Starting phenix.real_space_refine (version: dev) on Tue Apr 5 20:36:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mup_9251/04_2022/6mup_9251.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mup_9251/04_2022/6mup_9251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mup_9251/04_2022/6mup_9251.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mup_9251/04_2022/6mup_9251.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mup_9251/04_2022/6mup_9251.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mup_9251/04_2022/6mup_9251.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.008 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B ARG 23": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "G ARG 17": "NH1" <-> "NH2" Residue "M ARG 124": "NH1" <-> "NH2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "M ARG 196": "NH1" <-> "NH2" Residue "N ARG 134": "NH1" <-> "NH2" Residue "N ARG 196": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 15803 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 814 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 98} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 687 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 88} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 785 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 809 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 98} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 687 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 88} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 795 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2994 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3027 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 174 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 18} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 169 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "M" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1712 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain breaks: 1 Chain: "N" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1712 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain breaks: 1 Time building chain proxies: 9.52, per 1000 atoms: 0.60 Number of scatterers: 15803 At special positions: 0 Unit cell: (150.52, 126.14, 116.6, 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 24 16.00 P 292 15.00 O 3494 8.00 N 2892 7.00 C 9101 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 - 3.50 Amino acid : False - 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: 11.78 Conformation dependent library (CDL) restraints added in 1.5 seconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 54.0% alpha, 3.9% beta 63 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 5.49 Creating SS restraints... Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.547A pdb=" N ARG A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 94 through 114 removed outlier: 3.812A pdb=" N ALA A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N HIS A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 removed outlier: 4.001A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.798A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 63 removed outlier: 4.248A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 76 removed outlier: 3.839A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.896A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.516A pdb=" N ARG C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.658A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 60 removed outlier: 3.676A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 73 removed outlier: 3.517A pdb=" N ARG C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 removed outlier: 3.677A pdb=" N ALA C 86 " --> pdb=" O HIS C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.528A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.518A pdb=" N TYR D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 67 removed outlier: 3.799A pdb=" N SER D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 75 Processing helix chain 'D' and resid 76 through 84 removed outlier: 3.788A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.671A pdb=" N GLN D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 116 removed outlier: 3.595A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 55 removed outlier: 3.548A pdb=" N GLN E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.621A pdb=" N ARG E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG E 72 " --> pdb=" O SER E 68 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 114 removed outlier: 4.313A pdb=" N HIS E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP E 108 " --> pdb=" O HIS E 104 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 133 removed outlier: 4.387A pdb=" N LEU E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.535A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 63 removed outlier: 3.851A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 76 removed outlier: 3.828A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.784A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.512A pdb=" N HIS G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG G 35 " --> pdb=" O HIS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 67 removed outlier: 3.865A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 72 Processing helix chain 'G' and resid 80 through 88 removed outlier: 4.059A pdb=" N ALA G 86 " --> pdb=" O HIS G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.696A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.928A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 74 removed outlier: 3.718A pdb=" N VAL H 66 " --> pdb=" O MET H 62 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP H 68 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 84 Processing helix chain 'H' and resid 91 through 102 removed outlier: 3.610A pdb=" N GLN H 95 " --> pdb=" O SER H 91 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA H 97 " --> pdb=" O GLU H 93 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 123 removed outlier: 3.781A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR H 115 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR H 121 " --> pdb=" O ALA H 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 16 removed outlier: 3.507A pdb=" N LYS M 15 " --> pdb=" O ARG M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 19 No H-bonds generated for 'chain 'M' and resid 17 through 19' Processing helix chain 'M' and resid 20 through 29 removed outlier: 3.504A pdb=" N ILE M 24 " --> pdb=" O GLU M 20 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA M 27 " --> pdb=" O THR M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 37 Processing helix chain 'M' and resid 44 through 60 removed outlier: 3.973A pdb=" N GLN M 50 " --> pdb=" O GLU M 46 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS M 51 " --> pdb=" O SER M 47 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE M 53 " --> pdb=" O VAL M 49 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU M 55 " --> pdb=" O HIS M 51 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU M 58 " --> pdb=" O HIS M 54 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS M 59 " --> pdb=" O LEU M 55 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG M 60 " --> pdb=" O CYS M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 77 removed outlier: 4.604A pdb=" N LEU M 68 " --> pdb=" O SER M 64 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU M 69 " --> pdb=" O ASP M 65 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP M 70 " --> pdb=" O ALA M 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE M 76 " --> pdb=" O ILE M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 106 removed outlier: 3.853A pdb=" N ASN M 106 " --> pdb=" O LYS M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 183 removed outlier: 4.291A pdb=" N THR M 180 " --> pdb=" O GLY M 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 206 Processing helix chain 'M' and resid 206 through 211 removed outlier: 3.761A pdb=" N GLN M 211 " --> pdb=" O LYS M 207 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 15 removed outlier: 3.580A pdb=" N ARG N 11 " --> pdb=" O GLU N 7 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU N 14 " --> pdb=" O LYS N 10 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 19 removed outlier: 6.241A pdb=" N ASN N 19 " --> pdb=" O ILE N 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 16 through 19' Processing helix chain 'N' and resid 20 through 29 removed outlier: 3.614A pdb=" N ILE N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP N 29 " --> pdb=" O LEU N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 37 Processing helix chain 'N' and resid 44 through 60 removed outlier: 4.051A pdb=" N GLN N 50 " --> pdb=" O GLU N 46 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS N 51 " --> pdb=" O SER N 47 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU N 58 " --> pdb=" O HIS N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 76 removed outlier: 4.567A pdb=" N LEU N 68 " --> pdb=" O SER N 64 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU N 69 " --> pdb=" O ASP N 65 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE N 72 " --> pdb=" O LEU N 68 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET N 74 " --> pdb=" O ASP N 70 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE N 76 " --> pdb=" O ILE N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 107 Processing helix chain 'N' and resid 171 through 183 removed outlier: 4.097A pdb=" N GLY N 176 " --> pdb=" O THR N 172 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN N 177 " --> pdb=" O PRO N 173 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA N 178 " --> pdb=" O LEU N 174 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA N 182 " --> pdb=" O ALA N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 206 Processing helix chain 'N' and resid 206 through 211 removed outlier: 3.763A pdb=" N GLN N 211 " --> pdb=" O LYS N 207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 7.353A pdb=" N ASN A 85 " --> 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 'C' and resid 42 through 43 removed outlier: 7.484A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'E' and resid 85 through 86 removed outlier: 7.336A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.833A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'M' and resid 133 through 134 removed outlier: 5.072A pdb=" N TYR M 151 " --> pdb=" O SER M 164 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA M 161 " --> pdb=" O PHE M 86 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE M 86 " --> pdb=" O ALA M 161 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN M 87 " --> pdb=" O VAL M 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 133 through 134 removed outlier: 5.199A pdb=" N TYR N 151 " --> pdb=" O SER N 164 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 145 hydrogen bonds 286 hydrogen bond angles 0 basepair planarities 63 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 5.80 Time building geometry restraints manager: 11.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2736 1.32 - 1.45: 5656 1.45 - 1.57: 7685 1.57 - 1.69: 581 1.69 - 1.82: 44 Bond restraints: 16702 Sorted by residual: bond pdb=" C SER M 195 " pdb=" N ARG M 196 " ideal model delta sigma weight residual 1.331 1.496 -0.166 1.38e-02 5.25e+03 1.44e+02 bond pdb=" C VAL C 107 " pdb=" N LEU C 108 " ideal model delta sigma weight residual 1.331 1.238 0.093 1.48e-02 4.57e+03 3.95e+01 bond pdb=" N PRO K 527 " pdb=" CD PRO K 527 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.17e+01 bond pdb=" C LEU H 102 " pdb=" N PRO H 103 " ideal model delta sigma weight residual 1.328 1.289 0.039 1.25e-02 6.40e+03 9.62e+00 bond pdb=" CB THR E 113 " pdb=" CG2 THR E 113 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.19e+00 ... (remaining 16697 not shown) Histogram of bond angle deviations from ideal: 97.17 - 105.79: 1727 105.79 - 114.41: 10010 114.41 - 123.03: 10136 123.03 - 131.65: 1831 131.65 - 140.27: 115 Bond angle restraints: 23819 Sorted by residual: angle pdb=" CA SER M 195 " pdb=" C SER M 195 " pdb=" N ARG M 196 " ideal model delta sigma weight residual 115.90 133.64 -17.74 1.21e+00 6.83e-01 2.15e+02 angle pdb=" O SER M 195 " pdb=" C SER M 195 " pdb=" N ARG M 196 " ideal model delta sigma weight residual 122.59 104.83 17.76 1.35e+00 5.49e-01 1.73e+02 angle pdb=" C SER M 195 " pdb=" N ARG M 196 " pdb=" CA ARG M 196 " ideal model delta sigma weight residual 122.79 140.27 -17.48 1.78e+00 3.16e-01 9.64e+01 angle pdb=" N PRO G 117 " pdb=" CA PRO G 117 " pdb=" CB PRO G 117 " ideal model delta sigma weight residual 103.00 110.47 -7.47 1.10e+00 8.26e-01 4.61e+01 angle pdb=" C ARG K 521 " pdb=" N ARG K 522 " pdb=" CA ARG K 522 " ideal model delta sigma weight residual 122.93 132.61 -9.68 1.45e+00 4.76e-01 4.46e+01 ... (remaining 23814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 7609 35.00 - 70.00: 1329 70.00 - 105.00: 52 105.00 - 140.00: 0 140.00 - 175.01: 2 Dihedral angle restraints: 8992 sinusoidal: 5418 harmonic: 3574 Sorted by residual: dihedral pdb=" CA ARG B 23 " pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta harmonic sigma weight residual 180.00 111.61 68.39 0 5.00e+00 4.00e-02 1.87e+02 dihedral pdb=" CA LEU E 135 " pdb=" C LEU E 135 " pdb=" N GLU E 136 " pdb=" CA GLU E 136 " ideal model delta harmonic sigma weight residual 180.00 133.88 46.12 0 5.00e+00 4.00e-02 8.51e+01 dihedral pdb=" CA ARG F 23 " pdb=" C ARG F 23 " pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta harmonic sigma weight residual 180.00 133.96 46.04 0 5.00e+00 4.00e-02 8.48e+01 ... (remaining 8989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2152 0.074 - 0.149: 489 0.149 - 0.223: 39 0.223 - 0.297: 9 0.297 - 0.372: 1 Chirality restraints: 2690 Sorted by residual: chirality pdb=" CA SER K 528 " pdb=" N SER K 528 " pdb=" C SER K 528 " pdb=" CB SER K 528 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CB VAL D 66 " pdb=" CA VAL D 66 " pdb=" CG1 VAL D 66 " pdb=" CG2 VAL D 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2687 not shown) Planarity restraints: 1986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER N 195 " -0.025 2.00e-02 2.50e+03 5.30e-02 2.81e+01 pdb=" C SER N 195 " 0.092 2.00e-02 2.50e+03 pdb=" O SER N 195 " -0.036 2.00e-02 2.50e+03 pdb=" N ARG N 196 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 526 " -0.429 9.50e-02 1.11e+02 1.92e-01 2.26e+01 pdb=" NE ARG K 526 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG K 526 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG K 526 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG K 526 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP L 530 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.47e+00 pdb=" C TRP L 530 " -0.053 2.00e-02 2.50e+03 pdb=" O TRP L 530 " 0.020 2.00e-02 2.50e+03 pdb=" N TRP L 531 " 0.018 2.00e-02 2.50e+03 ... (remaining 1983 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 7 2.08 - 2.79: 3712 2.79 - 3.49: 20724 3.49 - 4.20: 41531 4.20 - 4.90: 62984 Nonbonded interactions: 128958 Sorted by model distance: nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG L 522 " model vdw 1.379 2.520 nonbonded pdb=" OD2 ASP G 90 " pdb=" NH2 ARG K 522 " model vdw 1.686 2.520 nonbonded pdb=" O TRP K 530 " pdb=" CE3 TRP K 531 " model vdw 1.789 3.340 nonbonded pdb=" CG ASP G 90 " pdb=" NH2 ARG K 522 " model vdw 1.796 3.350 nonbonded pdb=" OE1 GLU C 92 " pdb=" CZ ARG L 522 " model vdw 1.984 3.270 ... (remaining 128953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 139) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 116) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'K' and resid 519 through 537) selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 24 5.16 5 C 9101 2.51 5 N 2892 2.21 5 O 3494 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.100 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.980 Process input model: 51.870 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 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 : 0.013 0.166 16702 Z= 0.792 Angle : 1.189 17.758 23819 Z= 0.685 Chirality : 0.061 0.372 2690 Planarity : 0.008 0.192 1986 Dihedral : 25.790 175.006 6672 Min Nonbonded Distance : 1.379 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.28 % Favored : 89.21 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.68 % 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: -6.36 (0.16), residues: 1196 helix: -4.62 (0.09), residues: 669 sheet: -2.35 (0.63), residues: 60 loop : -3.59 (0.23), residues: 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 331 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 339 average time/residue: 0.3715 time to fit residues: 168.9144 Evaluate side-chains 227 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 225 time to evaluate : 1.495 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1541 time to fit residues: 2.2996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 50.0000 chunk 111 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 0.0030 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 93 GLN C 24 GLN C 73 ASN C 94 ASN D 47 GLN D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS G 94 ASN H 63 ASN H 67 ASN M 19 ASN M 40 ASN M 129 ASN M 145 ASN N 19 ASN N 129 ASN N 187 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 16702 Z= 0.226 Angle : 0.699 12.127 23819 Z= 0.400 Chirality : 0.039 0.280 2690 Planarity : 0.005 0.097 1986 Dihedral : 30.418 172.287 4292 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.94 % Favored : 91.97 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -4.86 (0.19), residues: 1196 helix: -3.20 (0.14), residues: 681 sheet: -2.37 (0.61), residues: 64 loop : -3.12 (0.25), residues: 451 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 261 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 17 residues processed: 278 average time/residue: 0.3303 time to fit residues: 126.8054 Evaluate side-chains 226 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 209 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1581 time to fit residues: 6.5881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 90 optimal weight: 30.0000 chunk 36 optimal weight: 0.1980 chunk 133 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 38 ASN C 73 ASN D 47 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN H 67 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 HIS N 51 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 16702 Z= 0.314 Angle : 0.683 12.457 23819 Z= 0.389 Chirality : 0.039 0.222 2690 Planarity : 0.005 0.082 1986 Dihedral : 30.406 172.467 4292 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.11 % Favored : 90.72 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -4.02 (0.21), residues: 1196 helix: -2.31 (0.17), residues: 684 sheet: -2.11 (0.61), residues: 64 loop : -3.13 (0.25), residues: 448 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 238 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 17 residues processed: 258 average time/residue: 0.3418 time to fit residues: 121.2192 Evaluate side-chains 211 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 194 time to evaluate : 1.395 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1700 time to fit residues: 6.6831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 24 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 47 GLN D 84 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 HIS M 145 ASN N 187 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.096 16702 Z= 0.291 Angle : 0.638 6.756 23819 Z= 0.368 Chirality : 0.038 0.193 2690 Planarity : 0.005 0.095 1986 Dihedral : 30.272 171.626 4292 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -3.51 (0.22), residues: 1196 helix: -1.86 (0.18), residues: 685 sheet: -1.97 (0.63), residues: 64 loop : -2.98 (0.26), residues: 447 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 220 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 236 average time/residue: 0.3236 time to fit residues: 106.3657 Evaluate side-chains 213 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 196 time to evaluate : 1.338 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1618 time to fit residues: 6.4556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 16702 Z= 0.273 Angle : 0.647 14.728 23819 Z= 0.369 Chirality : 0.037 0.179 2690 Planarity : 0.004 0.071 1986 Dihedral : 30.205 171.210 4292 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -3.20 (0.22), residues: 1196 helix: -1.59 (0.18), residues: 673 sheet: -1.87 (0.62), residues: 64 loop : -2.86 (0.26), residues: 459 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 218 average time/residue: 0.3346 time to fit residues: 101.2987 Evaluate side-chains 199 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 188 time to evaluate : 1.294 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1576 time to fit residues: 4.6351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN G 38 ASN M 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 16702 Z= 0.219 Angle : 0.592 7.787 23819 Z= 0.343 Chirality : 0.036 0.154 2690 Planarity : 0.005 0.104 1986 Dihedral : 30.003 170.806 4292 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -2.77 (0.23), residues: 1196 helix: -1.22 (0.19), residues: 688 sheet: -1.56 (0.66), residues: 64 loop : -2.76 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 217 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 18 residues processed: 230 average time/residue: 0.3638 time to fit residues: 115.4160 Evaluate side-chains 216 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 198 time to evaluate : 1.348 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1671 time to fit residues: 6.9422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 119 optimal weight: 30.0000 chunk 79 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 HIS M 75 GLN ** M 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.275 16702 Z= 0.598 Angle : 0.849 22.776 23819 Z= 0.469 Chirality : 0.047 0.196 2690 Planarity : 0.006 0.104 1986 Dihedral : 30.506 167.215 4292 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.29 % Favored : 88.55 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -3.24 (0.22), residues: 1196 helix: -1.61 (0.18), residues: 685 sheet: -1.72 (0.64), residues: 64 loop : -2.94 (0.26), residues: 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 208 time to evaluate : 1.395 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 220 average time/residue: 0.3717 time to fit residues: 111.9010 Evaluate side-chains 210 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 195 time to evaluate : 1.393 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1421 time to fit residues: 5.6462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 90 optimal weight: 30.0000 chunk 96 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 111 optimal weight: 0.3980 chunk 128 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** M 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.103 16702 Z= 0.190 Angle : 0.625 13.745 23819 Z= 0.356 Chirality : 0.036 0.149 2690 Planarity : 0.005 0.121 1986 Dihedral : 29.983 169.528 4292 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -2.40 (0.24), residues: 1196 helix: -0.93 (0.20), residues: 685 sheet: -1.60 (0.62), residues: 70 loop : -2.54 (0.29), residues: 441 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 227 time to evaluate : 1.542 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 233 average time/residue: 0.3402 time to fit residues: 109.3503 Evaluate side-chains 214 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 206 time to evaluate : 1.346 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2348 time to fit residues: 4.8028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 16702 Z= 0.307 Angle : 0.671 10.844 23819 Z= 0.374 Chirality : 0.038 0.167 2690 Planarity : 0.004 0.073 1986 Dihedral : 30.127 169.745 4292 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -2.40 (0.24), residues: 1196 helix: -0.87 (0.20), residues: 683 sheet: -1.61 (0.62), residues: 70 loop : -2.64 (0.28), residues: 443 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 205 time to evaluate : 1.576 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 206 average time/residue: 0.3605 time to fit residues: 101.5551 Evaluate side-chains 203 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 200 time to evaluate : 1.664 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1556 time to fit residues: 2.6440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 116 optimal weight: 0.0270 chunk 12 optimal weight: 0.8980 chunk 90 optimal weight: 30.0000 chunk 71 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** M 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 16702 Z= 0.268 Angle : 0.652 10.753 23819 Z= 0.365 Chirality : 0.037 0.162 2690 Planarity : 0.005 0.105 1986 Dihedral : 30.035 171.855 4292 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -2.24 (0.24), residues: 1196 helix: -0.72 (0.20), residues: 680 sheet: -1.60 (0.62), residues: 70 loop : -2.60 (0.28), residues: 446 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 201 time to evaluate : 1.343 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 203 average time/residue: 0.3470 time to fit residues: 97.1788 Evaluate side-chains 199 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 196 time to evaluate : 1.248 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1351 time to fit residues: 2.2922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 30.0000 chunk 35 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 0.1980 chunk 48 optimal weight: 0.0570 chunk 119 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 overall best weight: 0.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS ** M 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.185648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121886 restraints weight = 24764.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.125218 restraints weight = 12231.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127235 restraints weight = 8528.979| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.115 16702 Z= 0.186 Angle : 0.612 11.845 23819 Z= 0.346 Chirality : 0.035 0.153 2690 Planarity : 0.005 0.143 1986 Dihedral : 29.740 171.775 4292 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -1.78 (0.24), residues: 1196 helix: -0.30 (0.20), residues: 672 sheet: -1.51 (0.62), residues: 70 loop : -2.42 (0.29), residues: 454 =============================================================================== Job complete usr+sys time: 2845.60 seconds wall clock time: 52 minutes 45.57 seconds (3165.57 seconds total)