Starting phenix.real_space_refine (version: 1.21rc1) on Mon Aug 14 08:28:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy3_11548/08_2023/6zy3_11548_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy3_11548/08_2023/6zy3_11548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy3_11548/08_2023/6zy3_11548.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy3_11548/08_2023/6zy3_11548.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy3_11548/08_2023/6zy3_11548_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy3_11548/08_2023/6zy3_11548_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 71 5.16 5 C 10175 2.51 5 N 2639 2.21 5 O 2884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 7": "OE1" <-> "OE2" Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "I TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 85": "OE1" <-> "OE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 47": "OD1" <-> "OD2" Residue "J ASP 70": "OD1" <-> "OD2" Residue "J ASP 136": "OD1" <-> "OD2" Residue "J GLU 144": "OE1" <-> "OE2" Residue "K GLU 7": "OE1" <-> "OE2" Residue "K PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 47": "OD1" <-> "OD2" Residue "K ASP 70": "OD1" <-> "OD2" Residue "K GLU 85": "OE1" <-> "OE2" Residue "K GLU 109": "OE1" <-> "OE2" Residue "K GLU 119": "OE1" <-> "OE2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "L PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "L ASP 74": "OD1" <-> "OD2" Residue "L ASP 95": "OD1" <-> "OD2" Residue "L GLU 119": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B ASP 23": "OD1" <-> "OD2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B GLU 34": "OE1" <-> "OE2" Residue "B ASP 63": "OD1" <-> "OD2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B ASP 93": "OD1" <-> "OD2" Residue "C GLU 3": "OE1" <-> "OE2" Residue "C ASP 12": "OD1" <-> "OD2" Residue "C ASP 43": "OD1" <-> "OD2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "C ASP 63": "OD1" <-> "OD2" Residue "C ASP 93": "OD1" <-> "OD2" Residue "F ASP 10": "OD1" <-> "OD2" Residue "F ASP 99": "OD1" <-> "OD2" Residue "F GLU 112": "OE1" <-> "OE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F ASP 213": "OD1" <-> "OD2" Residue "F ASP 245": "OD1" <-> "OD2" Residue "F ARG 255": "NH1" <-> "NH2" Residue "G ASP 25": "OD1" <-> "OD2" Residue "G ARG 33": "NH1" <-> "NH2" Residue "G ASP 61": "OD1" <-> "OD2" Residue "G ASP 104": "OD1" <-> "OD2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 157": "NH1" <-> "NH2" Residue "G GLU 162": "OE1" <-> "OE2" Residue "G PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 176": "OD1" <-> "OD2" Residue "G ASP 220": "OD1" <-> "OD2" Residue "G ARG 255": "NH1" <-> "NH2" Residue "G TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 181": "OD1" <-> "OD2" Residue "E ARG 196": "NH1" <-> "NH2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "H ASP 198": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 15770 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1081 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1017 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 24 Chain: "J" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1093 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1111 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1078 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 2 Chain: "B" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 757 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "C" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 733 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1984 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 18, 'TRANS': 242} Chain: "G" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1989 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 18, 'TRANS': 243} Chain: "E" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1946 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "H" Number of atoms: 1993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1993 Unusual residues: {'PEE': 1} Classifications: {'peptide': 258, 'undetermined': 1} Link IDs: {'PTRANS': 7, 'TRANS': 250, None: 1} Not linked: pdbres="GLY H 259 " pdbres="PEE H 301 " Time building chain proxies: 8.31, per 1000 atoms: 0.53 Number of scatterers: 15770 At special positions: 0 Unit cell: (99.372, 125.736, 145.002, 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 71 16.00 P 1 15.00 O 2884 8.00 N 2639 7.00 C 10175 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: 5.68 Conformation dependent library (CDL) restraints added in 2.3 seconds 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3796 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 17 sheets defined 33.5% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 4 through 26 removed outlier: 3.635A pdb=" N ILE A 8 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP A 9 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 10 " --> pdb=" O ASN A 6 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 151 removed outlier: 3.517A pdb=" N GLY A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 9 removed outlier: 3.608A pdb=" N ILE D 8 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4 through 9' Processing helix chain 'D' and resid 11 through 26 removed outlier: 3.734A pdb=" N ALA D 17 " --> pdb=" O PHE D 13 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 151 removed outlier: 4.781A pdb=" N GLY D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 27 removed outlier: 3.894A pdb=" N VAL I 10 " --> pdb=" O ASN I 6 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N CYS I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU I 26 " --> pdb=" O LEU I 22 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS I 27 " --> pdb=" O PHE I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 151 removed outlier: 4.191A pdb=" N ILE I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY I 148 " --> pdb=" O GLU I 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 25 removed outlier: 3.703A pdb=" N TRP J 9 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL J 10 " --> pdb=" O ASN J 6 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 150 removed outlier: 3.897A pdb=" N ILE J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY J 148 " --> pdb=" O GLU J 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 19 Processing helix chain 'K' and resid 143 through 151 removed outlier: 3.680A pdb=" N GLY K 148 " --> pdb=" O GLU K 144 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE K 150 " --> pdb=" O LEU K 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 25 removed outlier: 3.748A pdb=" N ILE L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE L 13 " --> pdb=" O TRP L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 148 Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.624A pdb=" N GLU B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 26 through 30' Processing helix chain 'B' and resid 52 through 66 removed outlier: 3.537A pdb=" N ALA B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 88 removed outlier: 3.524A pdb=" N THR B 83 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS B 86 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 29 No H-bonds generated for 'chain 'C' and resid 26 through 29' Processing helix chain 'C' and resid 52 through 67 removed outlier: 3.632A pdb=" N ALA C 56 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C 67 " --> pdb=" O ASP C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 85 removed outlier: 3.600A pdb=" N LEU C 84 " --> pdb=" O LYS C 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 55 removed outlier: 3.828A pdb=" N ARG F 52 " --> pdb=" O THR F 48 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU F 53 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 48 through 55' Processing helix chain 'F' and resid 77 through 86 removed outlier: 3.510A pdb=" N TYR F 81 " --> pdb=" O ARG F 77 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR F 82 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS F 85 " --> pdb=" O TYR F 81 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'F' and resid 118 through 132 removed outlier: 3.505A pdb=" N HIS F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER F 123 " --> pdb=" O PRO F 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET F 126 " --> pdb=" O HIS F 122 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU F 130 " --> pdb=" O MET F 126 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA F 131 " --> pdb=" O MET F 127 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 158 removed outlier: 3.937A pdb=" N ARG F 151 " --> pdb=" O GLY F 147 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 192 removed outlier: 3.767A pdb=" N GLY F 181 " --> pdb=" O PRO F 177 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL F 182 " --> pdb=" O ILE F 178 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE F 187 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 243 No H-bonds generated for 'chain 'F' and resid 240 through 243' Processing helix chain 'G' and resid 50 through 55 removed outlier: 4.006A pdb=" N ILE G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 removed outlier: 4.011A pdb=" N LYS G 85 " --> pdb=" O TYR G 81 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG G 86 " --> pdb=" O THR G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 106 Processing helix chain 'G' and resid 109 through 112 No H-bonds generated for 'chain 'G' and resid 109 through 112' Processing helix chain 'G' and resid 118 through 132 removed outlier: 3.974A pdb=" N MET G 126 " --> pdb=" O HIS G 122 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N MET G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS G 128 " --> pdb=" O THR G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 158 removed outlier: 4.015A pdb=" N ARG G 151 " --> pdb=" O GLY G 147 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG G 152 " --> pdb=" O GLY G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 190 removed outlier: 3.602A pdb=" N VAL G 182 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL G 184 " --> pdb=" O MET G 180 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS G 185 " --> pdb=" O GLY G 181 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 208 No H-bonds generated for 'chain 'G' and resid 205 through 208' Processing helix chain 'G' and resid 238 through 241 No H-bonds generated for 'chain 'G' and resid 238 through 241' Processing helix chain 'G' and resid 261 through 264 No H-bonds generated for 'chain 'G' and resid 261 through 264' Processing helix chain 'E' and resid 2 through 30 removed outlier: 3.821A pdb=" N LEU E 6 " --> pdb=" O LEU E 2 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA E 7 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA E 30 " --> pdb=" O MET E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 removed outlier: 3.868A pdb=" N VAL E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG E 46 " --> pdb=" O PRO E 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 41 through 46' Processing helix chain 'E' and resid 57 through 73 removed outlier: 3.950A pdb=" N VAL E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER E 62 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL E 64 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE E 65 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 125 removed outlier: 3.702A pdb=" N GLY E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER E 114 " --> pdb=" O GLY E 110 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 120 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 133 Processing helix chain 'E' and resid 145 through 149 Processing helix chain 'E' and resid 151 through 170 removed outlier: 3.560A pdb=" N LEU E 155 " --> pdb=" O GLY E 151 " (cutoff:3.500A) Proline residue: E 156 - end of helix removed outlier: 3.897A pdb=" N VAL E 160 " --> pdb=" O PRO E 156 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 219 removed outlier: 4.045A pdb=" N ILE E 216 " --> pdb=" O THR E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 257 removed outlier: 4.163A pdb=" N SER E 232 " --> pdb=" O SER E 228 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL E 252 " --> pdb=" O GLY E 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 31 removed outlier: 3.601A pdb=" N ALA H 30 " --> pdb=" O MET H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 48 removed outlier: 3.770A pdb=" N VAL H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 72 removed outlier: 3.954A pdb=" N LEU H 57 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE H 58 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE H 59 " --> pdb=" O MET H 56 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL H 60 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N VAL H 61 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER H 62 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL H 64 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE H 66 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY H 67 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET H 68 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL H 69 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU H 70 " --> pdb=" O GLY H 67 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU H 72 " --> pdb=" O VAL H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 78 No H-bonds generated for 'chain 'H' and resid 76 through 78' Processing helix chain 'H' and resid 88 through 97 removed outlier: 3.911A pdb=" N LEU H 93 " --> pdb=" O MET H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 110 Processing helix chain 'H' and resid 112 through 125 removed outlier: 3.533A pdb=" N THR H 117 " --> pdb=" O GLY H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 134 Processing helix chain 'H' and resid 140 through 174 removed outlier: 3.544A pdb=" N ILE H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER H 145 " --> pdb=" O ARG H 141 " (cutoff:3.500A) Proline residue: H 146 - end of helix removed outlier: 3.969A pdb=" N LEU H 155 " --> pdb=" O GLY H 151 " (cutoff:3.500A) Proline residue: H 156 - end of helix removed outlier: 3.585A pdb=" N VAL H 160 " --> pdb=" O PRO H 156 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL H 173 " --> pdb=" O GLY H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 188 removed outlier: 3.665A pdb=" N SER H 187 " --> pdb=" O GLY H 183 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA H 188 " --> pdb=" O PHE H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 220 removed outlier: 3.599A pdb=" N SER H 206 " --> pdb=" O CYS H 202 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL H 207 " --> pdb=" O LEU H 203 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL H 208 " --> pdb=" O ILE H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 253 removed outlier: 3.898A pdb=" N VAL H 239 " --> pdb=" O THR H 235 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE H 251 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL H 252 " --> pdb=" O GLY H 248 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 71 through 73 Processing sheet with id= B, first strand: chain 'A' and resid 98 through 103 removed outlier: 3.681A pdb=" N SER A 98 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A 115 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 58 through 60 removed outlier: 3.613A pdb=" N GLY A 66 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 60 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 39 through 41 removed outlier: 3.825A pdb=" N ILE D 86 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 100 through 103 Processing sheet with id= F, first strand: chain 'I' and resid 43 through 45 Processing sheet with id= G, first strand: chain 'I' and resid 58 through 60 removed outlier: 3.846A pdb=" N GLY I 66 " --> pdb=" O VAL I 58 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE I 60 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL I 64 " --> pdb=" O ILE I 60 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 58 through 60 removed outlier: 9.296A pdb=" N SER J 59 " --> pdb=" O GLN J 110 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU J 112 " --> pdb=" O SER J 59 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'J' and resid 71 through 74 removed outlier: 3.653A pdb=" N LEU J 79 " --> pdb=" O ASP J 74 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 39 through 45 removed outlier: 3.715A pdb=" N ILE K 86 " --> pdb=" O TYR K 40 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU K 42 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA K 44 " --> pdb=" O VAL K 82 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 98 through 103 Processing sheet with id= L, first strand: chain 'K' and resid 58 through 60 removed outlier: 3.647A pdb=" N GLY K 66 " --> pdb=" O VAL K 58 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE K 60 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL K 64 " --> pdb=" O ILE K 60 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'L' and resid 84 through 86 removed outlier: 3.713A pdb=" N ARG L 67 " --> pdb=" O GLU L 85 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL L 63 " --> pdb=" O ILE L 60 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL L 58 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG L 67 " --> pdb=" O SER L 56 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER L 56 " --> pdb=" O ARG L 67 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 71 through 73 Processing sheet with id= O, first strand: chain 'L' and resid 98 through 103 Processing sheet with id= P, first strand: chain 'F' and resid 222 through 227 removed outlier: 7.169A pdb=" N ILE F 217 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N HIS F 226 " --> pdb=" O ALA F 215 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA F 215 " --> pdb=" O HIS F 226 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER F 202 " --> pdb=" O ILE F 39 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 222 through 225 removed outlier: 3.644A pdb=" N ALA G 219 " --> pdb=" O LYS G 222 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL G 224 " --> pdb=" O ILE G 217 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE G 217 " --> pdb=" O VAL G 224 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS G 214 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA G 38 " --> pdb=" O HIS G 214 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N CYS G 198 " --> pdb=" O THR G 37 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE G 39 " --> pdb=" O CYS G 198 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL G 200 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N GLY G 41 " --> pdb=" O VAL G 200 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1128 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: 3.91 Time building geometry restraints manager: 6.15 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: 4967 1.34 - 1.46: 2257 1.46 - 1.58: 8686 1.58 - 1.69: 2 1.69 - 1.81: 128 Bond restraints: 16040 Sorted by residual: bond pdb=" C30 PEE H 301 " pdb=" O3 PEE H 301 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C10 PEE H 301 " pdb=" O2 PEE H 301 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C TYR G 108 " pdb=" N PRO G 109 " ideal model delta sigma weight residual 1.336 1.384 -0.049 1.23e-02 6.61e+03 1.56e+01 bond pdb=" O4P PEE H 301 " pdb=" P PEE H 301 " ideal model delta sigma weight residual 1.653 1.610 0.043 2.00e-02 2.50e+03 4.61e+00 bond pdb=" C ILE G 72 " pdb=" N PRO G 73 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.54e+00 ... (remaining 16035 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.72: 448 106.72 - 113.55: 9092 113.55 - 120.39: 5852 120.39 - 127.22: 6229 127.22 - 134.05: 162 Bond angle restraints: 21783 Sorted by residual: angle pdb=" O3P PEE H 301 " pdb=" P PEE H 301 " pdb=" O4P PEE H 301 " ideal model delta sigma weight residual 92.91 109.45 -16.54 3.00e+00 1.11e-01 3.04e+01 angle pdb=" C VAL G 9 " pdb=" N ASP G 10 " pdb=" CA ASP G 10 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C ARG J 35 " pdb=" N THR J 36 " pdb=" CA THR J 36 " ideal model delta sigma weight residual 122.08 127.64 -5.56 1.47e+00 4.63e-01 1.43e+01 angle pdb=" C PRO F 171 " pdb=" N PHE F 172 " pdb=" CA PHE F 172 " ideal model delta sigma weight residual 122.46 127.66 -5.20 1.41e+00 5.03e-01 1.36e+01 angle pdb=" C GLU E 84 " pdb=" N THR E 85 " pdb=" CA THR E 85 " ideal model delta sigma weight residual 122.08 127.42 -5.34 1.47e+00 4.63e-01 1.32e+01 ... (remaining 21778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.36: 9162 24.36 - 48.72: 389 48.72 - 73.09: 20 73.09 - 97.45: 10 97.45 - 121.81: 3 Dihedral angle restraints: 9584 sinusoidal: 3684 harmonic: 5900 Sorted by residual: dihedral pdb=" CA TYR L 40 " pdb=" C TYR L 40 " pdb=" N THR L 41 " pdb=" CA THR L 41 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C21 PEE H 301 " pdb=" C22 PEE H 301 " pdb=" C23 PEE H 301 " pdb=" C24 PEE H 301 " ideal model delta sinusoidal sigma weight residual 180.10 58.29 121.81 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C23 PEE H 301 " pdb=" C24 PEE H 301 " pdb=" C25 PEE H 301 " pdb=" C26 PEE H 301 " ideal model delta sinusoidal sigma weight residual -179.89 -61.68 -118.21 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 9581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2112 0.052 - 0.104: 432 0.104 - 0.157: 96 0.157 - 0.209: 7 0.209 - 0.261: 2 Chirality restraints: 2649 Sorted by residual: chirality pdb=" C2 PEE H 301 " pdb=" C1 PEE H 301 " pdb=" C3 PEE H 301 " pdb=" O2 PEE H 301 " both_signs ideal model delta sigma weight residual False -2.33 -2.59 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB THR I 96 " pdb=" CA THR I 96 " pdb=" OG1 THR I 96 " pdb=" CG2 THR I 96 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE D 60 " pdb=" CA ILE D 60 " pdb=" CG1 ILE D 60 " pdb=" CG2 ILE D 60 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 9.98e-01 ... (remaining 2646 not shown) Planarity restraints: 2718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 26 " -0.038 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO B 27 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 27 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 27 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 155 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO E 156 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 156 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 156 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 155 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO H 156 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 156 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 156 " 0.026 5.00e-02 4.00e+02 ... (remaining 2715 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 5059 2.85 - 3.36: 13075 3.36 - 3.87: 24638 3.87 - 4.39: 27479 4.39 - 4.90: 48112 Nonbonded interactions: 118363 Sorted by model distance: nonbonded pdb=" O SER H 82 " pdb=" OG SER H 82 " model vdw 2.332 2.440 nonbonded pdb=" O LEU F 110 " pdb=" OG1 THR F 114 " model vdw 2.339 2.440 nonbonded pdb=" OH TYR K 40 " pdb=" O TYR K 90 " model vdw 2.340 2.440 nonbonded pdb=" O ILE H 231 " pdb=" OG1 THR H 235 " model vdw 2.342 2.440 nonbonded pdb=" O ALA E 83 " pdb=" OG SER E 86 " model vdw 2.345 2.440 ... (remaining 118358 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 29 or resid 38 through 89 or (resid 90 and (name \ N or name CA or name C or name O or name CB )) or resid 91 through 94 or (resid \ 95 through 96 and (name N or name CA or name C or name O or name CB )) or resid \ 97 through 108 or (resid 109 and (name N or name CA or name C or name O or name \ CB )) or resid 110 through 113 or resid 128 or (resid 129 and (name N or name C \ A or name C or name O or name CB )) or resid 130 through 131 or (resid 132 and ( \ name N or name CA or name C or name O or name CB )) or resid 133 through 135 or \ (resid 136 and (name N or name CA or name C or name O or name CB )) or resid 137 \ through 140 or (resid 141 and (name N or name CA or name C or name O or name CB \ )) or resid 142 through 144 or (resid 145 and (name N or name CA or name C or n \ ame O or name CB )) or resid 146 through 148 or (resid 149 and (name N or name C \ A or name C or name O or name CB )) or resid 150 through 152)) selection = (chain 'D' and (resid 3 through 26 or (resid 27 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 38 through 52 or (resid 53 through \ 55 and (name N or name CA or name C or name O or name CB )) or resid 56 through \ 89 or (resid 90 and (name N or name CA or name C or name O or name CB )) or resi \ d 91 or (resid 92 and (name N or name CA or name C or name O or name CB )) or re \ sid 93 through 94 or (resid 95 through 96 and (name N or name CA or name C or na \ me O or name CB )) or resid 97 through 108 or (resid 109 and (name N or name CA \ or name C or name O or name CB )) or resid 110 through 113 or resid 128 through \ 144 or (resid 145 and (name N or name CA or name C or name O or name CB )) or re \ sid 146 through 148 or (resid 149 and (name N or name CA or name C or name O or \ name CB )) or resid 150 through 152)) selection = (chain 'I' and (resid 3 through 26 or (resid 27 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 38 through 52 or (resid 53 through \ 55 and (name N or name CA or name C or name O or name CB )) or resid 56 through \ 91 or (resid 92 and (name N or name CA or name C or name O or name CB )) or resi \ d 93 through 95 or (resid 96 and (name N or name CA or name C or name O or name \ CB )) or resid 97 through 113 or resid 128 or (resid 129 and (name N or name CA \ or name C or name O or name CB )) or resid 130 through 131 or (resid 132 and (na \ me N or name CA or name C or name O or name CB )) or resid 133 through 140 or (r \ esid 141 and (name N or name CA or name C or name O or name CB )) or resid 142 t \ hrough 152)) selection = (chain 'J' and (resid 3 through 26 or (resid 27 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 38 through 52 or (resid 53 through \ 55 and (name N or name CA or name C or name O or name CB )) or resid 56 through \ 89 or (resid 90 and (name N or name CA or name C or name O or name CB )) or resi \ d 91 or (resid 92 and (name N or name CA or name C or name O or name CB )) or re \ sid 93 through 113 or resid 128 through 131 or (resid 132 and (name N or name CA \ or name C or name O or name CB )) or resid 133 through 135 or (resid 136 and (n \ ame N or name CA or name C or name O or name CB )) or resid 137 through 140 or ( \ resid 141 and (name N or name CA or name C or name O or name CB )) or resid 142 \ through 144 or (resid 145 and (name N or name CA or name C or name O or name CB \ )) or resid 146 through 148 or (resid 149 and (name N or name CA or name C or na \ me O or name CB )) or resid 150 through 152)) selection = (chain 'K' and (resid 3 through 29 or resid 38 through 52 or (resid 53 through 5 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 56 through 8 \ 9 or (resid 90 and (name N or name CA or name C or name O or name CB )) or resid \ 91 or (resid 92 and (name N or name CA or name C or name O or name CB )) or res \ id 93 through 94 or (resid 95 through 96 and (name N or name CA or name C or nam \ e O or name CB )) or resid 97 through 108 or (resid 109 and (name N or name CA o \ r name C or name O or name CB )) or resid 110 through 113 or resid 128 or (resid \ 129 and (name N or name CA or name C or name O or name CB )) or resid 130 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 through 135 or (resid 136 and (name N or name CA or name C or name O \ or name CB )) or resid 137 through 140 or (resid 141 and (name N or name CA or n \ ame C or name O or name CB )) or resid 142 through 144 or (resid 145 and (name N \ or name CA or name C or name O or name CB )) or resid 146 through 148 or (resid \ 149 and (name N or name CA or name C or name O or name CB )) or resid 150 throu \ gh 152)) selection = (chain 'L' and (resid 3 through 26 or (resid 27 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 38 through 52 or (resid 53 through \ 55 and (name N or name CA or name C or name O or name CB )) or resid 56 through \ 89 or (resid 90 and (name N or name CA or name C or name O or name CB )) or resi \ d 91 or (resid 92 and (name N or name CA or name C or name O or name CB )) or re \ sid 93 through 94 or (resid 95 through 96 and (name N or name CA or name C or na \ me O or name CB )) or resid 97 through 108 or (resid 109 and (name N or name CA \ or name C or name O or name CB )) or resid 110 through 113 or resid 128 or (resi \ d 129 and (name N or name CA or name C or name O or name CB )) or resid 130 thro \ ugh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) o \ r resid 133 through 135 or (resid 136 and (name N or name CA or name C or name O \ or name CB )) or resid 137 through 140 or (resid 141 and (name N or name CA or \ name C or name O or name CB )) or resid 142 through 144 or (resid 145 and (name \ N or name CA or name C or name O or name CB )) or resid 146 through 148 or (resi \ d 149 and (name N or name CA or name C or name O or name CB )) or resid 150 thro \ ugh 152)) } ncs_group { reference = (chain 'B' and resid 3 through 97) selection = chain 'C' } ncs_group { reference = (chain 'E' and resid 2 through 258) selection = (chain 'H' and resid 2 through 258) } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 7 through 267) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.010 Extract box with map and model: 5.020 Check model and map are aligned: 0.220 Set scattering table: 0.160 Process input model: 39.750 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 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 : 0.003 0.128 16040 Z= 0.207 Angle : 0.702 16.538 21783 Z= 0.369 Chirality : 0.045 0.261 2649 Planarity : 0.005 0.056 2718 Dihedral : 12.966 121.812 5788 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 0.18 % 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: -5.92 (0.12), residues: 2027 helix: -4.99 (0.04), residues: 727 sheet: -2.45 (0.33), residues: 206 loop : -3.52 (0.14), residues: 1094 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 386 time to evaluate : 1.859 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 389 average time/residue: 0.3170 time to fit residues: 174.0204 Evaluate side-chains 279 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.824 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 48 ASN K 135 GLN L 48 ASN L 88 GLN L 91 ASN B 70 ASN F 57 GLN F 262 HIS G 175 GLN E 47 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 16040 Z= 0.215 Angle : 0.558 11.556 21783 Z= 0.272 Chirality : 0.041 0.167 2649 Planarity : 0.004 0.039 2718 Dihedral : 5.701 87.859 2238 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 2.30 % 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: -4.15 (0.14), residues: 2027 helix: -2.77 (0.14), residues: 729 sheet: -2.01 (0.34), residues: 208 loop : -2.96 (0.15), residues: 1090 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 297 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 27 residues processed: 318 average time/residue: 0.2875 time to fit residues: 132.5277 Evaluate side-chains 289 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 262 time to evaluate : 1.847 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1387 time to fit residues: 9.5016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 147 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 16040 Z= 0.259 Angle : 0.580 12.758 21783 Z= 0.285 Chirality : 0.042 0.172 2649 Planarity : 0.004 0.041 2718 Dihedral : 5.675 85.380 2238 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 2.13 % 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: -3.05 (0.17), residues: 2027 helix: -1.35 (0.17), residues: 758 sheet: -1.85 (0.35), residues: 221 loop : -2.62 (0.16), residues: 1048 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 284 time to evaluate : 1.864 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 24 residues processed: 304 average time/residue: 0.2976 time to fit residues: 130.5777 Evaluate side-chains 293 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 269 time to evaluate : 1.867 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1465 time to fit residues: 9.3061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 184 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 262 HIS H 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 16040 Z= 0.230 Angle : 0.558 14.687 21783 Z= 0.271 Chirality : 0.041 0.169 2649 Planarity : 0.003 0.039 2718 Dihedral : 5.687 86.088 2238 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 2.01 % 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: -2.44 (0.18), residues: 2027 helix: -0.70 (0.19), residues: 776 sheet: -1.70 (0.35), residues: 227 loop : -2.37 (0.18), residues: 1024 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 282 time to evaluate : 1.766 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 302 average time/residue: 0.2783 time to fit residues: 123.1040 Evaluate side-chains 284 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 265 time to evaluate : 1.825 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1460 time to fit residues: 7.5464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 48 ASN F 262 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 16040 Z= 0.196 Angle : 0.525 12.957 21783 Z= 0.257 Chirality : 0.041 0.176 2649 Planarity : 0.003 0.038 2718 Dihedral : 5.499 85.151 2238 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 1.54 % 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: -2.00 (0.18), residues: 2027 helix: -0.20 (0.20), residues: 768 sheet: -1.49 (0.36), residues: 225 loop : -2.22 (0.18), residues: 1034 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 276 time to evaluate : 1.687 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 19 residues processed: 291 average time/residue: 0.2871 time to fit residues: 121.2427 Evaluate side-chains 285 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 266 time to evaluate : 1.785 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1425 time to fit residues: 7.4233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 102 optimal weight: 0.0980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 262 HIS ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 16040 Z= 0.203 Angle : 0.532 11.548 21783 Z= 0.260 Chirality : 0.041 0.184 2649 Planarity : 0.003 0.035 2718 Dihedral : 5.573 86.965 2238 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.19), residues: 2027 helix: 0.05 (0.20), residues: 774 sheet: -1.20 (0.37), residues: 207 loop : -2.11 (0.18), residues: 1046 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 271 time to evaluate : 1.856 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 282 average time/residue: 0.2962 time to fit residues: 120.5918 Evaluate side-chains 271 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 262 time to evaluate : 1.817 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1477 time to fit residues: 4.9604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 0.6980 chunk 22 optimal weight: 0.0670 chunk 111 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 164 optimal weight: 0.0040 chunk 109 optimal weight: 0.5980 chunk 194 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 overall best weight: 0.4130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 262 HIS G 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 16040 Z= 0.125 Angle : 0.493 10.588 21783 Z= 0.241 Chirality : 0.039 0.184 2649 Planarity : 0.003 0.034 2718 Dihedral : 5.322 88.412 2238 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.19), residues: 2027 helix: 0.43 (0.20), residues: 772 sheet: -1.08 (0.38), residues: 205 loop : -2.03 (0.18), residues: 1050 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 268 time to evaluate : 1.773 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 280 average time/residue: 0.3049 time to fit residues: 126.7084 Evaluate side-chains 268 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 261 time to evaluate : 1.895 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1460 time to fit residues: 4.5476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 0.0870 chunk 77 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 96 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 262 HIS H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 16040 Z= 0.195 Angle : 0.527 10.406 21783 Z= 0.258 Chirality : 0.041 0.172 2649 Planarity : 0.003 0.033 2718 Dihedral : 5.552 86.924 2238 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.19), residues: 2027 helix: 0.50 (0.20), residues: 776 sheet: -1.08 (0.37), residues: 213 loop : -1.92 (0.19), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 261 time to evaluate : 1.825 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 270 average time/residue: 0.3037 time to fit residues: 118.1575 Evaluate side-chains 262 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 256 time to evaluate : 1.779 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1398 time to fit residues: 4.0383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 0.2980 chunk 186 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 142 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 262 HIS H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 16040 Z= 0.166 Angle : 0.509 9.980 21783 Z= 0.249 Chirality : 0.040 0.154 2649 Planarity : 0.003 0.070 2718 Dihedral : 5.504 89.243 2238 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 0.59 % 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: -1.18 (0.19), residues: 2027 helix: 0.58 (0.20), residues: 779 sheet: -1.21 (0.36), residues: 228 loop : -1.81 (0.19), residues: 1020 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 265 time to evaluate : 1.615 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 270 average time/residue: 0.3154 time to fit residues: 125.8636 Evaluate side-chains 268 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 262 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2186 time to fit residues: 4.6526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 185 optimal weight: 0.0970 chunk 160 optimal weight: 0.0470 chunk 16 optimal weight: 9.9990 chunk 123 optimal weight: 0.1980 chunk 98 optimal weight: 0.6980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 HIS H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 16040 Z= 0.124 Angle : 0.495 9.613 21783 Z= 0.241 Chirality : 0.039 0.146 2649 Planarity : 0.003 0.060 2718 Dihedral : 5.291 89.459 2238 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 0.24 % 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: -0.99 (0.19), residues: 2027 helix: 0.83 (0.20), residues: 774 sheet: -1.08 (0.37), residues: 218 loop : -1.77 (0.19), residues: 1035 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 264 time to evaluate : 1.975 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 266 average time/residue: 0.2867 time to fit residues: 111.8017 Evaluate side-chains 264 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 262 time to evaluate : 2.121 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1372 time to fit residues: 3.2492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 147 optimal weight: 0.0970 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 0.0170 chunk 67 optimal weight: 0.0980 chunk 164 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 0.3980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 HIS H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.189709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.147098 restraints weight = 18728.589| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.59 r_work: 0.3081 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 16040 Z= 0.119 Angle : 0.486 9.478 21783 Z= 0.236 Chirality : 0.039 0.136 2649 Planarity : 0.003 0.054 2718 Dihedral : 5.128 88.534 2238 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 0.18 % 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: -0.86 (0.20), residues: 2027 helix: 1.02 (0.20), residues: 775 sheet: -0.97 (0.38), residues: 209 loop : -1.78 (0.19), residues: 1043 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3500.22 seconds wall clock time: 63 minutes 51.04 seconds (3831.04 seconds total)