Starting phenix.real_space_refine on Sat Mar 16 20:39:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bxt_30237/03_2024/7bxt_30237.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bxt_30237/03_2024/7bxt_30237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bxt_30237/03_2024/7bxt_30237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bxt_30237/03_2024/7bxt_30237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bxt_30237/03_2024/7bxt_30237.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bxt_30237/03_2024/7bxt_30237.pdb" } resolution = 4.2 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= 0.005 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 289 5.49 5 S 28 5.16 5 C 9015 2.51 5 N 2927 2.21 5 O 3437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E ARG 118": "NH1" <-> "NH2" Residue "E ASP 126": "OD1" <-> "OD2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 51": "OD1" <-> "OD2" Residue "L ARG 661": "NH1" <-> "NH2" Residue "M ASP 2": "OD1" <-> "OD2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M GLU 20": "OE1" <-> "OE2" Residue "M GLU 33": "OE1" <-> "OE2" Residue "M ASP 70": "OD1" <-> "OD2" Residue "M ARG 81": "NH1" <-> "NH2" Residue "M ARG 101": "NH1" <-> "NH2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "M ARG 109": "NH1" <-> "NH2" Residue "M GLU 126": "OE1" <-> "OE2" Residue "M ARG 133": "NH1" <-> "NH2" Residue "M PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N ARG 81": "NH1" <-> "NH2" Residue "N ARG 101": "NH1" <-> "NH2" Residue "N ARG 108": "NH1" <-> "NH2" Residue "N ARG 109": "NH1" <-> "NH2" Residue "N GLU 126": "OE1" <-> "OE2" Residue "N ARG 133": "NH1" <-> "NH2" Residue "N TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15696 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 854 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain breaks: 1 Chain: "D" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 737 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 854 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 737 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2953 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2989 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 174 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "L" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 174 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "M" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1645 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1651 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Time building chain proxies: 8.66, per 1000 atoms: 0.55 Number of scatterers: 15696 At special positions: 0 Unit cell: (124.95, 152.88, 116.13, 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 289 15.00 O 3437 8.00 N 2927 7.00 C 9015 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: 8.38 Conformation dependent library (CDL) restraints added in 1.5 seconds 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2278 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 8 sheets defined 56.8% alpha, 6.8% beta 146 base pairs and 214 stacking pairs defined. Time for finding SS restraints: 6.38 Creating SS restraints... Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.936A pdb=" N ILE A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N CYS A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 117 removed outlier: 3.591A pdb=" N LEU A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N HIS A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 117 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.535A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.694A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 4.411A pdb=" N ALA B 89 " --> pdb=" O ASP B 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 46 through 64 Processing helix chain 'C' and resid 67 through 74 removed outlier: 4.285A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.546A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 Processing helix chain 'D' and resid 37 through 47 removed outlier: 3.648A pdb=" N LYS D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 65 Processing helix chain 'D' and resid 65 through 84 removed outlier: 4.350A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.782A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.688A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.838A pdb=" N LEU E 49 " --> pdb=" O GLY E 45 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 80 removed outlier: 4.083A pdb=" N ILE E 75 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS E 76 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU E 77 " --> pdb=" O ARG E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 117 removed outlier: 3.955A pdb=" N GLU E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS E 105 " --> pdb=" O ALA E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 133 Processing helix chain 'F' and resid 32 through 39 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.905A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL F 57 " --> pdb=" O GLU F 53 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 4.403A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.243A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.751A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 95 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.753A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 4.045A pdb=" N VAL H 66 " --> pdb=" O MET H 62 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.780A pdb=" N GLN H 95 " --> pdb=" O SER H 91 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA H 97 " --> pdb=" O GLU H 93 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU H 102 " --> pdb=" O VAL H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 123 removed outlier: 4.188A pdb=" N LYS H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 15 removed outlier: 3.774A pdb=" N VAL M 6 " --> pdb=" O ASP M 2 " (cutoff:3.500A) removed outlier: 3.525A 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 Processing helix chain 'M' and resid 32 through 37 Processing helix chain 'M' and resid 44 through 59 Processing helix chain 'M' and resid 62 through 77 Processing helix chain 'M' and resid 102 through 111 removed outlier: 3.885A pdb=" N ARG M 108 " --> pdb=" O LYS M 104 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG M 109 " --> pdb=" O LYS M 105 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN M 110 " --> pdb=" O LYS M 106 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE M 111 " --> pdb=" O PHE M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 182 Processing helix chain 'N' and resid 3 through 14 Processing helix chain 'N' and resid 20 through 29 Processing helix chain 'N' and resid 32 through 37 Processing helix chain 'N' and resid 44 through 60 Processing helix chain 'N' and resid 63 through 77 removed outlier: 3.513A pdb=" N ALA N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 112 Processing helix chain 'N' and resid 170 through 182 Processing helix chain 'N' and resid 196 through 207 removed outlier: 3.838A pdb=" N LEU N 200 " --> pdb=" O CYS N 196 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 removed outlier: 7.322A pdb=" N ARG A 86 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.447A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 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 86 through 87 removed outlier: 7.641A pdb=" N ARG E 86 " --> 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: 7.371A 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 'M' and resid 119 through 124 removed outlier: 3.659A pdb=" N THR M 119 " --> pdb=" O ALA M 135 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N HIS M 154 " --> pdb=" O TYR M 159 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TYR M 159 " --> pdb=" O HIS M 154 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL M 85 " --> pdb=" O LEU M 192 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU M 192 " --> pdb=" O VAL M 85 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N HIS M 87 " --> pdb=" O MET M 190 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET M 190 " --> pdb=" O HIS M 87 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ASN M 89 " --> pdb=" O HIS M 188 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N HIS M 188 " --> pdb=" O ASN M 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 119 through 124 removed outlier: 3.947A pdb=" N TYR N 150 " --> pdb=" O SER N 163 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N HIS N 154 " --> pdb=" O TYR N 159 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N TYR N 159 " --> pdb=" O HIS N 154 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL N 85 " --> pdb=" O LEU N 192 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU N 192 " --> pdb=" O VAL N 85 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N HIS N 87 " --> pdb=" O MET N 190 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N MET N 190 " --> pdb=" O HIS N 87 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN N 89 " --> pdb=" O HIS N 188 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N HIS N 188 " --> pdb=" O ASN N 89 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1380 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 732 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 214 stacking parallelities Total time for adding SS restraints: 5.27 Time building geometry restraints manager: 8.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3442 1.33 - 1.45: 4947 1.45 - 1.57: 7576 1.57 - 1.69: 577 1.69 - 1.81: 46 Bond restraints: 16588 Sorted by residual: bond pdb=" CB TRP A 87 " pdb=" CG TRP A 87 " ideal model delta sigma weight residual 1.498 1.430 0.068 3.10e-02 1.04e+03 4.87e+00 bond pdb=" CG LEU C 83 " pdb=" CD2 LEU C 83 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.41e+00 bond pdb=" CB TRP M 83 " pdb=" CG TRP M 83 " ideal model delta sigma weight residual 1.498 1.441 0.057 3.10e-02 1.04e+03 3.33e+00 bond pdb=" CB TYR N 150 " pdb=" CG TYR N 150 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.20e-02 2.07e+03 3.27e+00 bond pdb=" CB VAL B 81 " pdb=" CG2 VAL B 81 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.17e+00 ... (remaining 16583 not shown) Histogram of bond angle deviations from ideal: 97.25 - 104.64: 1262 104.64 - 112.02: 8836 112.02 - 119.40: 5484 119.40 - 126.78: 7209 126.78 - 134.16: 855 Bond angle restraints: 23646 Sorted by residual: angle pdb=" C VAL L 654 " pdb=" N ARG L 655 " pdb=" CA ARG L 655 " ideal model delta sigma weight residual 122.44 114.72 7.72 1.19e+00 7.06e-01 4.20e+01 angle pdb=" N ARG K 655 " pdb=" CA ARG K 655 " pdb=" C ARG K 655 " ideal model delta sigma weight residual 110.80 101.91 8.89 2.13e+00 2.20e-01 1.74e+01 angle pdb=" N VAL L 654 " pdb=" CA VAL L 654 " pdb=" C VAL L 654 " ideal model delta sigma weight residual 113.47 109.40 4.07 1.01e+00 9.80e-01 1.63e+01 angle pdb=" CA LEU L 662 " pdb=" CB LEU L 662 " pdb=" CG LEU L 662 " ideal model delta sigma weight residual 116.30 129.63 -13.33 3.50e+00 8.16e-02 1.45e+01 angle pdb=" C ASP N 127 " pdb=" N ASN N 128 " pdb=" CA ASN N 128 " ideal model delta sigma weight residual 121.54 128.73 -7.19 1.91e+00 2.74e-01 1.42e+01 ... (remaining 23641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.32: 6711 24.32 - 48.64: 1659 48.64 - 72.96: 794 72.96 - 97.27: 67 97.27 - 121.59: 1 Dihedral angle restraints: 9232 sinusoidal: 5710 harmonic: 3522 Sorted by residual: dihedral pdb=" CA ARG L 661 " pdb=" C ARG L 661 " pdb=" N LEU L 662 " pdb=" CA LEU L 662 " ideal model delta harmonic sigma weight residual -180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLU C 92 " pdb=" C GLU C 92 " pdb=" N LEU C 93 " pdb=" CA LEU C 93 " ideal model delta harmonic sigma weight residual 180.00 156.19 23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ALA H 117 " pdb=" C ALA H 117 " pdb=" N VAL H 118 " pdb=" CA VAL H 118 " ideal model delta harmonic sigma weight residual -180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 9229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2161 0.067 - 0.133: 441 0.133 - 0.200: 53 0.200 - 0.266: 3 0.266 - 0.333: 1 Chirality restraints: 2659 Sorted by residual: chirality pdb=" CB ILE M 134 " pdb=" CA ILE M 134 " pdb=" CG1 ILE M 134 " pdb=" CG2 ILE M 134 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB ILE H 54 " pdb=" CA ILE H 54 " pdb=" CG1 ILE H 54 " pdb=" CG2 ILE H 54 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB ILE N 130 " pdb=" CA ILE N 130 " pdb=" CG1 ILE N 130 " pdb=" CG2 ILE N 130 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2656 not shown) Planarity restraints: 1979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR K 667 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C TYR K 667 " 0.060 2.00e-02 2.50e+03 pdb=" O TYR K 667 " -0.022 2.00e-02 2.50e+03 pdb=" N TRP K 668 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 667 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C TYR L 667 " -0.058 2.00e-02 2.50e+03 pdb=" O TYR L 667 " 0.022 2.00e-02 2.50e+03 pdb=" N TRP L 668 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS L 663 " 0.052 5.00e-02 4.00e+02 7.80e-02 9.74e+00 pdb=" N PRO L 664 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO L 664 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO L 664 " 0.044 5.00e-02 4.00e+02 ... (remaining 1976 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 14 2.31 - 2.96: 6885 2.96 - 3.60: 26831 3.60 - 4.25: 40274 4.25 - 4.90: 59246 Nonbonded interactions: 133250 Sorted by model distance: nonbonded pdb=" NE2 HIS H 109 " pdb=" O LYS K 658 " model vdw 1.659 2.520 nonbonded pdb=" OE2 GLU G 61 " pdb=" OG1 THR K 657 " model vdw 1.915 2.440 nonbonded pdb=" CD2 HIS H 109 " pdb=" O LYS K 658 " model vdw 2.039 3.260 nonbonded pdb=" OE1 GLU C 64 " pdb=" NH2 ARG L 661 " model vdw 2.126 2.520 nonbonded pdb=" ND2 ASN C 38 " pdb=" OE2 GLU G 41 " model vdw 2.143 2.520 ... (remaining 133245 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 11 through 64 or resid 66 through 118)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = (chain 'N' and (resid 1 through 206 or (resid 207 and (name N or name CA or name \ C or name O or name CB )))) } 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 2.540 Check model and map are aligned: 0.250 Set scattering table: 0.130 Process input model: 47.420 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 : 0.010 0.068 16588 Z= 0.571 Angle : 0.942 13.331 23646 Z= 0.535 Chirality : 0.053 0.333 2659 Planarity : 0.008 0.078 1979 Dihedral : 28.647 121.593 6954 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.39 % Allowed : 12.74 % Favored : 86.87 % 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: -4.26 (0.19), residues: 1171 helix: -2.98 (0.13), residues: 668 sheet: -0.91 (0.53), residues: 82 loop : -2.65 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP K 668 HIS 0.010 0.002 HIS N 188 PHE 0.017 0.003 PHE B 61 TYR 0.023 0.003 TYR H 42 ARG 0.008 0.001 ARG K 659 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 357 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7964 (mm-30) REVERT: A 74 GLU cc_start: 0.8193 (tt0) cc_final: 0.7115 (tt0) REVERT: A 105 HIS cc_start: 0.8107 (m-70) cc_final: 0.7812 (m170) REVERT: B 25 ASN cc_start: 0.8303 (t0) cc_final: 0.7546 (t0) REVERT: C 24 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7602 (tp40) REVERT: C 34 LEU cc_start: 0.9483 (tp) cc_final: 0.8918 (tp) REVERT: C 43 VAL cc_start: 0.9414 (t) cc_final: 0.9179 (t) REVERT: C 87 ILE cc_start: 0.9714 (mm) cc_final: 0.9463 (mt) REVERT: C 99 ARG cc_start: 0.7320 (ptt-90) cc_final: 0.6763 (ptp-170) REVERT: D 57 LYS cc_start: 0.9151 (mmmt) cc_final: 0.8773 (mptt) REVERT: D 71 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7909 (tm-30) REVERT: D 83 TYR cc_start: 0.8580 (m-10) cc_final: 0.8075 (m-10) REVERT: D 85 LYS cc_start: 0.8783 (mttt) cc_final: 0.8552 (mmtt) REVERT: D 121 TYR cc_start: 0.9199 (t80) cc_final: 0.8919 (t80) REVERT: E 108 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8232 (tm-30) REVERT: E 123 TYR cc_start: 0.8930 (m-80) cc_final: 0.8437 (m-10) REVERT: E 139 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7875 (mt-10) REVERT: F 25 ASN cc_start: 0.7509 (t0) cc_final: 0.6056 (t0) REVERT: G 38 ASN cc_start: 0.8572 (t0) cc_final: 0.8207 (p0) REVERT: G 95 LYS cc_start: 0.8699 (tttm) cc_final: 0.8157 (ttmm) REVERT: H 51 ASP cc_start: 0.8020 (m-30) cc_final: 0.7696 (t0) REVERT: H 57 LYS cc_start: 0.9109 (mmtt) cc_final: 0.8784 (mptt) REVERT: H 59 MET cc_start: 0.8914 (tpp) cc_final: 0.8425 (tpp) REVERT: K 665 LEU cc_start: 0.8793 (tt) cc_final: 0.8538 (tt) REVERT: M 3 GLU cc_start: 0.8607 (mp0) cc_final: 0.8311 (mp0) REVERT: M 20 GLU cc_start: 0.8360 (mp0) cc_final: 0.7543 (mp0) REVERT: M 35 GLN cc_start: 0.8191 (mt0) cc_final: 0.7824 (mt0) REVERT: M 46 GLU cc_start: 0.7954 (pp20) cc_final: 0.7459 (pp20) REVERT: M 50 HIS cc_start: 0.8986 (m-70) cc_final: 0.7977 (m-70) REVERT: M 74 ASN cc_start: 0.8854 (m-40) cc_final: 0.8570 (m-40) REVERT: M 79 ASN cc_start: 0.8825 (m-40) cc_final: 0.8058 (t0) REVERT: M 183 ASN cc_start: 0.8441 (m110) cc_final: 0.7816 (p0) REVERT: N 22 MET cc_start: 0.8204 (mpp) cc_final: 0.8001 (mpp) REVERT: N 30 PHE cc_start: 0.8448 (t80) cc_final: 0.8214 (t80) REVERT: N 204 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8201 (p) outliers start: 4 outliers final: 1 residues processed: 361 average time/residue: 0.3447 time to fit residues: 168.8726 Evaluate side-chains 232 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 230 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN C 73 ASN D 63 ASN D 95 GLN D 109 HIS E 40 HIS E 96 GLN G 73 ASN G 110 ASN H 63 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 GLN M 128 ASN M 144 ASN M 188 HIS N 35 GLN N 50 HIS N 74 ASN N 128 ASN N 170 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16588 Z= 0.198 Angle : 0.637 8.474 23646 Z= 0.367 Chirality : 0.039 0.208 2659 Planarity : 0.005 0.069 1979 Dihedral : 32.059 115.317 4522 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.29 % Allowed : 4.63 % Favored : 95.08 % 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: -2.25 (0.22), residues: 1171 helix: -1.08 (0.18), residues: 671 sheet: -0.54 (0.52), residues: 82 loop : -2.20 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 668 HIS 0.009 0.001 HIS B 75 PHE 0.013 0.002 PHE N 30 TYR 0.015 0.001 TYR A 111 ARG 0.011 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 321 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8224 (tt0) cc_final: 0.7962 (tt0) REVERT: A 96 GLN cc_start: 0.9452 (tp40) cc_final: 0.9197 (tp40) REVERT: C 24 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7530 (tp40) REVERT: C 34 LEU cc_start: 0.9405 (tp) cc_final: 0.8887 (tp) REVERT: C 41 GLU cc_start: 0.8637 (pm20) cc_final: 0.8262 (mp0) REVERT: C 56 GLU cc_start: 0.8128 (tt0) cc_final: 0.7651 (tt0) REVERT: D 57 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8756 (mptt) REVERT: D 67 ASN cc_start: 0.9035 (m-40) cc_final: 0.8418 (t0) REVERT: D 71 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7961 (tm-30) REVERT: D 76 GLU cc_start: 0.8834 (tp30) cc_final: 0.8522 (mm-30) REVERT: D 85 LYS cc_start: 0.8851 (mttt) cc_final: 0.8536 (mmtt) REVERT: D 95 GLN cc_start: 0.9054 (tp40) cc_final: 0.8667 (tp-100) REVERT: D 108 LYS cc_start: 0.9285 (tttt) cc_final: 0.8912 (ttpp) REVERT: D 121 TYR cc_start: 0.9106 (t80) cc_final: 0.8896 (t80) REVERT: E 108 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7987 (tm-30) REVERT: E 123 TYR cc_start: 0.8759 (m-80) cc_final: 0.8366 (m-10) REVERT: E 139 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8169 (mt-10) REVERT: F 29 ILE cc_start: 0.9202 (mm) cc_final: 0.8988 (mt) REVERT: F 51 TYR cc_start: 0.8311 (m-10) cc_final: 0.8024 (m-10) REVERT: G 38 ASN cc_start: 0.8488 (t0) cc_final: 0.8076 (p0) REVERT: G 95 LYS cc_start: 0.8433 (tttm) cc_final: 0.7850 (ttmm) REVERT: H 46 LYS cc_start: 0.9102 (mmpt) cc_final: 0.8334 (mmmt) REVERT: H 57 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8777 (mptt) REVERT: H 95 GLN cc_start: 0.8549 (tp-100) cc_final: 0.8349 (tp40) REVERT: K 658 LYS cc_start: 0.7781 (mmmt) cc_final: 0.7438 (mmtt) REVERT: K 665 LEU cc_start: 0.8638 (tt) cc_final: 0.8379 (tt) REVERT: M 46 GLU cc_start: 0.8424 (pp20) cc_final: 0.8084 (pp20) REVERT: M 50 HIS cc_start: 0.9151 (m-70) cc_final: 0.8238 (m-70) REVERT: M 79 ASN cc_start: 0.8691 (m-40) cc_final: 0.7887 (t0) REVERT: M 183 ASN cc_start: 0.8320 (m110) cc_final: 0.7653 (p0) REVERT: M 188 HIS cc_start: 0.6935 (m90) cc_final: 0.6390 (m170) REVERT: N 20 GLU cc_start: 0.8644 (mp0) cc_final: 0.8437 (mp0) REVERT: N 22 MET cc_start: 0.8230 (mpp) cc_final: 0.8009 (mpp) REVERT: N 87 HIS cc_start: 0.7903 (t70) cc_final: 0.7667 (t70) REVERT: N 119 THR cc_start: 0.9537 (m) cc_final: 0.9075 (p) outliers start: 3 outliers final: 1 residues processed: 323 average time/residue: 0.3031 time to fit residues: 137.4431 Evaluate side-chains 238 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 0.0770 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN C 104 GLN E 96 GLN G 73 ASN H 49 HIS H 84 ASN M 35 GLN N 35 GLN N 40 ASN N 50 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16588 Z= 0.190 Angle : 0.603 7.215 23646 Z= 0.348 Chirality : 0.038 0.207 2659 Planarity : 0.005 0.056 1979 Dihedral : 31.524 114.492 4522 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.10 % Allowed : 4.73 % Favored : 95.17 % 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: -1.16 (0.24), residues: 1171 helix: -0.07 (0.20), residues: 653 sheet: -0.42 (0.54), residues: 86 loop : -1.85 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 668 HIS 0.004 0.001 HIS M 185 PHE 0.009 0.001 PHE C 25 TYR 0.016 0.001 TYR A 111 ARG 0.006 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 307 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8244 (tt0) cc_final: 0.7531 (tt0) REVERT: B 31 LYS cc_start: 0.8610 (tmtt) cc_final: 0.8372 (ttmt) REVERT: B 68 ASP cc_start: 0.8311 (m-30) cc_final: 0.7966 (m-30) REVERT: C 24 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7532 (tp40) REVERT: C 34 LEU cc_start: 0.9361 (tp) cc_final: 0.9050 (tp) REVERT: C 41 GLU cc_start: 0.8665 (pm20) cc_final: 0.8253 (mp0) REVERT: C 56 GLU cc_start: 0.7993 (tt0) cc_final: 0.7546 (tt0) REVERT: D 57 LYS cc_start: 0.9317 (mmmt) cc_final: 0.8834 (mptt) REVERT: D 67 ASN cc_start: 0.8943 (m-40) cc_final: 0.8472 (t0) REVERT: D 71 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8025 (tm-30) REVERT: D 85 LYS cc_start: 0.8950 (mttt) cc_final: 0.8625 (mmtt) REVERT: D 90 THR cc_start: 0.9131 (p) cc_final: 0.8924 (p) REVERT: D 108 LYS cc_start: 0.9215 (tttt) cc_final: 0.8866 (ttpp) REVERT: D 113 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8395 (mm-30) REVERT: D 120 LYS cc_start: 0.9075 (mmmm) cc_final: 0.8825 (mtpt) REVERT: D 121 TYR cc_start: 0.9130 (t80) cc_final: 0.8906 (t80) REVERT: E 97 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8541 (mm-30) REVERT: E 111 TYR cc_start: 0.9469 (t80) cc_final: 0.9054 (t80) REVERT: E 123 TYR cc_start: 0.8669 (m-80) cc_final: 0.8356 (m-10) REVERT: E 139 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7862 (mt-10) REVERT: F 59 LYS cc_start: 0.8936 (ttmt) cc_final: 0.8305 (ttpt) REVERT: F 61 PHE cc_start: 0.9113 (t80) cc_final: 0.8763 (t80) REVERT: F 98 TYR cc_start: 0.9045 (m-10) cc_final: 0.8663 (m-10) REVERT: G 38 ASN cc_start: 0.8304 (t0) cc_final: 0.7994 (p0) REVERT: G 50 TYR cc_start: 0.9013 (t80) cc_final: 0.8776 (t80) REVERT: G 92 GLU cc_start: 0.7767 (pm20) cc_final: 0.7437 (pm20) REVERT: G 95 LYS cc_start: 0.8537 (tttm) cc_final: 0.7959 (ttmm) REVERT: H 46 LYS cc_start: 0.8907 (mmpt) cc_final: 0.8688 (mmmt) REVERT: H 57 LYS cc_start: 0.9130 (mmtt) cc_final: 0.8806 (mptt) REVERT: H 95 GLN cc_start: 0.8577 (tp-100) cc_final: 0.8221 (tp-100) REVERT: H 121 TYR cc_start: 0.9308 (t80) cc_final: 0.8912 (t80) REVERT: K 658 LYS cc_start: 0.7880 (mmmt) cc_final: 0.7475 (mmtt) REVERT: K 660 ILE cc_start: 0.8217 (mm) cc_final: 0.7981 (mm) REVERT: M 7 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8375 (tt0) REVERT: M 35 GLN cc_start: 0.8108 (mt0) cc_final: 0.7041 (mp10) REVERT: M 50 HIS cc_start: 0.9073 (m-70) cc_final: 0.8372 (m-70) REVERT: M 54 GLN cc_start: 0.8801 (pp30) cc_final: 0.7701 (pp30) REVERT: M 57 GLU cc_start: 0.8475 (pt0) cc_final: 0.7861 (pp20) REVERT: M 58 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6076 (mm-30) REVERT: M 79 ASN cc_start: 0.8638 (m-40) cc_final: 0.7981 (t0) REVERT: M 178 MET cc_start: 0.7715 (ttt) cc_final: 0.7287 (tmm) REVERT: M 183 ASN cc_start: 0.8120 (m110) cc_final: 0.7603 (p0) REVERT: N 22 MET cc_start: 0.8195 (mpp) cc_final: 0.7948 (mpp) REVERT: N 46 GLU cc_start: 0.9002 (pp20) cc_final: 0.8642 (pp20) REVERT: N 87 HIS cc_start: 0.7960 (t70) cc_final: 0.7590 (t70) REVERT: N 107 PHE cc_start: 0.8474 (t80) cc_final: 0.8267 (t80) REVERT: N 134 ILE cc_start: 0.8886 (tp) cc_final: 0.8679 (tt) REVERT: N 178 MET cc_start: 0.7727 (ttp) cc_final: 0.7396 (ttp) outliers start: 1 outliers final: 1 residues processed: 308 average time/residue: 0.2984 time to fit residues: 129.9149 Evaluate side-chains 235 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 121 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN C 104 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 128 ASN M 188 HIS N 35 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16588 Z= 0.306 Angle : 0.660 7.567 23646 Z= 0.374 Chirality : 0.040 0.212 2659 Planarity : 0.005 0.052 1979 Dihedral : 31.517 116.011 4522 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.19 % Allowed : 4.63 % Favored : 95.17 % 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: -0.98 (0.24), residues: 1171 helix: 0.04 (0.20), residues: 665 sheet: -0.55 (0.54), residues: 88 loop : -1.69 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 668 HIS 0.006 0.001 HIS C 31 PHE 0.014 0.002 PHE N 205 TYR 0.035 0.002 TYR D 83 ARG 0.016 0.001 ARG K 659 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 274 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8379 (tt0) cc_final: 0.7818 (tt0) REVERT: C 24 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7599 (tp-100) REVERT: C 41 GLU cc_start: 0.8698 (pm20) cc_final: 0.8258 (mp0) REVERT: C 56 GLU cc_start: 0.8043 (tt0) cc_final: 0.7565 (tt0) REVERT: D 62 MET cc_start: 0.9184 (mmm) cc_final: 0.8403 (tpp) REVERT: D 67 ASN cc_start: 0.9012 (m-40) cc_final: 0.8586 (t0) REVERT: D 71 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8025 (tm-30) REVERT: D 76 GLU cc_start: 0.9029 (tp30) cc_final: 0.8731 (tp30) REVERT: D 85 LYS cc_start: 0.9013 (mttt) cc_final: 0.8632 (mmtt) REVERT: D 108 LYS cc_start: 0.9296 (tttt) cc_final: 0.9002 (ttpp) REVERT: D 121 TYR cc_start: 0.9180 (t80) cc_final: 0.8910 (t80) REVERT: E 97 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8587 (mm-30) REVERT: E 123 TYR cc_start: 0.8815 (m-80) cc_final: 0.8589 (m-10) REVERT: G 38 ASN cc_start: 0.8637 (t0) cc_final: 0.8401 (p0) REVERT: G 95 LYS cc_start: 0.8758 (tttm) cc_final: 0.8119 (ttmm) REVERT: G 99 ARG cc_start: 0.8266 (mtt180) cc_final: 0.7951 (mtt180) REVERT: H 46 LYS cc_start: 0.8916 (mmpt) cc_final: 0.8652 (mmmt) REVERT: H 57 LYS cc_start: 0.9159 (mmtt) cc_final: 0.8810 (mptt) REVERT: H 71 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7658 (tm-30) REVERT: H 93 GLU cc_start: 0.7981 (pp20) cc_final: 0.7606 (tm-30) REVERT: M 7 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8413 (tt0) REVERT: M 50 HIS cc_start: 0.8986 (m-70) cc_final: 0.8715 (m-70) REVERT: M 57 GLU cc_start: 0.8551 (pt0) cc_final: 0.7941 (pp20) REVERT: M 58 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6324 (mm-30) REVERT: M 79 ASN cc_start: 0.8673 (m-40) cc_final: 0.7987 (t0) REVERT: M 183 ASN cc_start: 0.7994 (m110) cc_final: 0.7564 (p0) REVERT: M 188 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.6933 (m-70) REVERT: N 46 GLU cc_start: 0.8872 (pp20) cc_final: 0.8586 (pp20) REVERT: N 87 HIS cc_start: 0.7939 (t70) cc_final: 0.7416 (t70) REVERT: N 107 PHE cc_start: 0.8534 (t80) cc_final: 0.8281 (t80) REVERT: N 178 MET cc_start: 0.7829 (ttp) cc_final: 0.7577 (ttt) outliers start: 2 outliers final: 0 residues processed: 275 average time/residue: 0.3212 time to fit residues: 126.4695 Evaluate side-chains 217 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 chunk 115 optimal weight: 0.0040 chunk 93 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 121 optimal weight: 0.0770 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 overall best weight: 0.5550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS C 73 ASN C 104 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 104 GLN H 82 HIS M 117 ASN M 128 ASN M 188 HIS N 35 GLN N 50 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16588 Z= 0.155 Angle : 0.579 7.864 23646 Z= 0.333 Chirality : 0.037 0.180 2659 Planarity : 0.004 0.050 1979 Dihedral : 31.049 108.094 4522 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.10 % Allowed : 2.12 % Favored : 97.78 % 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: -0.38 (0.25), residues: 1171 helix: 0.60 (0.21), residues: 669 sheet: -0.13 (0.55), residues: 86 loop : -1.63 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 87 HIS 0.006 0.001 HIS N 50 PHE 0.008 0.001 PHE C 25 TYR 0.038 0.001 TYR D 83 ARG 0.006 0.000 ARG L 669 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 289 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9411 (tp40) cc_final: 0.9128 (tp40) REVERT: B 25 ASN cc_start: 0.8045 (t0) cc_final: 0.7483 (t0) REVERT: C 24 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7598 (tp40) REVERT: C 41 GLU cc_start: 0.8585 (pm20) cc_final: 0.8125 (mp0) REVERT: C 56 GLU cc_start: 0.7652 (tt0) cc_final: 0.7302 (tt0) REVERT: D 67 ASN cc_start: 0.8977 (m-40) cc_final: 0.8568 (t0) REVERT: D 76 GLU cc_start: 0.8768 (tp30) cc_final: 0.8429 (mm-30) REVERT: D 85 LYS cc_start: 0.8929 (mttt) cc_final: 0.8526 (mmtt) REVERT: D 90 THR cc_start: 0.9078 (p) cc_final: 0.8878 (p) REVERT: D 108 LYS cc_start: 0.9338 (tttt) cc_final: 0.8979 (ttpp) REVERT: D 121 TYR cc_start: 0.9194 (t80) cc_final: 0.8873 (t80) REVERT: E 97 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8530 (mm-30) REVERT: E 100 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8460 (mm-30) REVERT: E 111 TYR cc_start: 0.9449 (t80) cc_final: 0.9043 (t80) REVERT: F 31 LYS cc_start: 0.8925 (tptt) cc_final: 0.8440 (tptt) REVERT: F 61 PHE cc_start: 0.9172 (t80) cc_final: 0.8930 (t80) REVERT: G 38 ASN cc_start: 0.8255 (t0) cc_final: 0.7982 (p0) REVERT: G 41 GLU cc_start: 0.8586 (mp0) cc_final: 0.8342 (mt-10) REVERT: G 95 LYS cc_start: 0.8645 (tttm) cc_final: 0.8011 (ttmm) REVERT: H 46 LYS cc_start: 0.8813 (mmpt) cc_final: 0.8583 (mmmt) REVERT: H 57 LYS cc_start: 0.8993 (mmtt) cc_final: 0.8665 (mptt) REVERT: M 22 MET cc_start: 0.8583 (pmm) cc_final: 0.8326 (pmm) REVERT: M 57 GLU cc_start: 0.8397 (pt0) cc_final: 0.7854 (pp20) REVERT: M 58 GLU cc_start: 0.7522 (mm-30) cc_final: 0.6611 (mm-30) REVERT: M 79 ASN cc_start: 0.8658 (m-40) cc_final: 0.8002 (t0) REVERT: M 183 ASN cc_start: 0.8075 (m110) cc_final: 0.7859 (p0) REVERT: N 22 MET cc_start: 0.8341 (mpp) cc_final: 0.7926 (mpp) REVERT: N 87 HIS cc_start: 0.7924 (t70) cc_final: 0.7394 (t70) REVERT: N 107 PHE cc_start: 0.8502 (t80) cc_final: 0.8271 (t80) outliers start: 1 outliers final: 1 residues processed: 290 average time/residue: 0.3001 time to fit residues: 124.4244 Evaluate side-chains 224 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN G 104 GLN M 50 HIS M 128 ASN M 188 HIS N 35 GLN N 50 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16588 Z= 0.177 Angle : 0.576 8.108 23646 Z= 0.331 Chirality : 0.037 0.219 2659 Planarity : 0.004 0.049 1979 Dihedral : 31.016 103.335 4522 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.10 % Allowed : 2.70 % Favored : 97.20 % 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: -0.17 (0.25), residues: 1171 helix: 0.74 (0.20), residues: 671 sheet: -0.18 (0.56), residues: 88 loop : -1.46 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 87 HIS 0.006 0.001 HIS N 50 PHE 0.010 0.001 PHE E 79 TYR 0.045 0.001 TYR D 83 ARG 0.003 0.000 ARG L 669 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 279 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8357 (tt0) cc_final: 0.7743 (tt0) REVERT: B 63 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8091 (mt-10) REVERT: C 24 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7722 (tp40) REVERT: C 41 GLU cc_start: 0.8549 (pm20) cc_final: 0.8166 (mp0) REVERT: C 56 GLU cc_start: 0.7688 (tt0) cc_final: 0.7276 (tt0) REVERT: D 57 LYS cc_start: 0.9348 (mmmm) cc_final: 0.8714 (mptt) REVERT: D 67 ASN cc_start: 0.9027 (m-40) cc_final: 0.8587 (t0) REVERT: D 76 GLU cc_start: 0.8695 (tp30) cc_final: 0.8295 (mm-30) REVERT: D 85 LYS cc_start: 0.8873 (mttt) cc_final: 0.8467 (mmtt) REVERT: D 108 LYS cc_start: 0.9247 (tttt) cc_final: 0.8960 (ttpp) REVERT: D 121 TYR cc_start: 0.9138 (t80) cc_final: 0.8840 (t80) REVERT: E 97 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8130 (mm-30) REVERT: E 100 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8566 (mm-30) REVERT: E 111 TYR cc_start: 0.9379 (t80) cc_final: 0.9047 (t80) REVERT: E 137 GLN cc_start: 0.8513 (mp10) cc_final: 0.8273 (mm-40) REVERT: F 61 PHE cc_start: 0.9144 (t80) cc_final: 0.8913 (t80) REVERT: G 38 ASN cc_start: 0.8274 (t0) cc_final: 0.8063 (p0) REVERT: G 56 GLU cc_start: 0.7835 (pt0) cc_final: 0.7623 (pt0) REVERT: G 95 LYS cc_start: 0.8631 (tttm) cc_final: 0.8064 (ttmm) REVERT: G 99 ARG cc_start: 0.8403 (mtt180) cc_final: 0.8179 (mtp180) REVERT: H 46 LYS cc_start: 0.8890 (mmpt) cc_final: 0.8629 (mmmt) REVERT: H 57 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8725 (mptt) REVERT: H 95 GLN cc_start: 0.8939 (tp-100) cc_final: 0.8444 (tp-100) REVERT: M 22 MET cc_start: 0.8661 (pmm) cc_final: 0.8432 (pmm) REVERT: M 57 GLU cc_start: 0.8378 (pt0) cc_final: 0.7923 (pp20) REVERT: M 58 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6664 (mm-30) REVERT: M 62 ASP cc_start: 0.8737 (t0) cc_final: 0.8535 (t0) REVERT: M 79 ASN cc_start: 0.8596 (m-40) cc_final: 0.7984 (t0) REVERT: M 192 LEU cc_start: 0.8079 (pp) cc_final: 0.7870 (pt) REVERT: N 22 MET cc_start: 0.8296 (mpp) cc_final: 0.7894 (mpp) REVERT: N 87 HIS cc_start: 0.7905 (t70) cc_final: 0.7387 (t70) outliers start: 1 outliers final: 1 residues processed: 279 average time/residue: 0.3113 time to fit residues: 126.2848 Evaluate side-chains 218 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS G 31 HIS H 82 HIS ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 GLN M 50 HIS M 128 ASN N 35 GLN ** N 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.077 16588 Z= 0.591 Angle : 0.871 12.104 23646 Z= 0.476 Chirality : 0.048 0.189 2659 Planarity : 0.006 0.057 1979 Dihedral : 31.739 111.552 4522 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.24), residues: 1171 helix: -0.27 (0.19), residues: 661 sheet: -0.57 (0.55), residues: 88 loop : -1.68 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP M 131 HIS 0.009 0.003 HIS A 105 PHE 0.017 0.003 PHE E 79 TYR 0.052 0.003 TYR H 83 ARG 0.007 0.001 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8403 (tt0) cc_final: 0.7663 (tt0) REVERT: B 43 VAL cc_start: 0.9421 (t) cc_final: 0.9078 (p) REVERT: B 59 LYS cc_start: 0.8971 (ttpt) cc_final: 0.8385 (ttpt) REVERT: C 24 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7864 (tp-100) REVERT: C 34 LEU cc_start: 0.9464 (tp) cc_final: 0.9247 (tp) REVERT: C 41 GLU cc_start: 0.8687 (pm20) cc_final: 0.8151 (mp0) REVERT: C 56 GLU cc_start: 0.7992 (tt0) cc_final: 0.7702 (tt0) REVERT: C 57 TYR cc_start: 0.8788 (t80) cc_final: 0.8497 (t80) REVERT: D 67 ASN cc_start: 0.9164 (m-40) cc_final: 0.8751 (t0) REVERT: D 76 GLU cc_start: 0.9209 (tp30) cc_final: 0.8980 (tp30) REVERT: D 85 LYS cc_start: 0.9118 (mttt) cc_final: 0.8652 (mmtt) REVERT: D 86 ARG cc_start: 0.8973 (mmt90) cc_final: 0.8406 (ttm-80) REVERT: D 108 LYS cc_start: 0.9261 (tttt) cc_final: 0.8988 (ttpp) REVERT: D 121 TYR cc_start: 0.9192 (t80) cc_final: 0.8920 (t80) REVERT: E 90 MET cc_start: 0.8612 (mmm) cc_final: 0.8286 (mmt) REVERT: E 97 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8779 (mm-30) REVERT: G 95 LYS cc_start: 0.8730 (tttm) cc_final: 0.8086 (ttmm) REVERT: H 51 ASP cc_start: 0.8382 (t0) cc_final: 0.8181 (t0) REVERT: H 57 LYS cc_start: 0.9225 (mmtt) cc_final: 0.8949 (mptt) REVERT: H 83 TYR cc_start: 0.9106 (m-10) cc_final: 0.8519 (m-80) REVERT: N 22 MET cc_start: 0.8402 (mpp) cc_final: 0.8022 (mpp) REVERT: N 122 PHE cc_start: 0.7755 (m-80) cc_final: 0.7294 (m-80) REVERT: N 191 GLU cc_start: 0.8394 (pm20) cc_final: 0.8095 (pm20) REVERT: N 195 HIS cc_start: 0.8266 (p-80) cc_final: 0.7860 (p-80) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.3131 time to fit residues: 103.1157 Evaluate side-chains 183 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 0.0050 chunk 106 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 104 GLN D 82 HIS H 49 HIS H 82 HIS M 128 ASN M 188 HIS N 35 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16588 Z= 0.204 Angle : 0.638 9.284 23646 Z= 0.361 Chirality : 0.039 0.182 2659 Planarity : 0.004 0.047 1979 Dihedral : 31.168 113.615 4522 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.10 % Allowed : 1.64 % Favored : 98.26 % 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: -0.42 (0.25), residues: 1171 helix: 0.49 (0.20), residues: 656 sheet: -0.24 (0.56), residues: 88 loop : -1.42 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP M 131 HIS 0.009 0.001 HIS N 50 PHE 0.012 0.001 PHE C 25 TYR 0.042 0.001 TYR H 83 ARG 0.011 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8493 (tt0) cc_final: 0.7923 (tt0) REVERT: A 108 GLU cc_start: 0.8558 (tt0) cc_final: 0.7709 (tm-30) REVERT: A 109 ASP cc_start: 0.8347 (m-30) cc_final: 0.7718 (m-30) REVERT: C 24 GLN cc_start: 0.8360 (mm-40) cc_final: 0.7854 (tp-100) REVERT: C 41 GLU cc_start: 0.8714 (pm20) cc_final: 0.8220 (mp0) REVERT: C 56 GLU cc_start: 0.7527 (tt0) cc_final: 0.7192 (tt0) REVERT: C 57 TYR cc_start: 0.8864 (t80) cc_final: 0.8604 (t80) REVERT: D 67 ASN cc_start: 0.9063 (m-40) cc_final: 0.8667 (t0) REVERT: D 85 LYS cc_start: 0.8979 (mttt) cc_final: 0.8633 (mmtt) REVERT: D 121 TYR cc_start: 0.9154 (t80) cc_final: 0.8854 (t80) REVERT: E 97 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8614 (mm-30) REVERT: F 58 LEU cc_start: 0.9605 (tp) cc_final: 0.9380 (tp) REVERT: G 56 GLU cc_start: 0.7847 (pt0) cc_final: 0.7592 (pt0) REVERT: G 95 LYS cc_start: 0.8621 (tttm) cc_final: 0.8032 (ttmm) REVERT: G 99 ARG cc_start: 0.8390 (mtt180) cc_final: 0.7917 (ttm170) REVERT: H 46 LYS cc_start: 0.8660 (mmpt) cc_final: 0.8410 (mmmt) REVERT: H 57 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8744 (mptt) REVERT: H 67 ASN cc_start: 0.8833 (m-40) cc_final: 0.8328 (t0) REVERT: H 71 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7806 (tm-30) REVERT: M 22 MET cc_start: 0.8676 (pmm) cc_final: 0.8465 (pmm) REVERT: M 57 GLU cc_start: 0.8532 (pt0) cc_final: 0.7948 (pp20) REVERT: M 58 GLU cc_start: 0.7331 (mm-30) cc_final: 0.5840 (mm-30) REVERT: M 62 ASP cc_start: 0.8756 (t0) cc_final: 0.8382 (t0) REVERT: M 79 ASN cc_start: 0.8590 (m-40) cc_final: 0.8265 (m-40) REVERT: M 196 CYS cc_start: 0.7539 (t) cc_final: 0.7169 (t) REVERT: N 22 MET cc_start: 0.8286 (mpp) cc_final: 0.7945 (mpp) REVERT: N 191 GLU cc_start: 0.8233 (pm20) cc_final: 0.7892 (pm20) outliers start: 1 outliers final: 1 residues processed: 276 average time/residue: 0.2871 time to fit residues: 114.1804 Evaluate side-chains 216 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 98 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 50 HIS M 128 ASN N 35 GLN N 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 16588 Z= 0.386 Angle : 0.724 9.210 23646 Z= 0.403 Chirality : 0.042 0.178 2659 Planarity : 0.005 0.050 1979 Dihedral : 31.369 118.839 4522 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.77 (0.24), residues: 1171 helix: 0.17 (0.20), residues: 674 sheet: -0.31 (0.56), residues: 88 loop : -1.60 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 668 HIS 0.005 0.001 HIS E 105 PHE 0.019 0.002 PHE E 79 TYR 0.050 0.003 TYR H 83 ARG 0.009 0.001 ARG L 669 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8536 (tt0) cc_final: 0.7819 (tt0) REVERT: C 24 GLN cc_start: 0.8420 (mm-40) cc_final: 0.8036 (tp-100) REVERT: C 41 GLU cc_start: 0.8758 (pm20) cc_final: 0.8233 (mp0) REVERT: D 67 ASN cc_start: 0.9128 (m-40) cc_final: 0.8770 (t0) REVERT: D 85 LYS cc_start: 0.9066 (mttt) cc_final: 0.8634 (mmtt) REVERT: D 121 TYR cc_start: 0.9193 (t80) cc_final: 0.8884 (t80) REVERT: E 96 GLN cc_start: 0.9288 (tp-100) cc_final: 0.9057 (mm-40) REVERT: E 97 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8645 (mm-30) REVERT: G 15 LYS cc_start: 0.8992 (ttmt) cc_final: 0.8672 (ttpt) REVERT: G 23 LEU cc_start: 0.9068 (mm) cc_final: 0.8579 (mm) REVERT: G 95 LYS cc_start: 0.8666 (tttm) cc_final: 0.8107 (ttmm) REVERT: H 46 LYS cc_start: 0.8926 (mmpt) cc_final: 0.8308 (mmmt) REVERT: H 57 LYS cc_start: 0.9139 (mmtt) cc_final: 0.8819 (mptt) REVERT: H 83 TYR cc_start: 0.8774 (m-80) cc_final: 0.8384 (m-80) REVERT: M 22 MET cc_start: 0.8698 (pmm) cc_final: 0.8457 (pmm) REVERT: M 196 CYS cc_start: 0.7884 (t) cc_final: 0.7679 (t) REVERT: N 22 MET cc_start: 0.8270 (mpp) cc_final: 0.7949 (mpp) REVERT: N 122 PHE cc_start: 0.7692 (m-80) cc_final: 0.7317 (m-80) REVERT: N 191 GLU cc_start: 0.8156 (pm20) cc_final: 0.7920 (pm20) REVERT: N 195 HIS cc_start: 0.8141 (p-80) cc_final: 0.7703 (p-80) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2975 time to fit residues: 106.1353 Evaluate side-chains 199 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN M 50 HIS M 128 ASN M 188 HIS N 35 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 16588 Z= 0.401 Angle : 0.744 9.326 23646 Z= 0.414 Chirality : 0.042 0.141 2659 Planarity : 0.005 0.054 1979 Dihedral : 31.431 131.991 4522 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.10 % Allowed : 0.58 % Favored : 99.32 % 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: -0.96 (0.24), residues: 1171 helix: -0.04 (0.19), residues: 683 sheet: -0.48 (0.54), residues: 88 loop : -1.58 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP M 131 HIS 0.007 0.002 HIS N 50 PHE 0.021 0.002 PHE A 79 TYR 0.044 0.003 TYR H 83 ARG 0.006 0.001 ARG K 669 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8430 (tt0) cc_final: 0.7663 (tt0) REVERT: B 59 LYS cc_start: 0.8964 (ttpt) cc_final: 0.8719 (ttpt) REVERT: C 24 GLN cc_start: 0.8426 (mm-40) cc_final: 0.7964 (tp-100) REVERT: C 41 GLU cc_start: 0.8788 (pm20) cc_final: 0.8248 (mp0) REVERT: D 67 ASN cc_start: 0.9156 (m-40) cc_final: 0.8733 (t0) REVERT: D 85 LYS cc_start: 0.9084 (mttt) cc_final: 0.8691 (mmtt) REVERT: D 121 TYR cc_start: 0.9198 (t80) cc_final: 0.8879 (t80) REVERT: E 96 GLN cc_start: 0.9358 (tp-100) cc_final: 0.9048 (mm-40) REVERT: E 97 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8641 (mm-30) REVERT: G 15 LYS cc_start: 0.8963 (ttmt) cc_final: 0.8564 (ttpt) REVERT: G 91 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7745 (tm-30) REVERT: G 95 LYS cc_start: 0.8804 (tttm) cc_final: 0.8000 (ttmm) REVERT: H 57 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8818 (mptt) REVERT: H 71 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7972 (tm-30) REVERT: M 22 MET cc_start: 0.8774 (pmm) cc_final: 0.8491 (pmm) REVERT: M 56 CYS cc_start: 0.7851 (m) cc_final: 0.7495 (m) REVERT: M 186 ASP cc_start: 0.7287 (t70) cc_final: 0.7029 (t70) REVERT: M 188 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.7141 (m-70) REVERT: M 190 MET cc_start: 0.7146 (mmp) cc_final: 0.6943 (mmp) REVERT: M 191 GLU cc_start: 0.7871 (pm20) cc_final: 0.7521 (pm20) REVERT: M 196 CYS cc_start: 0.7892 (t) cc_final: 0.7686 (t) REVERT: N 22 MET cc_start: 0.8361 (mpp) cc_final: 0.8079 (mpp) REVERT: N 122 PHE cc_start: 0.7688 (m-80) cc_final: 0.7267 (m-80) REVERT: N 174 LEU cc_start: 0.9389 (tp) cc_final: 0.9185 (tt) REVERT: N 191 GLU cc_start: 0.8259 (pm20) cc_final: 0.8011 (pm20) REVERT: N 195 HIS cc_start: 0.7765 (p-80) cc_final: 0.7504 (p-80) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.3065 time to fit residues: 106.2874 Evaluate side-chains 203 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 50 HIS M 128 ASN M 185 HIS N 35 GLN N 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.076303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.058177 restraints weight = 51668.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.058529 restraints weight = 35673.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.058869 restraints weight = 30936.033| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16588 Z= 0.182 Angle : 0.629 9.406 23646 Z= 0.355 Chirality : 0.038 0.148 2659 Planarity : 0.004 0.048 1979 Dihedral : 31.034 133.191 4522 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.32 (0.25), residues: 1171 helix: 0.60 (0.20), residues: 665 sheet: -0.18 (0.56), residues: 86 loop : -1.47 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 668 HIS 0.007 0.001 HIS M 50 PHE 0.016 0.001 PHE E 79 TYR 0.029 0.001 TYR D 83 ARG 0.008 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2861.04 seconds wall clock time: 52 minutes 33.13 seconds (3153.13 seconds total)