110 ASN R 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25507 Z= 0.236 Angle : 0.624 7.876 36757 Z= 0.369 Chirality : 0.036 0.151 4161 Planarity : 0.004 0.050 2744 Dihedral : 32.090 179.900 7955 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.91 % Favored : 95.90 % Rotamer: Outliers : 4.67 % Allowed : 23.27 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.21), residues: 1561 helix: -0.16 (0.17), residues: 999 sheet: None (None), residues: 0 loop : -1.67 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 79 PHE 0.012 0.001 PHE E 78 TYR 0.024 0.002 TYR B 88 ARG 0.006 0.000 ARG R 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 161 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. REVERT: B 27 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7810 (mp10) REVERT: C 13 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.6737 (tptt) REVERT: C 74 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8018 (mtpt) REVERT: D 30 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7154 (mtp-110) REVERT: H 35 SER cc_start: 0.9157 (m) cc_final: 0.8710 (t) REVERT: H 113 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7216 (ttpp) REVERT: K 129 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7188 (ttm170) REVERT: M 13 LYS cc_start: 0.6750 (OUTLIER) cc_final: 0.6487 (ptmt) REVERT: N 90 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: O 37 LYS cc_start: 0.5990 (OUTLIER) cc_final: 0.5106 (tttt) REVERT: O 86 SER cc_start: 0.7499 (t) cc_final: 0.6779 (m) REVERT: O 123 ASP cc_start: 0.8836 (m-30) cc_final: 0.8565 (m-30) REVERT: P 92 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8126 (ttp80) REVERT: R 110 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7647 (tm-30) outliers start: 62 outliers final: 38 residues processed: 210 average time/residue: 0.4041 time to fit residues: 125.1726 Evaluate side-chains 190 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 141 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain O residue 37 LYS Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 110 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 0.0970 chunk 140 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN D 81 ASN G 104 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 84 GLN R 46 HIS R 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25507 Z= 0.163 Angle : 0.553 6.231 36757 Z= 0.333 Chirality : 0.033 0.163 4161 Planarity : 0.004 0.036 2744 Dihedral : 31.642 176.699 7937 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.01 % Favored : 96.80 % Rotamer: Outliers : 4.22 % Allowed : 23.87 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.21), residues: 1561 helix: 0.14 (0.17), residues: 1003 sheet: None (None), residues: 0 loop : -1.44 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.006 0.001 PHE H 62 TYR 0.015 0.001 TYR R 80 ARG 0.010 0.000 ARG K 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 163 time to evaluate : 1.764 Fit side-chains TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. REVERT: A 86 SER cc_start: 0.7463 (t) cc_final: 0.6603 (m) REVERT: B 27 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7831 (mp10) REVERT: B 75 HIS cc_start: 0.9141 (t70) cc_final: 0.8920 (t-90) REVERT: C 13 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.6711 (tptt) REVERT: C 23 LEU cc_start: 0.8153 (mt) cc_final: 0.7948 (mp) REVERT: C 74 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7235 (tmtt) REVERT: C 112 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7101 (mt0) REVERT: D 30 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6934 (mtp-110) REVERT: D 56 MET cc_start: 0.7353 (tpp) cc_final: 0.6986 (tpt) REVERT: G 34 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9091 (tt) REVERT: H 113 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7202 (ttpt) REVERT: K 129 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7162 (ttm170) REVERT: M 29 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8169 (mmm160) REVERT: M 92 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7220 (mm-30) REVERT: N 79 HIS cc_start: 0.7049 (m-70) cc_final: 0.6849 (m-70) REVERT: N 98 LEU cc_start: 0.8255 (tt) cc_final: 0.7556 (mt) REVERT: O 86 SER cc_start: 0.7209 (t) cc_final: 0.6807 (m) REVERT: O 131 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7567 (mtp-110) REVERT: P 34 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8780 (mt) REVERT: R 80 TYR cc_start: 0.7373 (m-80) cc_final: 0.6824 (m-10) outliers start: 56 outliers final: 27 residues processed: 209 average time/residue: 0.3934 time to fit residues: 122.8466 Evaluate side-chains 180 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 142 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 112 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 136 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 177 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 104 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 84 GLN Q 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25507 Z= 0.321 Angle : 0.652 6.419 36757 Z= 0.381 Chirality : 0.038 0.197 4161 Planarity : 0.005 0.048 2744 Dihedral : 31.720 177.449 7925 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.93 % Favored : 94.81 % Rotamer: Outliers : 5.72 % Allowed : 23.80 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.21), residues: 1561 helix: -0.40 (0.17), residues: 1017 sheet: None (None), residues: 0 loop : -1.86 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.014 0.002 PHE N 67 TYR 0.020 0.002 TYR N 34 ARG 0.008 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 150 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7886 (mp10) REVERT: C 13 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.6798 (tptt) REVERT: C 74 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7887 (mtpt) REVERT: C 112 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7460 (mt0) REVERT: D 30 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7166 (mtp-110) REVERT: D 90 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8388 (mm-30) REVERT: D 98 LEU cc_start: 0.8857 (tt) cc_final: 0.7988 (mt) REVERT: H 35 SER cc_start: 0.9107 (m) cc_final: 0.8640 (t) REVERT: H 59 MET cc_start: 0.9012 (mmm) cc_final: 0.8803 (mmt) REVERT: H 113 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7167 (tttt) REVERT: K 129 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.6859 (ttm170) REVERT: M 24 GLN cc_start: 0.7485 (mm-40) cc_final: 0.7220 (mp10) REVERT: O 86 SER cc_start: 0.7336 (t) cc_final: 0.6642 (m) REVERT: P 34 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8901 (mt) REVERT: P 92 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8090 (ttp80) REVERT: Q 84 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8124 (tp-100) REVERT: R 110 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7811 (tm-30) outliers start: 76 outliers final: 44 residues processed: 216 average time/residue: 0.4441 time to fit residues: 140.9598 Evaluate side-chains 198 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 142 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 84 GLN Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain R residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 0.9990 chunk 178 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 116 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 73 ASN D 46 HIS D 81 ASN G 104 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 25507 Z= 0.171 Angle : 0.556 7.064 36757 Z= 0.331 Chirality : 0.033 0.269 4161 Planarity : 0.004 0.034 2744 Dihedral : 31.422 176.040 7919 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.54 % Allowed : 26.13 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.21), residues: 1561 helix: 0.01 (0.17), residues: 1013 sheet: None (None), residues: 0 loop : -1.59 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.006 0.001 PHE D 67 TYR 0.015 0.001 TYR N 37 ARG 0.007 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 151 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.7566 (t) cc_final: 0.6662 (m) REVERT: B 25 ASN cc_start: 0.7731 (m-40) cc_final: 0.7525 (m110) REVERT: B 27 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7854 (mp10) REVERT: C 13 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.6743 (tptt) REVERT: D 30 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6955 (mtp-110) REVERT: D 98 LEU cc_start: 0.8676 (tt) cc_final: 0.7902 (mt) REVERT: F 59 LYS cc_start: 0.8209 (tppt) cc_final: 0.7188 (ttmt) REVERT: H 35 SER cc_start: 0.8921 (m) cc_final: 0.8521 (t) REVERT: H 113 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7239 (ttpt) REVERT: K 129 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.6995 (ttm170) REVERT: M 24 GLN cc_start: 0.7497 (mm-40) cc_final: 0.7280 (mp10) REVERT: O 86 SER cc_start: 0.7179 (t) cc_final: 0.6615 (m) REVERT: O 131 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7326 (mtp-110) REVERT: P 34 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8822 (mt) REVERT: R 110 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7528 (tm-30) outliers start: 47 outliers final: 24 residues processed: 188 average time/residue: 0.4101 time to fit residues: 115.9990 Evaluate side-chains 171 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 110 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS G 104 GLN K 68 GLN ** M 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 ASN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25507 Z= 0.249 Angle : 0.609 7.248 36757 Z= 0.355 Chirality : 0.036 0.153 4161 Planarity : 0.004 0.041 2744 Dihedral : 31.476 176.797 7904 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.77 % Favored : 94.17 % Rotamer: Outliers : 4.14 % Allowed : 26.43 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.21), residues: 1561 helix: -0.19 (0.17), residues: 1010 sheet: None (None), residues: 0 loop : -1.76 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 79 PHE 0.014 0.002 PHE B 100 TYR 0.019 0.002 TYR N 34 ARG 0.007 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 144 time to evaluate : 1.901 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.7603 (t) cc_final: 0.6687 (m) REVERT: B 27 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7948 (mp10) REVERT: C 13 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.6780 (tptt) REVERT: C 112 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7244 (mt0) REVERT: D 98 LEU cc_start: 0.8825 (tt) cc_final: 0.7858 (mt) REVERT: H 35 SER cc_start: 0.9012 (m) cc_final: 0.8569 (t) REVERT: H 113 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7140 (tttt) REVERT: K 129 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.6798 (ttm170) REVERT: M 24 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7218 (mp10) REVERT: O 86 SER cc_start: 0.7199 (t) cc_final: 0.6607 (m) REVERT: O 131 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7226 (mtp-110) REVERT: P 34 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8876 (mt) REVERT: P 92 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8082 (ttp80) REVERT: R 110 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7790 (tm-30) outliers start: 55 outliers final: 36 residues processed: 191 average time/residue: 0.3833 time to fit residues: 110.6698 Evaluate side-chains 181 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 136 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain N residue 39 TYR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 110 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 0.0060 chunk 78 optimal weight: 6.9990 chunk 118 optimal weight: 0.1980 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 134 optimal weight: 0.0020 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 155 optimal weight: 0.2980 chunk 179 optimal weight: 3.9990 overall best weight: 0.3004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN D 81 ASN G 104 GLN ** M 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25507 Z= 0.157 Angle : 0.545 8.464 36757 Z= 0.322 Chirality : 0.032 0.173 4161 Planarity : 0.004 0.037 2744 Dihedral : 31.167 176.874 7900 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.91 % Favored : 96.03 % Rotamer: Outliers : 2.64 % Allowed : 27.33 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.22), residues: 1561 helix: 0.30 (0.18), residues: 1000 sheet: None (None), residues: 0 loop : -1.53 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 124 PHE 0.012 0.001 PHE E 67 TYR 0.014 0.001 TYR R 80 ARG 0.006 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 150 time to evaluate : 1.769 Fit side-chains TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7758 (mp10) REVERT: B 35 ARG cc_start: 0.8669 (mtm-85) cc_final: 0.8443 (mtm110) REVERT: C 13 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.6830 (tptt) REVERT: D 98 LEU cc_start: 0.8559 (tt) cc_final: 0.7758 (mt) REVERT: H 35 SER cc_start: 0.8828 (m) cc_final: 0.8451 (t) REVERT: H 56 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8147 (mmm) REVERT: H 113 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7199 (ttpt) REVERT: K 129 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7071 (ttm170) REVERT: M 24 GLN cc_start: 0.7401 (mm-40) cc_final: 0.7183 (mp10) REVERT: O 86 SER cc_start: 0.7033 (t) cc_final: 0.6547 (m) REVERT: P 34 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8740 (mt) REVERT: P 84 MET cc_start: 0.7927 (mmm) cc_final: 0.7312 (tpt) outliers start: 35 outliers final: 24 residues processed: 178 average time/residue: 0.3823 time to fit residues: 102.6150 Evaluate side-chains 170 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 140 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 120 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 5.9990 chunk 172 optimal weight: 0.4980 chunk 184 optimal weight: 4.9990 chunk 110 optimal weight: 0.0000 chunk 80 optimal weight: 0.0570 chunk 144 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.9106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 81 ASN Q 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.5977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25507 Z= 0.189 Angle : 0.560 8.058 36757 Z= 0.329 Chirality : 0.033 0.149 4161 Planarity : 0.004 0.033 2744 Dihedral : 31.205 178.187 7896 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.86 % Allowed : 27.71 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.22), residues: 1561 helix: 0.20 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -1.57 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 79 PHE 0.009 0.001 PHE E 78 TYR 0.024 0.001 TYR H 80 ARG 0.008 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 140 time to evaluate : 1.836 Fit side-chains TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.7305 (t) cc_final: 0.6546 (m) REVERT: B 27 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7885 (mp10) REVERT: C 13 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.6881 (tptt) REVERT: D 98 LEU cc_start: 0.8726 (tt) cc_final: 0.7804 (mt) REVERT: H 35 SER cc_start: 0.8897 (m) cc_final: 0.8503 (t) REVERT: H 113 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7205 (ttpt) REVERT: K 129 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.6766 (ttm170) REVERT: M 24 GLN cc_start: 0.7495 (mm-40) cc_final: 0.7267 (mp10) REVERT: O 86 SER cc_start: 0.7135 (t) cc_final: 0.6596 (m) REVERT: P 34 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8841 (mt) REVERT: Q 84 GLN cc_start: 0.8794 (tp-100) cc_final: 0.8273 (tm-30) REVERT: R 110 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7627 (tm-30) outliers start: 38 outliers final: 28 residues processed: 172 average time/residue: 0.3839 time to fit residues: 100.6451 Evaluate side-chains 167 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain R residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25507 Z= 0.230 Angle : 0.590 10.252 36757 Z= 0.343 Chirality : 0.035 0.149 4161 Planarity : 0.004 0.037 2744 Dihedral : 31.218 177.135 7896 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.32 % Favored : 94.62 % Rotamer: Outliers : 2.94 % Allowed : 27.79 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1561 helix: 0.00 (0.17), residues: 1011 sheet: None (None), residues: 0 loop : -1.69 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS D 79 PHE 0.009 0.001 PHE P 100 TYR 0.025 0.002 TYR H 80 ARG 0.009 0.000 ARG A 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 136 time to evaluate : 1.675 Fit side-chains TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 38 PRO cc_start: 0.6891 (Cg_endo) cc_final: 0.6621 (Cg_exo) REVERT: A 86 SER cc_start: 0.7357 (t) cc_final: 0.6527 (m) REVERT: B 27 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7945 (mp10) REVERT: C 13 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.6867 (tptt) REVERT: C 112 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7170 (mt0) REVERT: H 35 SER cc_start: 0.8905 (m) cc_final: 0.8487 (t) REVERT: H 113 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7149 (tttt) REVERT: K 129 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.6737 (ttm170) REVERT: O 86 SER cc_start: 0.7125 (t) cc_final: 0.6456 (m) REVERT: P 34 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8854 (mt) REVERT: R 110 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7876 (tm-30) outliers start: 39 outliers final: 30 residues processed: 172 average time/residue: 0.3841 time to fit residues: 99.9857 Evaluate side-chains 166 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain N residue 39 TYR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain R residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 24 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 162 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 167 optimal weight: 0.4980 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.175098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.135855 restraints weight = 35234.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135073 restraints weight = 86509.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.135568 restraints weight = 75136.188| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.6210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25507 Z= 0.198 Angle : 0.567 8.421 36757 Z= 0.332 Chirality : 0.034 0.218 4161 Planarity : 0.004 0.064 2744 Dihedral : 31.115 177.833 7896 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 2.94 % Allowed : 27.86 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.21), residues: 1561 helix: 0.09 (0.17), residues: 1009 sheet: None (None), residues: 0 loop : -1.71 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE D 67 TYR 0.024 0.001 TYR H 80 ARG 0.008 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3540.48 seconds wall clock time: 69 minutes 59.13 seconds (4199.13 seconds total)