Starting phenix.real_space_refine on Sat Mar 16 22:26:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch0_30367/03_2024/7ch0_30367_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch0_30367/03_2024/7ch0_30367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch0_30367/03_2024/7ch0_30367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch0_30367/03_2024/7ch0_30367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch0_30367/03_2024/7ch0_30367_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch0_30367/03_2024/7ch0_30367_updated.pdb" } resolution = 3.7 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= 0.001 sd= 0.010 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 6 5.49 5 S 68 5.16 5 C 10164 2.51 5 N 2666 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A GLU 36": "OE1" <-> "OE2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ASP 260": "OD1" <-> "OD2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 33": "NH1" <-> "NH2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E ARG 255": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 97": "NH1" <-> "NH2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ARG 97": "NH1" <-> "NH2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G GLU 119": "OE1" <-> "OE2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H GLU 122": "OE1" <-> "OE2" Residue "I ARG 55": "NH1" <-> "NH2" Residue "I GLU 122": "OE1" <-> "OE2" Residue "I GLU 144": "OE1" <-> "OE2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "K GLU 37": "OE1" <-> "OE2" Residue "K ARG 55": "NH1" <-> "NH2" Residue "K ARG 89": "NH1" <-> "NH2" Residue "K GLU 122": "OE1" <-> "OE2" Residue "K GLU 144": "OE1" <-> "OE2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "L GLU 87": "OE1" <-> "OE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15856 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1934 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "B" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1995 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 244} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1995 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 244} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1934 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "C" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 725 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "F" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 725 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "G" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "H" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "I" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1033 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "J" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "K" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "L" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1033 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.92, per 1000 atoms: 0.56 Number of scatterers: 15856 At special positions: 0 Unit cell: (108.7, 105.439, 150.006, 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 68 16.00 P 6 15.00 O 2952 8.00 N 2666 7.00 C 10164 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: 5.43 Conformation dependent library (CDL) restraints added in 3.0 seconds 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3824 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 15 sheets defined 34.4% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.42 Creating SS restraints... Processing helix chain 'A' and resid 4 through 31 removed outlier: 3.538A pdb=" N SER A 8 " --> pdb=" O ASN A 4 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 51 removed outlier: 3.617A pdb=" N VAL A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 76 removed outlier: 4.161A pdb=" N LEU A 57 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 58 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 59 " --> pdb=" O MET A 56 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL A 61 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A 62 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 64 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE A 65 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 66 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL A 69 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 70 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 72 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLN A 73 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY A 74 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU A 76 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 88 through 97 removed outlier: 4.001A pdb=" N LEU A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 125 removed outlier: 3.538A pdb=" N VAL A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 removed outlier: 4.042A pdb=" N MET A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 142 No H-bonds generated for 'chain 'A' and resid 139 through 142' Processing helix chain 'A' and resid 145 through 152 removed outlier: 3.586A pdb=" N TRP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 173 removed outlier: 4.034A pdb=" N VAL A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 192 removed outlier: 3.913A pdb=" N ASN A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 219 removed outlier: 3.806A pdb=" N LYS A 205 " --> pdb=" O ASN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 256 removed outlier: 3.865A pdb=" N SER A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 55 removed outlier: 3.733A pdb=" N ILE B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 removed outlier: 3.795A pdb=" N TYR B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS B 85 " --> pdb=" O TYR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.941A pdb=" N TYR B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 131 removed outlier: 4.013A pdb=" N GLU B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 156 removed outlier: 3.665A pdb=" N ALA B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 188 removed outlier: 3.580A pdb=" N VAL B 184 " --> pdb=" O MET B 180 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'E' and resid 48 through 55 removed outlier: 3.732A pdb=" N ILE E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 85 removed outlier: 3.794A pdb=" N TYR E 81 " --> pdb=" O ARG E 77 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR E 82 " --> pdb=" O SER E 78 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS E 85 " --> pdb=" O TYR E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.941A pdb=" N TYR E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 131 removed outlier: 4.014A pdb=" N GLU E 130 " --> pdb=" O MET E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 156 removed outlier: 3.665A pdb=" N ALA E 154 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA E 156 " --> pdb=" O ARG E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 188 removed outlier: 3.580A pdb=" N VAL E 184 " --> pdb=" O MET E 180 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS E 185 " --> pdb=" O GLY E 181 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE E 187 " --> pdb=" O LEU E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing helix chain 'E' and resid 262 through 264 No H-bonds generated for 'chain 'E' and resid 262 through 264' Processing helix chain 'D' and resid 4 through 31 removed outlier: 3.537A pdb=" N SER D 8 " --> pdb=" O ASN D 4 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU D 9 " --> pdb=" O ALA D 5 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY D 10 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR D 16 " --> pdb=" O LYS D 12 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 51 removed outlier: 3.617A pdb=" N VAL D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG D 46 " --> pdb=" O PRO D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 76 removed outlier: 4.161A pdb=" N LEU D 57 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 58 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE D 59 " --> pdb=" O MET D 56 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D 60 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL D 61 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 62 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL D 64 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE D 65 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE D 66 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL D 69 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU D 70 " --> pdb=" O GLY D 67 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 72 " --> pdb=" O VAL D 69 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N GLN D 73 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY D 74 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU D 76 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 88 through 97 removed outlier: 4.001A pdb=" N LEU D 93 " --> pdb=" O MET D 89 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 125 removed outlier: 3.538A pdb=" N VAL D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 135 removed outlier: 4.041A pdb=" N MET D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 142 No H-bonds generated for 'chain 'D' and resid 139 through 142' Processing helix chain 'D' and resid 145 through 152 removed outlier: 3.586A pdb=" N TRP D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 173 removed outlier: 4.034A pdb=" N VAL D 160 " --> pdb=" O PRO D 156 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL D 173 " --> pdb=" O GLY D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 192 removed outlier: 3.913A pdb=" N ASN D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 219 removed outlier: 3.805A pdb=" N LYS D 205 " --> pdb=" O ASN D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 256 removed outlier: 3.865A pdb=" N SER D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 236 " --> pdb=" O SER D 232 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL D 246 " --> pdb=" O SER D 242 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU D 247 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 30 Processing helix chain 'C' and resid 52 through 61 removed outlier: 5.122A pdb=" N LEU C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 58 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 removed outlier: 3.723A pdb=" N LYS C 67 " --> pdb=" O ASP C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 63 through 67' Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 52 through 61 removed outlier: 5.121A pdb=" N LEU F 57 " --> pdb=" O GLY F 53 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU F 58 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 67 removed outlier: 3.723A pdb=" N LYS F 67 " --> pdb=" O ASP F 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 63 through 67' Processing helix chain 'G' and resid 5 through 27 removed outlier: 4.001A pdb=" N TRP G 9 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL G 10 " --> pdb=" O ASN G 6 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU G 15 " --> pdb=" O GLY G 11 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 151 removed outlier: 3.606A pdb=" N ILE G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN G 149 " --> pdb=" O ASP G 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 9 No H-bonds generated for 'chain 'H' and resid 6 through 9' Processing helix chain 'H' and resid 11 through 23 Processing helix chain 'H' and resid 143 through 150 Processing helix chain 'I' and resid 9 through 27 removed outlier: 4.015A pdb=" N LEU I 14 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 150 removed outlier: 4.062A pdb=" N GLY I 148 " --> pdb=" O GLU I 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 11 removed outlier: 3.796A pdb=" N GLY J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 27 removed outlier: 4.292A pdb=" N LEU J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA J 21 " --> pdb=" O ALA J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 151 removed outlier: 3.526A pdb=" N GLY J 148 " --> pdb=" O GLU J 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 27 removed outlier: 4.494A pdb=" N PHE K 13 " --> pdb=" O TRP K 9 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 151 Processing helix chain 'L' and resid 7 through 17 removed outlier: 3.700A pdb=" N ALA L 17 " --> pdb=" O PHE L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 27 removed outlier: 4.190A pdb=" N CYS L 25 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 151 Processing sheet with id= A, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.542A pdb=" N VAL B 31 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 37 through 39 removed outlier: 3.522A pdb=" N THR B 37 " --> pdb=" O CYS B 198 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.542A pdb=" N VAL E 31 " --> pdb=" O LEU E 8 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 37 through 39 removed outlier: 3.521A pdb=" N THR E 37 " --> pdb=" O CYS E 198 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 215 through 218 removed outlier: 3.653A pdb=" N ALA E 215 " --> pdb=" O GLY E 227 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY E 227 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA E 225 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 39 through 45 removed outlier: 3.588A pdb=" N ALA G 44 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP G 70 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLU G 85 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL G 68 " --> pdb=" O GLU G 85 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLU G 87 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY G 66 " --> pdb=" O GLU G 87 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL G 63 " --> pdb=" O ILE G 60 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL G 58 " --> pdb=" O VAL G 65 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU G 112 " --> pdb=" O SER G 59 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 132 through 134 removed outlier: 4.747A pdb=" N THR H 45 " --> pdb=" O ILE H 134 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 100 through 103 Processing sheet with id= I, first strand: chain 'I' and resid 39 through 43 removed outlier: 4.130A pdb=" N ASP I 70 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU I 85 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL I 68 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU I 87 " --> pdb=" O GLY I 66 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLY I 66 " --> pdb=" O GLU I 87 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL I 63 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL I 58 " --> pdb=" O VAL I 65 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 112 through 115 removed outlier: 6.913A pdb=" N ASP I 136 " --> pdb=" O LEU I 99 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ILE I 101 " --> pdb=" O ASP I 136 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LYS I 138 " --> pdb=" O ILE I 101 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'J' and resid 39 through 45 removed outlier: 3.676A pdb=" N ALA J 44 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP J 70 " --> pdb=" O THR J 83 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU J 85 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL J 68 " --> pdb=" O GLU J 85 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLU J 87 " --> pdb=" O GLY J 66 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY J 66 " --> pdb=" O GLU J 87 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL J 63 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL J 58 " --> pdb=" O VAL J 65 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'J' and resid 98 through 100 Processing sheet with id= M, first strand: chain 'K' and resid 43 through 45 removed outlier: 3.780A pdb=" N ASP K 70 " --> pdb=" O THR K 83 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU K 85 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL K 68 " --> pdb=" O GLU K 85 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL K 63 " --> pdb=" O ILE K 60 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL K 58 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU K 112 " --> pdb=" O SER K 59 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG K 102 " --> pdb=" O TYR K 111 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN K 115 " --> pdb=" O SER K 98 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER K 98 " --> pdb=" O ASN K 115 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 39 through 45 removed outlier: 3.697A pdb=" N ARG L 67 " --> pdb=" O GLU L 85 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N VAL L 65 " --> pdb=" O GLU L 87 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL L 58 " --> pdb=" O VAL L 65 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'L' and resid 98 through 103 411 hydrogen bonds defined for protein. 1170 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.90 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5082 1.34 - 1.46: 2652 1.46 - 1.57: 8266 1.57 - 1.69: 10 1.69 - 1.81: 124 Bond restraints: 16134 Sorted by residual: bond pdb=" C4 ATP E 301 " pdb=" C5 ATP E 301 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.26e+01 bond pdb=" C4 ATP B 301 " pdb=" C5 ATP B 301 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.17e+01 bond pdb=" C5 ATP B 301 " pdb=" C6 ATP B 301 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.48e+01 bond pdb=" C5 ATP E 301 " pdb=" C6 ATP E 301 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.44e+01 bond pdb=" C5 ATP E 301 " pdb=" N7 ATP E 301 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.31e+01 ... (remaining 16129 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.49: 495 106.49 - 113.77: 9291 113.77 - 121.04: 7498 121.04 - 128.32: 4551 128.32 - 135.60: 117 Bond angle restraints: 21952 Sorted by residual: angle pdb=" PB ATP E 301 " pdb=" O3B ATP E 301 " pdb=" PG ATP E 301 " ideal model delta sigma weight residual 139.87 120.92 18.95 1.00e+00 1.00e+00 3.59e+02 angle pdb=" PB ATP B 301 " pdb=" O3B ATP B 301 " pdb=" PG ATP B 301 " ideal model delta sigma weight residual 139.87 120.94 18.93 1.00e+00 1.00e+00 3.58e+02 angle pdb=" PA ATP E 301 " pdb=" O3A ATP E 301 " pdb=" PB ATP E 301 " ideal model delta sigma weight residual 136.83 119.25 17.58 1.00e+00 1.00e+00 3.09e+02 angle pdb=" PA ATP B 301 " pdb=" O3A ATP B 301 " pdb=" PB ATP B 301 " ideal model delta sigma weight residual 136.83 119.31 17.52 1.00e+00 1.00e+00 3.07e+02 angle pdb=" C5 ATP E 301 " pdb=" C4 ATP E 301 " pdb=" N3 ATP E 301 " ideal model delta sigma weight residual 126.80 118.28 8.52 1.00e+00 1.00e+00 7.26e+01 ... (remaining 21947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8532 17.94 - 35.88: 847 35.88 - 53.82: 226 53.82 - 71.77: 57 71.77 - 89.71: 12 Dihedral angle restraints: 9674 sinusoidal: 3720 harmonic: 5954 Sorted by residual: dihedral pdb=" CA THR J 77 " pdb=" C THR J 77 " pdb=" N TYR J 78 " pdb=" CA TYR J 78 " ideal model delta harmonic sigma weight residual -180.00 -153.22 -26.78 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ASP G 95 " pdb=" C ASP G 95 " pdb=" N THR G 96 " pdb=" CA THR G 96 " ideal model delta harmonic sigma weight residual 180.00 154.56 25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA THR L 77 " pdb=" C THR L 77 " pdb=" N TYR L 78 " pdb=" CA TYR L 78 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 9671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2335 0.083 - 0.165: 298 0.165 - 0.248: 13 0.248 - 0.331: 3 0.331 - 0.414: 3 Chirality restraints: 2652 Sorted by residual: chirality pdb=" CB ILE L 71 " pdb=" CA ILE L 71 " pdb=" CG1 ILE L 71 " pdb=" CG2 ILE L 71 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CB ILE I 71 " pdb=" CA ILE I 71 " pdb=" CG1 ILE I 71 " pdb=" CG2 ILE I 71 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CB ILE H 71 " pdb=" CA ILE H 71 " pdb=" CG1 ILE H 71 " pdb=" CG2 ILE H 71 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 2649 not shown) Planarity restraints: 2764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 26 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO C 27 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 27 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 27 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 26 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO F 27 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO F 27 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 27 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 41 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO D 42 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 42 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 42 " -0.036 5.00e-02 4.00e+02 ... (remaining 2761 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 80 2.51 - 3.11: 10113 3.11 - 3.70: 22740 3.70 - 4.30: 31887 4.30 - 4.90: 53883 Nonbonded interactions: 118703 Sorted by model distance: nonbonded pdb=" O GLY B 259 " pdb=" O ASP B 260 " model vdw 1.910 3.040 nonbonded pdb=" N GLN E 230 " pdb=" OE1 GLN E 230 " model vdw 2.036 2.520 nonbonded pdb=" O HIS B 226 " pdb=" ND1 HIS B 226 " model vdw 2.129 2.520 nonbonded pdb=" OD1 ASP B 260 " pdb=" N TYR B 261 " model vdw 2.232 2.520 nonbonded pdb=" O TYR E 261 " pdb=" N ALA E 263 " model vdw 2.272 2.520 ... (remaining 118698 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 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = (chain 'G' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = (chain 'H' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = chain 'I' selection = (chain 'J' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = (chain 'K' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.190 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: 2.640 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 42.990 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 16134 Z= 0.505 Angle : 1.105 18.950 21952 Z= 0.658 Chirality : 0.056 0.414 2652 Planarity : 0.007 0.079 2764 Dihedral : 16.223 89.707 5850 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.75 % Favored : 89.01 % Rotamer: Outliers : 6.24 % Allowed : 10.34 % Favored : 83.41 % 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: -6.21 (0.12), residues: 2056 helix: -4.84 (0.06), residues: 811 sheet: -3.29 (0.26), residues: 290 loop : -3.65 (0.16), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 7 HIS 0.003 0.001 HIS E 122 PHE 0.020 0.002 PHE B 254 TYR 0.036 0.002 TYR J 111 ARG 0.008 0.001 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 387 time to evaluate : 1.676 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6980 (tp) REVERT: A 72 LEU cc_start: 0.8444 (mm) cc_final: 0.8040 (mt) REVERT: A 111 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8629 (tmm160) REVERT: A 122 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8317 (tp) REVERT: A 203 LEU cc_start: 0.8732 (mt) cc_final: 0.8437 (mt) REVERT: B 130 GLU cc_start: 0.8649 (mm-30) cc_final: 0.7888 (tt0) REVERT: B 176 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8417 (p0) REVERT: B 222 LYS cc_start: 0.8345 (pttt) cc_final: 0.7548 (ptmm) REVERT: B 242 GLN cc_start: 0.6892 (tm-30) cc_final: 0.6486 (tm-30) REVERT: E 139 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8325 (mmtp) REVERT: E 207 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7847 (mm-30) REVERT: E 222 LYS cc_start: 0.8292 (pttt) cc_final: 0.7908 (ptpp) REVERT: D 38 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6491 (mmt180) REVERT: D 129 LEU cc_start: 0.9296 (mt) cc_final: 0.9079 (mt) REVERT: D 134 MET cc_start: 0.8799 (tpt) cc_final: 0.8585 (tpt) REVERT: C 32 ARG cc_start: 0.6746 (ptt90) cc_final: 0.6545 (ptt-90) REVERT: C 81 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8649 (m) REVERT: F 83 THR cc_start: 0.8914 (t) cc_final: 0.8714 (m) REVERT: G 74 ASP cc_start: 0.7947 (t0) cc_final: 0.7712 (t0) REVERT: G 134 ILE cc_start: 0.8664 (mt) cc_final: 0.8450 (mp) REVERT: H 102 ARG cc_start: 0.8339 (mtt180) cc_final: 0.7910 (mtm-85) REVERT: J 30 ASN cc_start: 0.6046 (OUTLIER) cc_final: 0.5539 (m-40) REVERT: J 85 GLU cc_start: 0.8111 (tt0) cc_final: 0.7564 (tt0) REVERT: K 48 ASN cc_start: 0.8274 (m110) cc_final: 0.8013 (t0) outliers start: 105 outliers final: 21 residues processed: 457 average time/residue: 0.3010 time to fit residues: 194.3787 Evaluate side-chains 330 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 301 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 230 GLN Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain J residue 30 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 159 optimal weight: 0.0030 chunk 61 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 29 ASN A 73 GLN A 128 GLN ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN B 92 GLN B 230 GLN E 57 GLN E 62 HIS D 4 ASN D 29 ASN D 73 GLN D 128 GLN D 191 ASN D 241 HIS C 70 ASN F 70 ASN G 91 ASN H 149 GLN I 91 ASN K 6 ASN K 48 ASN L 91 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16134 Z= 0.194 Angle : 0.631 9.470 21952 Z= 0.326 Chirality : 0.042 0.177 2652 Planarity : 0.005 0.062 2764 Dihedral : 8.683 87.216 2350 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.59 % Favored : 92.36 % Rotamer: Outliers : 3.33 % Allowed : 16.53 % Favored : 80.14 % 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: -4.95 (0.15), residues: 2056 helix: -3.33 (0.13), residues: 847 sheet: -2.92 (0.28), residues: 288 loop : -3.26 (0.17), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 216 HIS 0.016 0.001 HIS E 62 PHE 0.015 0.001 PHE G 13 TYR 0.014 0.001 TYR K 40 ARG 0.006 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 327 time to evaluate : 2.032 Fit side-chains REVERT: A 26 MET cc_start: 0.9011 (ttt) cc_final: 0.8782 (ttp) REVERT: A 72 LEU cc_start: 0.8312 (mm) cc_final: 0.8083 (mt) REVERT: A 111 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.6208 (tmm160) REVERT: A 158 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8704 (mp) REVERT: A 191 ASN cc_start: 0.8457 (p0) cc_final: 0.8199 (p0) REVERT: B 100 MET cc_start: 0.7847 (ttp) cc_final: 0.7598 (mtm) REVERT: B 130 GLU cc_start: 0.8546 (mm-30) cc_final: 0.7755 (tt0) REVERT: B 141 MET cc_start: 0.8349 (mmm) cc_final: 0.7981 (mmm) REVERT: B 222 LYS cc_start: 0.8315 (pttt) cc_final: 0.7464 (ptmm) REVERT: B 242 GLN cc_start: 0.6988 (tm-30) cc_final: 0.6448 (tm-30) REVERT: E 40 MET cc_start: 0.8067 (mtp) cc_final: 0.7792 (mtt) REVERT: E 207 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7844 (mm-30) REVERT: E 222 LYS cc_start: 0.8252 (pttt) cc_final: 0.7812 (ptpp) REVERT: D 38 ARG cc_start: 0.7100 (mtt180) cc_final: 0.6693 (mmt180) REVERT: D 129 LEU cc_start: 0.9238 (mt) cc_final: 0.9023 (mt) REVERT: D 231 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8656 (mp) REVERT: G 74 ASP cc_start: 0.7837 (t0) cc_final: 0.7577 (t0) REVERT: H 88 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7582 (mm-40) REVERT: J 30 ASN cc_start: 0.6127 (OUTLIER) cc_final: 0.5577 (m-40) REVERT: J 85 GLU cc_start: 0.8092 (tt0) cc_final: 0.7824 (tt0) REVERT: K 9 TRP cc_start: 0.7671 (t-100) cc_final: 0.6486 (t60) outliers start: 56 outliers final: 34 residues processed: 365 average time/residue: 0.2701 time to fit residues: 145.6607 Evaluate side-chains 322 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 284 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 111 TYR Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain L residue 100 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 154 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 185 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 63 optimal weight: 0.2980 chunk 148 optimal weight: 30.0000 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN E 62 HIS D 191 ASN H 149 GLN I 91 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 16134 Z= 0.445 Angle : 0.756 9.761 21952 Z= 0.386 Chirality : 0.048 0.278 2652 Planarity : 0.006 0.059 2764 Dihedral : 7.884 77.501 2315 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.97 % Favored : 89.98 % Rotamer: Outliers : 4.93 % Allowed : 20.10 % Favored : 74.97 % 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: -4.34 (0.16), residues: 2056 helix: -2.64 (0.15), residues: 846 sheet: -2.63 (0.30), residues: 274 loop : -3.13 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 177 HIS 0.013 0.002 HIS E 62 PHE 0.030 0.002 PHE G 13 TYR 0.022 0.002 TYR K 40 ARG 0.005 0.001 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 287 time to evaluate : 1.846 Fit side-chains REVERT: B 141 MET cc_start: 0.8258 (mmm) cc_final: 0.7902 (mmm) REVERT: B 222 LYS cc_start: 0.8658 (pttt) cc_final: 0.7770 (ptmm) REVERT: B 242 GLN cc_start: 0.7346 (tm-30) cc_final: 0.7114 (tm-30) REVERT: E 40 MET cc_start: 0.8228 (mtp) cc_final: 0.7912 (mtt) REVERT: E 207 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8267 (mm-30) REVERT: E 222 LYS cc_start: 0.8436 (pttt) cc_final: 0.7965 (ptpp) REVERT: D 38 ARG cc_start: 0.7515 (mtt180) cc_final: 0.6855 (mmt180) REVERT: C 31 MET cc_start: 0.7036 (mtp) cc_final: 0.6779 (mtp) REVERT: F 37 LYS cc_start: 0.5912 (OUTLIER) cc_final: 0.5605 (pttp) REVERT: G 74 ASP cc_start: 0.7785 (t0) cc_final: 0.7526 (t0) REVERT: I 91 ASN cc_start: 0.7885 (OUTLIER) cc_final: 0.7668 (p0) REVERT: I 138 LYS cc_start: 0.8555 (mttt) cc_final: 0.8311 (mttt) REVERT: J 85 GLU cc_start: 0.8112 (tt0) cc_final: 0.7671 (tt0) REVERT: J 111 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8207 (p90) REVERT: K 6 ASN cc_start: 0.7649 (t0) cc_final: 0.7291 (t0) REVERT: K 7 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8284 (pt0) REVERT: K 151 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6925 (pp) outliers start: 83 outliers final: 59 residues processed: 341 average time/residue: 0.2705 time to fit residues: 136.3963 Evaluate side-chains 328 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 264 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 91 ASN Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 111 TYR Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 141 MET Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 142 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 96 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 124 optimal weight: 30.0000 chunk 186 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS B 62 HIS D 191 ASN K 6 ASN ** L 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16134 Z= 0.146 Angle : 0.568 8.525 21952 Z= 0.292 Chirality : 0.041 0.203 2652 Planarity : 0.004 0.052 2764 Dihedral : 6.863 68.730 2305 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.21 % Allowed : 22.35 % Favored : 74.44 % 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: -3.69 (0.17), residues: 2056 helix: -1.94 (0.17), residues: 840 sheet: -2.41 (0.30), residues: 288 loop : -2.89 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 7 HIS 0.005 0.001 HIS I 92 PHE 0.008 0.001 PHE A 162 TYR 0.015 0.001 TYR J 152 ARG 0.005 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 281 time to evaluate : 1.937 Fit side-chains REVERT: A 191 ASN cc_start: 0.8300 (p0) cc_final: 0.8090 (p0) REVERT: B 141 MET cc_start: 0.8150 (mmm) cc_final: 0.7808 (mmm) REVERT: B 222 LYS cc_start: 0.8522 (pttt) cc_final: 0.7670 (ptmm) REVERT: B 242 GLN cc_start: 0.7269 (tm-30) cc_final: 0.6830 (tm-30) REVERT: E 222 LYS cc_start: 0.8373 (pttt) cc_final: 0.7860 (ptpp) REVERT: D 38 ARG cc_start: 0.7333 (mtt180) cc_final: 0.6747 (mmt180) REVERT: D 134 MET cc_start: 0.8434 (tpt) cc_final: 0.8113 (tpt) REVERT: C 8 MET cc_start: 0.5807 (mmt) cc_final: 0.5457 (mmt) REVERT: F 37 LYS cc_start: 0.5617 (OUTLIER) cc_final: 0.5350 (pttp) REVERT: G 74 ASP cc_start: 0.7796 (t0) cc_final: 0.7521 (t0) REVERT: I 85 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6271 (mp0) REVERT: I 138 LYS cc_start: 0.8468 (mttt) cc_final: 0.8238 (mttt) REVERT: J 30 ASN cc_start: 0.6538 (OUTLIER) cc_final: 0.5774 (m-40) REVERT: J 85 GLU cc_start: 0.8003 (tt0) cc_final: 0.7706 (tt0) REVERT: K 151 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6488 (pp) outliers start: 54 outliers final: 29 residues processed: 319 average time/residue: 0.2653 time to fit residues: 126.3968 Evaluate side-chains 294 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 261 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 123 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 0.9990 chunk 176 optimal weight: 0.0070 chunk 49 optimal weight: 20.0000 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN B 233 GLN D 191 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16134 Z= 0.153 Angle : 0.562 8.688 21952 Z= 0.285 Chirality : 0.041 0.173 2652 Planarity : 0.004 0.046 2764 Dihedral : 6.542 67.060 2305 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.57 % Allowed : 22.83 % Favored : 73.60 % 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: -3.25 (0.18), residues: 2056 helix: -1.56 (0.18), residues: 834 sheet: -2.15 (0.30), residues: 284 loop : -2.66 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 216 HIS 0.012 0.001 HIS B 62 PHE 0.011 0.001 PHE E 254 TYR 0.015 0.001 TYR K 40 ARG 0.004 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 273 time to evaluate : 1.849 Fit side-chains REVERT: A 72 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8021 (mt) REVERT: A 191 ASN cc_start: 0.8313 (p0) cc_final: 0.8108 (p0) REVERT: B 141 MET cc_start: 0.8154 (mmm) cc_final: 0.7797 (mmm) REVERT: B 222 LYS cc_start: 0.8471 (pttt) cc_final: 0.7606 (ptmm) REVERT: B 242 GLN cc_start: 0.7294 (tm-30) cc_final: 0.6839 (tm-30) REVERT: E 222 LYS cc_start: 0.8385 (pttt) cc_final: 0.7833 (ptpp) REVERT: D 38 ARG cc_start: 0.7284 (mtt180) cc_final: 0.6737 (mmt180) REVERT: D 134 MET cc_start: 0.8416 (tpt) cc_final: 0.8105 (tpt) REVERT: C 31 MET cc_start: 0.7017 (mtp) cc_final: 0.6695 (ttm) REVERT: C 49 ARG cc_start: 0.7758 (ptm-80) cc_final: 0.7403 (ptm-80) REVERT: F 22 GLN cc_start: 0.8229 (mt0) cc_final: 0.7912 (mt0) REVERT: F 37 LYS cc_start: 0.5662 (OUTLIER) cc_final: 0.5418 (pttp) REVERT: G 74 ASP cc_start: 0.7900 (t0) cc_final: 0.7683 (t0) REVERT: I 84 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8467 (mt) REVERT: I 85 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6348 (mp0) REVERT: J 30 ASN cc_start: 0.6466 (OUTLIER) cc_final: 0.5788 (m-40) REVERT: J 85 GLU cc_start: 0.8008 (tt0) cc_final: 0.7705 (tt0) REVERT: K 79 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7423 (pp) REVERT: K 151 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6477 (pp) outliers start: 60 outliers final: 40 residues processed: 312 average time/residue: 0.2697 time to fit residues: 125.0193 Evaluate side-chains 304 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 257 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 111 TYR Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 123 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS D 191 ASN J 92 HIS ** K 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16134 Z= 0.329 Angle : 0.652 10.842 21952 Z= 0.330 Chirality : 0.044 0.201 2652 Planarity : 0.004 0.044 2764 Dihedral : 6.879 70.184 2303 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 4.82 % Allowed : 22.47 % Favored : 72.71 % 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: -3.22 (0.18), residues: 2056 helix: -1.60 (0.17), residues: 836 sheet: -1.89 (0.31), residues: 286 loop : -2.68 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 216 HIS 0.003 0.001 HIS A 241 PHE 0.022 0.002 PHE G 13 TYR 0.020 0.002 TYR K 40 ARG 0.015 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 262 time to evaluate : 1.737 Fit side-chains REVERT: A 72 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8094 (mt) REVERT: A 191 ASN cc_start: 0.8512 (p0) cc_final: 0.8241 (p0) REVERT: A 231 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8979 (mm) REVERT: B 141 MET cc_start: 0.8089 (mmm) cc_final: 0.7860 (mmm) REVERT: B 222 LYS cc_start: 0.8618 (pttt) cc_final: 0.7757 (ptmm) REVERT: B 242 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7243 (tm-30) REVERT: E 207 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7870 (mm-30) REVERT: E 222 LYS cc_start: 0.8428 (pttt) cc_final: 0.7923 (ptpp) REVERT: D 38 ARG cc_start: 0.7368 (mtt180) cc_final: 0.6772 (mmt180) REVERT: D 134 MET cc_start: 0.8485 (tpt) cc_final: 0.8066 (tpt) REVERT: F 37 LYS cc_start: 0.5785 (OUTLIER) cc_final: 0.5476 (pttp) REVERT: G 143 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7811 (pt) REVERT: H 8 ILE cc_start: 0.8431 (mt) cc_final: 0.7840 (mt) REVERT: I 55 ARG cc_start: 0.7823 (mmm160) cc_final: 0.7599 (mmm160) REVERT: J 85 GLU cc_start: 0.8043 (tt0) cc_final: 0.7714 (tt0) REVERT: J 111 TYR cc_start: 0.8776 (OUTLIER) cc_final: 0.8263 (p90) REVERT: K 9 TRP cc_start: 0.7834 (t-100) cc_final: 0.6327 (t60) REVERT: K 79 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7493 (pp) REVERT: K 92 HIS cc_start: 0.8206 (t-90) cc_final: 0.7877 (t-90) REVERT: K 151 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6652 (pp) outliers start: 81 outliers final: 61 residues processed: 318 average time/residue: 0.2723 time to fit residues: 128.0642 Evaluate side-chains 322 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 254 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 177 TRP Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 89 ARG Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 111 TYR Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 141 MET Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 123 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 50.0000 chunk 22 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 196 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 191 ASN C 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16134 Z= 0.182 Angle : 0.581 10.470 21952 Z= 0.296 Chirality : 0.042 0.220 2652 Planarity : 0.004 0.044 2764 Dihedral : 6.570 65.829 2303 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 4.52 % Allowed : 22.89 % Favored : 72.59 % 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: -2.91 (0.18), residues: 2056 helix: -1.26 (0.18), residues: 844 sheet: -1.77 (0.32), residues: 284 loop : -2.58 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 216 HIS 0.002 0.001 HIS E 262 PHE 0.012 0.001 PHE G 13 TYR 0.016 0.001 TYR K 40 ARG 0.007 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 267 time to evaluate : 1.816 Fit side-chains REVERT: A 72 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8074 (mt) REVERT: A 191 ASN cc_start: 0.8395 (p0) cc_final: 0.8176 (p0) REVERT: B 141 MET cc_start: 0.8104 (mmm) cc_final: 0.7892 (mmm) REVERT: B 222 LYS cc_start: 0.8583 (pttt) cc_final: 0.7757 (ptmm) REVERT: B 242 GLN cc_start: 0.7423 (tm-30) cc_final: 0.6976 (tm-30) REVERT: E 207 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7829 (mm-30) REVERT: E 222 LYS cc_start: 0.8416 (pttt) cc_final: 0.7905 (ptpp) REVERT: D 38 ARG cc_start: 0.7356 (mtt180) cc_final: 0.6755 (mmt180) REVERT: D 134 MET cc_start: 0.8410 (tpt) cc_final: 0.8122 (tpt) REVERT: C 8 MET cc_start: 0.5343 (mmt) cc_final: 0.4385 (ptm) REVERT: F 37 LYS cc_start: 0.5831 (OUTLIER) cc_final: 0.5521 (pttp) REVERT: H 8 ILE cc_start: 0.8255 (mt) cc_final: 0.7813 (mt) REVERT: I 85 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6244 (mp0) REVERT: J 85 GLU cc_start: 0.8002 (tt0) cc_final: 0.7722 (tt0) REVERT: J 111 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.8363 (p90) REVERT: K 55 ARG cc_start: 0.8542 (mmm160) cc_final: 0.8270 (mmp80) REVERT: K 79 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7523 (pp) REVERT: K 92 HIS cc_start: 0.8151 (t-90) cc_final: 0.7911 (t-90) REVERT: K 151 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6498 (pp) outliers start: 76 outliers final: 57 residues processed: 321 average time/residue: 0.2619 time to fit residues: 126.1777 Evaluate side-chains 322 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 259 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 111 TYR Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 123 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 133 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 262 HIS D 191 ASN K 6 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16134 Z= 0.163 Angle : 0.568 9.906 21952 Z= 0.289 Chirality : 0.041 0.180 2652 Planarity : 0.004 0.045 2764 Dihedral : 6.292 64.290 2303 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.52 % Allowed : 23.25 % Favored : 72.24 % 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: -2.62 (0.18), residues: 2056 helix: -0.97 (0.18), residues: 834 sheet: -1.61 (0.31), residues: 304 loop : -2.47 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 216 HIS 0.002 0.000 HIS E 62 PHE 0.010 0.001 PHE G 13 TYR 0.015 0.001 TYR K 40 ARG 0.005 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 269 time to evaluate : 1.736 Fit side-chains REVERT: A 72 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8040 (mt) REVERT: A 127 GLU cc_start: 0.7424 (tp30) cc_final: 0.7023 (tp30) REVERT: B 126 MET cc_start: 0.8686 (mmt) cc_final: 0.8307 (mmm) REVERT: B 222 LYS cc_start: 0.8352 (pttt) cc_final: 0.7525 (ptmm) REVERT: B 242 GLN cc_start: 0.7480 (tm-30) cc_final: 0.6883 (tm-30) REVERT: E 207 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7809 (mm-30) REVERT: E 222 LYS cc_start: 0.8406 (pttt) cc_final: 0.7892 (ptpp) REVERT: D 38 ARG cc_start: 0.7354 (mtt180) cc_final: 0.6754 (mmt180) REVERT: D 134 MET cc_start: 0.8409 (tpt) cc_final: 0.8188 (tpt) REVERT: F 37 LYS cc_start: 0.6083 (OUTLIER) cc_final: 0.5787 (pttp) REVERT: H 60 ILE cc_start: 0.8654 (mt) cc_final: 0.8408 (mt) REVERT: I 85 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6238 (mp0) REVERT: J 85 GLU cc_start: 0.7999 (tt0) cc_final: 0.7722 (tt0) REVERT: K 79 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7478 (pp) REVERT: K 92 HIS cc_start: 0.8138 (t-90) cc_final: 0.7917 (t-90) REVERT: K 151 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6462 (pp) outliers start: 76 outliers final: 60 residues processed: 323 average time/residue: 0.2809 time to fit residues: 136.2739 Evaluate side-chains 327 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 262 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 177 TRP Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 123 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.8980 chunk 171 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 110 optimal weight: 0.0570 chunk 79 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 173 optimal weight: 0.0000 chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 overall best weight: 0.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 191 ASN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16134 Z= 0.137 Angle : 0.552 7.649 21952 Z= 0.282 Chirality : 0.040 0.152 2652 Planarity : 0.004 0.048 2764 Dihedral : 5.983 70.061 2302 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.86 % Allowed : 23.96 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.31 (0.19), residues: 2056 helix: -0.59 (0.19), residues: 812 sheet: -1.44 (0.31), residues: 304 loop : -2.42 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 9 HIS 0.001 0.000 HIS B 262 PHE 0.015 0.001 PHE H 150 TYR 0.012 0.001 TYR K 40 ARG 0.017 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 276 time to evaluate : 1.876 Fit side-chains REVERT: A 72 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8042 (mt) REVERT: B 222 LYS cc_start: 0.8263 (pttt) cc_final: 0.7481 (ptmm) REVERT: B 242 GLN cc_start: 0.7440 (tm-30) cc_final: 0.6767 (tm-30) REVERT: E 130 GLU cc_start: 0.8870 (tp30) cc_final: 0.8654 (tp30) REVERT: E 207 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7750 (mm-30) REVERT: E 222 LYS cc_start: 0.8401 (pttt) cc_final: 0.7847 (ptpp) REVERT: D 38 ARG cc_start: 0.7376 (mtt180) cc_final: 0.6857 (mmt180) REVERT: D 134 MET cc_start: 0.8409 (tpt) cc_final: 0.8192 (tpt) REVERT: C 8 MET cc_start: 0.5115 (mmt) cc_final: 0.4435 (ptm) REVERT: F 8 MET cc_start: 0.5682 (OUTLIER) cc_final: 0.5465 (pmm) REVERT: F 37 LYS cc_start: 0.6123 (OUTLIER) cc_final: 0.5822 (pttp) REVERT: G 77 THR cc_start: 0.7930 (OUTLIER) cc_final: 0.7663 (p) REVERT: I 85 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6267 (mp0) REVERT: J 85 GLU cc_start: 0.7976 (tt0) cc_final: 0.7727 (tt0) REVERT: K 79 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7418 (pp) REVERT: K 92 HIS cc_start: 0.8147 (t-90) cc_final: 0.7943 (t-90) REVERT: K 151 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6355 (pp) outliers start: 65 outliers final: 49 residues processed: 321 average time/residue: 0.2551 time to fit residues: 123.5417 Evaluate side-chains 320 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 264 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain F residue 8 MET Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 111 TYR Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 125 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN ** K 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16134 Z= 0.231 Angle : 0.604 7.423 21952 Z= 0.309 Chirality : 0.042 0.160 2652 Planarity : 0.004 0.059 2764 Dihedral : 6.230 68.925 2301 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 3.98 % Allowed : 24.08 % Favored : 71.94 % 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: -2.37 (0.18), residues: 2056 helix: -0.68 (0.19), residues: 830 sheet: -1.49 (0.32), residues: 290 loop : -2.41 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 216 HIS 0.003 0.001 HIS A 241 PHE 0.017 0.001 PHE G 13 TYR 0.018 0.001 TYR K 40 ARG 0.011 0.000 ARG A 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 269 time to evaluate : 1.566 Fit side-chains REVERT: A 72 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8062 (mt) REVERT: B 141 MET cc_start: 0.8324 (mmm) cc_final: 0.7847 (mmm) REVERT: B 222 LYS cc_start: 0.8367 (pttt) cc_final: 0.7519 (ptmm) REVERT: B 242 GLN cc_start: 0.7488 (tm-30) cc_final: 0.6810 (tm-30) REVERT: E 222 LYS cc_start: 0.8417 (pttt) cc_final: 0.7870 (ptpp) REVERT: D 38 ARG cc_start: 0.7373 (mtt180) cc_final: 0.6738 (mmt180) REVERT: D 134 MET cc_start: 0.8448 (tpt) cc_final: 0.8229 (mmm) REVERT: C 8 MET cc_start: 0.5236 (mmt) cc_final: 0.4502 (ptm) REVERT: G 76 LYS cc_start: 0.7056 (tttm) cc_final: 0.6538 (ptpp) REVERT: G 77 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7785 (p) REVERT: I 85 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6188 (mp0) REVERT: J 85 GLU cc_start: 0.7966 (tt0) cc_final: 0.7692 (tt0) REVERT: K 79 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7436 (pp) REVERT: K 151 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6460 (pp) outliers start: 67 outliers final: 54 residues processed: 318 average time/residue: 0.2717 time to fit residues: 128.0950 Evaluate side-chains 327 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 268 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.138638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.121733 restraints weight = 21624.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.118833 restraints weight = 25892.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.117548 restraints weight = 26541.024| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 16134 Z= 0.254 Angle : 0.793 59.195 21952 Z= 0.446 Chirality : 0.045 0.794 2652 Planarity : 0.005 0.133 2764 Dihedral : 6.250 68.939 2301 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 3.86 % Allowed : 24.32 % Favored : 71.82 % Cbeta Deviations : 0.05 % 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: -2.37 (0.18), residues: 2056 helix: -0.69 (0.19), residues: 830 sheet: -1.49 (0.32), residues: 290 loop : -2.41 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 216 HIS 0.003 0.001 HIS B 262 PHE 0.016 0.001 PHE G 13 TYR 0.018 0.001 TYR K 40 ARG 0.007 0.000 ARG I 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3231.40 seconds wall clock time: 59 minutes 3.72 seconds (3543.72 seconds total)