Starting phenix.real_space_refine (version: dev) on Tue Feb 21 13:28:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy4_11549/02_2023/6zy4_11549_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy4_11549/02_2023/6zy4_11549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy4_11549/02_2023/6zy4_11549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy4_11549/02_2023/6zy4_11549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy4_11549/02_2023/6zy4_11549_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy4_11549/02_2023/6zy4_11549_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Process input model Symmetric amino acids flipped Residue "A ASP 70": "OD1" <-> "OD2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 144": "OE1" <-> "OE2" Residue "I PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 130": "OD1" <-> "OD2" Residue "K TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 93": "OD1" <-> "OD2" Residue "F ASP 10": "OD1" <-> "OD2" Residue "F ARG 33": "NH1" <-> "NH2" Residue "F PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 99": "OD1" <-> "OD2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F ASP 164": "OD1" <-> "OD2" Residue "F PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 207": "OE1" <-> "OE2" Residue "F ASP 220": "OD1" <-> "OD2" Residue "F ARG 255": "NH1" <-> "NH2" Residue "G ASP 10": "OD1" <-> "OD2" Residue "G ARG 33": "NH1" <-> "NH2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 104": "OD1" <-> "OD2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 157": "NH1" <-> "NH2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G GLU 170": "OE1" <-> "OE2" Residue "G GLU 189": "OE1" <-> "OE2" Residue "G ASP 220": "OD1" <-> "OD2" Residue "G PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 255": "NH1" <-> "NH2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E ASP 181": "OD1" <-> "OD2" Residue "E ARG 196": "NH1" <-> "NH2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "H ASP 181": "OD1" <-> "OD2" Residue "H ARG 196": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14902 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1013 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 793 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 999 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "J" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 999 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "K" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 794 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "L" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 941 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain breaks: 2 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 724 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 734 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1982 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 243} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1972 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 243} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1946 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 251} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1949 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 7, 'TRANS': 251} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.33, per 1000 atoms: 0.56 Number of scatterers: 14902 At special positions: 0 Unit cell: (99.372, 126.75, 145.002, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 69 16.00 P 4 15.00 Mg 2 11.99 O 2726 8.00 N 2504 7.00 C 9597 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: 5.84 Conformation dependent library (CDL) restraints added in 2.4 seconds 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3610 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 16 sheets defined 29.4% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 5 through 25 removed outlier: 3.621A pdb=" N LEU A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 151 removed outlier: 3.653A pdb=" N ILE A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 151 removed outlier: 3.737A pdb=" N ILE D 147 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 23 removed outlier: 3.865A pdb=" N VAL I 10 " --> pdb=" O ASN I 6 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY I 11 " --> pdb=" O GLU I 7 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE I 13 " --> pdb=" O TRP I 9 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA I 21 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 150 removed outlier: 3.508A pdb=" N ILE I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY I 148 " --> pdb=" O GLU I 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 22 removed outlier: 3.525A pdb=" N TRP J 9 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE J 12 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU J 15 " --> pdb=" O GLY J 11 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA J 16 " --> pdb=" O ILE J 12 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 151 Processing helix chain 'K' and resid 143 through 151 removed outlier: 3.513A pdb=" N ILE K 147 " --> pdb=" O LEU K 143 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY K 148 " --> pdb=" O GLU K 144 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN K 149 " --> pdb=" O ASP K 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 23 removed outlier: 3.738A pdb=" N PHE L 13 " --> pdb=" O TRP L 9 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA L 20 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA L 21 " --> pdb=" O ALA L 17 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU L 22 " --> pdb=" O LEU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 151 removed outlier: 3.689A pdb=" N LEU L 151 " --> pdb=" O ILE L 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 80 through 87 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 56 through 59 No H-bonds generated for 'chain 'C' and resid 56 through 59' Processing helix chain 'C' and resid 80 through 83 No H-bonds generated for 'chain 'C' and resid 80 through 83' Processing helix chain 'F' and resid 51 through 55 Processing helix chain 'F' and resid 77 through 86 removed outlier: 3.926A pdb=" N THR F 82 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL F 83 " --> pdb=" O ARG F 79 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS F 85 " --> pdb=" O TYR F 81 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ARG F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.636A pdb=" N VAL F 106 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA F 107 " --> pdb=" O PHE F 103 " (cutoff:3.500A) Proline residue: F 109 - end of helix removed outlier: 4.125A pdb=" N GLU F 112 " --> pdb=" O TYR F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 125 removed outlier: 3.506A pdb=" N HIS F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER F 123 " --> pdb=" O PRO F 119 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 149 through 156 Processing helix chain 'F' and resid 177 through 193 removed outlier: 4.348A pdb=" N GLY F 181 " --> pdb=" O PRO F 177 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL F 182 " --> pdb=" O ILE F 178 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL F 184 " --> pdb=" O MET F 180 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS F 185 " --> pdb=" O GLY F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 210 removed outlier: 4.027A pdb=" N LEU F 209 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER F 210 " --> pdb=" O PRO F 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 205 through 210' Processing helix chain 'F' and resid 241 through 244 No H-bonds generated for 'chain 'F' and resid 241 through 244' Processing helix chain 'G' and resid 48 through 55 Processing helix chain 'G' and resid 78 through 84 removed outlier: 3.728A pdb=" N THR G 82 " --> pdb=" O SER G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 106 removed outlier: 3.750A pdb=" N VAL G 106 " --> pdb=" O VAL G 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 102 through 106' Processing helix chain 'G' and resid 118 through 125 removed outlier: 3.507A pdb=" N HIS G 122 " --> pdb=" O ALA G 118 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER G 123 " --> pdb=" O PRO G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 132 removed outlier: 3.843A pdb=" N VAL G 132 " --> pdb=" O LEU G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 156 Processing helix chain 'G' and resid 177 through 180 No H-bonds generated for 'chain 'G' and resid 177 through 180' Processing helix chain 'G' and resid 183 through 191 removed outlier: 3.857A pdb=" N ILE G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER G 188 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 244 No H-bonds generated for 'chain 'G' and resid 241 through 244' Processing helix chain 'E' and resid 7 through 10 No H-bonds generated for 'chain 'E' and resid 7 through 10' Processing helix chain 'E' and resid 12 through 28 removed outlier: 3.552A pdb=" N THR E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU E 17 " --> pdb=" O GLY E 13 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR E 19 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE E 20 " --> pdb=" O THR E 16 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY E 24 " --> pdb=" O PHE E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 47 No H-bonds generated for 'chain 'E' and resid 44 through 47' Processing helix chain 'E' and resid 59 through 73 removed outlier: 4.973A pdb=" N VAL E 64 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE E 65 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 69 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E 70 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU E 72 " --> pdb=" O MET E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 90 removed outlier: 3.660A pdb=" N LEU E 87 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLY E 88 " --> pdb=" O THR E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 No H-bonds generated for 'chain 'E' and resid 93 through 96' Processing helix chain 'E' and resid 100 through 111 removed outlier: 3.869A pdb=" N ALA E 105 " --> pdb=" O PRO E 101 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 125 removed outlier: 3.540A pdb=" N THR E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE E 120 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 135 removed outlier: 3.801A pdb=" N MET E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 145 through 149 Processing helix chain 'E' and resid 151 through 174 removed outlier: 3.673A pdb=" N LEU E 155 " --> pdb=" O GLY E 151 " (cutoff:3.500A) Proline residue: E 156 - end of helix removed outlier: 3.668A pdb=" N VAL E 160 " --> pdb=" O PRO E 156 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA E 164 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL E 165 " --> pdb=" O ILE E 161 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY E 166 " --> pdb=" O PHE E 162 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL E 173 " --> pdb=" O GLY E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 191 removed outlier: 3.971A pdb=" N MET E 189 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN E 190 " --> pdb=" O TRP E 186 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN E 191 " --> pdb=" O SER E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 204 No H-bonds generated for 'chain 'E' and resid 201 through 204' Processing helix chain 'E' and resid 206 through 222 removed outlier: 3.778A pdb=" N THR E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE E 216 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 246 removed outlier: 3.675A pdb=" N THR E 235 " --> pdb=" O ILE E 231 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 240 " --> pdb=" O THR E 236 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER E 242 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 244 " --> pdb=" O VAL E 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 10 No H-bonds generated for 'chain 'H' and resid 7 through 10' Processing helix chain 'H' and resid 12 through 28 removed outlier: 3.648A pdb=" N THR H 19 " --> pdb=" O LYS H 15 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE H 20 " --> pdb=" O THR H 16 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY H 21 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY H 24 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU H 27 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 47 No H-bonds generated for 'chain 'H' and resid 44 through 47' Processing helix chain 'H' and resid 64 through 72 removed outlier: 4.289A pdb=" N VAL H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU H 70 " --> pdb=" O ILE H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 91 removed outlier: 3.836A pdb=" N LEU H 87 " --> pdb=" O GLU H 84 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLY H 88 " --> pdb=" O THR H 85 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL H 91 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 111 removed outlier: 3.667A pdb=" N ALA H 104 " --> pdb=" O GLY H 100 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ALA H 105 " --> pdb=" O PRO H 101 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU H 106 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG H 111 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 125 removed outlier: 3.689A pdb=" N ALA H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 133 removed outlier: 3.866A pdb=" N GLU H 133 " --> pdb=" O LEU H 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 129 through 133' Processing helix chain 'H' and resid 145 through 152 Processing helix chain 'H' and resid 159 through 174 removed outlier: 3.742A pdb=" N ALA H 164 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY H 166 " --> pdb=" O PHE H 162 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE H 167 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL H 173 " --> pdb=" O GLY H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 188 Processing helix chain 'H' and resid 199 through 205 removed outlier: 3.573A pdb=" N LEU H 203 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE H 204 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 220 removed outlier: 3.820A pdb=" N THR H 212 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE H 216 " --> pdb=" O THR H 212 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE H 219 " --> pdb=" O TRP H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 246 removed outlier: 4.389A pdb=" N VAL H 239 " --> pdb=" O THR H 235 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL H 240 " --> pdb=" O THR H 236 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER H 242 " --> pdb=" O THR H 238 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU H 244 " --> pdb=" O VAL H 240 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA H 245 " --> pdb=" O HIS H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 254 Processing sheet with id= A, first strand: chain 'A' and resid 41 through 45 removed outlier: 3.729A pdb=" N ASP A 70 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU A 85 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N VAL A 68 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 99 through 103 removed outlier: 4.043A pdb=" N GLY A 66 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE A 60 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 81 through 87 removed outlier: 6.544A pdb=" N ASP D 132 " --> pdb=" O TYR D 43 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N THR D 45 " --> pdb=" O ASP D 132 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE D 134 " --> pdb=" O THR D 45 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 98 through 103 removed outlier: 3.860A pdb=" N SER D 100 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA D 113 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 57 through 60 removed outlier: 3.719A pdb=" N GLY D 66 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE D 60 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'I' and resid 98 through 103 Processing sheet with id= G, first strand: chain 'I' and resid 66 through 73 removed outlier: 3.577A pdb=" N ARG I 67 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR I 83 " --> pdb=" O ALA I 69 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE I 71 " --> pdb=" O ARG I 81 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ARG I 81 " --> pdb=" O ILE I 71 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 39 through 42 removed outlier: 3.511A pdb=" N LEU J 42 " --> pdb=" O LEU J 84 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU J 84 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR J 83 " --> pdb=" O ASP J 70 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP J 70 " --> pdb=" O THR J 83 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLU J 85 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL J 68 " --> pdb=" O GLU J 85 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLU J 87 " --> pdb=" O GLY J 66 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLY J 66 " --> pdb=" O GLU J 87 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL J 58 " --> pdb=" O VAL J 65 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N SER J 59 " --> pdb=" O GLN J 110 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU J 112 " --> pdb=" O SER J 59 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 71 through 73 Processing sheet with id= J, first strand: chain 'K' and resid 98 through 103 removed outlier: 3.562A pdb=" N SER K 100 " --> pdb=" O ALA K 113 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 40 through 45 removed outlier: 3.601A pdb=" N LEU L 84 " --> pdb=" O LEU L 42 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 98 through 103 Processing sheet with id= M, first strand: chain 'L' and resid 57 through 59 removed outlier: 3.865A pdb=" N GLY L 66 " --> pdb=" O VAL L 58 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 28 through 30 removed outlier: 3.579A pdb=" N GLU F 64 " --> pdb=" O ARG F 12 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 214 through 216 removed outlier: 3.655A pdb=" N HIS F 214 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS F 198 " --> pdb=" O THR F 37 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE F 39 " --> pdb=" O CYS F 198 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL F 200 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE F 166 " --> pdb=" O THR F 197 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 214 through 216 removed outlier: 3.621A pdb=" N HIS G 214 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS G 198 " --> pdb=" O THR G 37 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE G 39 " --> pdb=" O CYS G 198 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL G 200 " --> pdb=" O ILE G 39 " (cutoff:3.500A) 274 hydrogen bonds defined for protein. 774 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: 3.66 Time building geometry restraints manager: 6.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4759 1.34 - 1.46: 2897 1.46 - 1.58: 7373 1.58 - 1.69: 6 1.69 - 1.81: 126 Bond restraints: 15161 Sorted by residual: bond pdb=" C TYR F 108 " pdb=" N PRO F 109 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.50e+00 bond pdb=" C GLU K 37 " pdb=" N PRO K 38 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.94e+00 bond pdb=" CA THR J 39 " pdb=" C THR J 39 " ideal model delta sigma weight residual 1.522 1.540 -0.018 1.08e-02 8.57e+03 2.71e+00 bond pdb=" CA GLY B 11 " pdb=" C GLY B 11 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.34e+00 bond pdb=" N PHE G 172 " pdb=" CA PHE G 172 " ideal model delta sigma weight residual 1.460 1.482 -0.022 1.54e-02 4.22e+03 2.05e+00 ... (remaining 15156 not shown) Histogram of bond angle deviations from ideal: 100.21 - 107.65: 557 107.65 - 115.08: 9296 115.08 - 122.52: 8805 122.52 - 129.95: 1875 129.95 - 137.39: 96 Bond angle restraints: 20629 Sorted by residual: angle pdb=" CA LEU F 265 " pdb=" CB LEU F 265 " pdb=" CG LEU F 265 " ideal model delta sigma weight residual 116.30 131.91 -15.61 3.50e+00 8.16e-02 1.99e+01 angle pdb=" N VAL F 205 " pdb=" CA VAL F 205 " pdb=" C VAL F 205 " ideal model delta sigma weight residual 108.88 118.36 -9.48 2.16e+00 2.14e-01 1.93e+01 angle pdb=" CA LEU G 265 " pdb=" CB LEU G 265 " pdb=" CG LEU G 265 " ideal model delta sigma weight residual 116.30 130.73 -14.43 3.50e+00 8.16e-02 1.70e+01 angle pdb=" C ASP G 220 " pdb=" N LYS G 221 " pdb=" CA LYS G 221 " ideal model delta sigma weight residual 121.54 129.39 -7.85 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C ALA F 107 " pdb=" N TYR F 108 " pdb=" CA TYR F 108 " ideal model delta sigma weight residual 120.58 125.62 -5.04 1.32e+00 5.74e-01 1.46e+01 ... (remaining 20624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.94: 8788 31.94 - 63.88: 205 63.88 - 95.83: 8 95.83 - 127.77: 2 127.77 - 159.71: 4 Dihedral angle restraints: 9007 sinusoidal: 3385 harmonic: 5622 Sorted by residual: dihedral pdb=" C5' ADP G 301 " pdb=" O5' ADP G 301 " pdb=" PA ADP G 301 " pdb=" O2A ADP G 301 " ideal model delta sinusoidal sigma weight residual -60.00 99.71 -159.71 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C5' ADP F 301 " pdb=" O5' ADP F 301 " pdb=" PA ADP F 301 " pdb=" O2A ADP F 301 " ideal model delta sinusoidal sigma weight residual -60.00 99.68 -159.68 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O2A ADP G 301 " pdb=" O3A ADP G 301 " pdb=" PA ADP G 301 " pdb=" PB ADP G 301 " ideal model delta sinusoidal sigma weight residual -60.00 74.69 -134.69 1 2.00e+01 2.50e-03 4.09e+01 ... (remaining 9004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1945 0.051 - 0.101: 434 0.101 - 0.152: 115 0.152 - 0.202: 25 0.202 - 0.253: 2 Chirality restraints: 2521 Sorted by residual: chirality pdb=" CB ILE A 60 " pdb=" CA ILE A 60 " pdb=" CG1 ILE A 60 " pdb=" CG2 ILE A 60 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE A 93 " pdb=" CA ILE A 93 " pdb=" CG1 ILE A 93 " pdb=" CG2 ILE A 93 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE G 65 " pdb=" CA ILE G 65 " pdb=" CG1 ILE G 65 " pdb=" CG2 ILE G 65 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2518 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 145 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO E 146 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 146 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 146 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 205 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO G 206 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO G 206 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 206 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 145 " -0.036 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO H 146 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO H 146 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 146 " -0.030 5.00e-02 4.00e+02 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4654 2.83 - 3.35: 12002 3.35 - 3.87: 23653 3.87 - 4.38: 25783 4.38 - 4.90: 43761 Nonbonded interactions: 109853 Sorted by model distance: nonbonded pdb=" OG1 THR I 39 " pdb=" O ILE I 86 " model vdw 2.314 2.440 nonbonded pdb=" O ASN B 89 " pdb=" OH TYR G 261 " model vdw 2.322 2.440 nonbonded pdb=" O LEU H 90 " pdb=" OG SER H 94 " model vdw 2.323 2.440 nonbonded pdb=" O ILE H 58 " pdb=" OG SER H 62 " model vdw 2.331 2.440 nonbonded pdb=" O ILE E 58 " pdb=" OG SER E 62 " model vdw 2.333 2.440 ... (remaining 109848 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 25 or resid 40 through 69 or (resid 70 through 7 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 73 or (resid \ 74 and (name N or name CA or name C or name O or name CB )) or resid 75 or (res \ id 76 and (name N or name CA or name C or name O or name CB )) or resid 77 throu \ gh 84 or (resid 85 and (name N or name CA or name C or name O or name CB )) or r \ esid 86 or (resid 87 through 88 and (name N or name CA or name C or name O or na \ me CB )) or resid 89 through 90 or (resid 91 through 92 and (name N or name CA o \ r name C or name O or name CB )) or resid 93 through 94 or (resid 95 and (name N \ or name CA or name C or name O or name CB )) or resid 96 through 108 or (resid \ 109 and (name N or name CA or name C or name O or name CB )) or resid 110 throug \ h 116 or (resid 130 and (name N or name CA or name C or name O or name CB )) or \ resid 131 through 140 or (resid 141 and (name N or name CA or name C or name O o \ r name CB )) or resid 142 through 143 or (resid 144 through 145 and (name N or n \ ame CA or name C or name O or name CB )) or resid 146 through 152)) selection = (chain 'I' and (resid 3 through 25 or resid 40 through 66 or (resid 67 and (name \ N or name CA or name C or name O or name CB )) or resid 68 through 71 or (resid \ 72 and (name N or name CA or name C or name O or name CB )) or resid 73 or (res \ id 74 and (name N or name CA or name C or name O or name CB )) or resid 75 or (r \ esid 76 and (name N or name CA or name C or name O or name CB )) or resid 77 thr \ ough 84 or (resid 85 and (name N or name CA or name C or name O or name CB )) or \ resid 86 through 87 or (resid 88 and (name N or name CA or name C or name O or \ name CB )) or resid 89 through 91 or (resid 92 and (name N or name CA or name C \ or name O or name CB )) or resid 93 through 94 or (resid 95 and (name N or name \ CA or name C or name O or name CB )) or resid 96 through 116 or (resid 130 throu \ gh 132 and (name N or name CA or name C or name O or name CB )) or resid 133 thr \ ough 140 or (resid 141 and (name N or name CA or name C or name O or name CB )) \ or resid 142 or (resid 143 through 145 and (name N or name CA or name C or name \ O or name CB )) or resid 146 through 152)) selection = (chain 'J' and (resid 3 through 25 or resid 40 through 70 or (resid 71 through 7 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 73 or (resid \ 74 and (name N or name CA or name C or name O or name CB )) or resid 75 or (res \ id 76 and (name N or name CA or name C or name O or name CB )) or resid 77 throu \ gh 86 or (resid 87 through 88 and (name N or name CA or name C or name O or name \ CB )) or resid 89 through 90 or (resid 91 through 92 and (name N or name CA or \ name C or name O or name CB )) or resid 93 through 116 or (resid 130 and (name N \ or name CA or name C or name O or name CB )) or resid 131 or (resid 132 and (na \ me N or name CA or name C or name O or name CB )) or resid 133 through 142 or (r \ esid 143 through 145 and (name N or name CA or name C or name O or name CB )) or \ resid 146 through 152)) selection = (chain 'L' and (resid 3 through 25 or resid 40 through 66 or (resid 67 and (name \ N or name CA or name C or name O or name CB )) or resid 68 through 70 or (resid \ 71 through 72 and (name N or name CA or name C or name O or name CB )) or resid \ 73 through 84 or (resid 85 and (name N or name CA or name C or name O or name C \ B )) or resid 86 or (resid 87 through 88 and (name N or name CA or name C or nam \ e O or name CB )) or resid 89 through 90 or (resid 91 through 92 and (name N or \ name CA or name C or name O or name CB )) or resid 93 through 116 or (resid 130 \ and (name N or name CA or name C or name O or name CB )) or resid 131 through 14 \ 0 or (resid 141 and (name N or name CA or name C or name O or name CB )) or resi \ d 142 through 143 or (resid 144 through 145 and (name N or name CA or name C or \ name O or name CB )) or resid 146 through 152)) } ncs_group { reference = (chain 'B' and (resid 4 through 96 or (resid 97 and (name N or name CA or name C \ or name O or name CB )) or resid 98)) selection = (chain 'C' and (resid 4 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB )) or resid 34 through 50 or (resid 51 and (name N or name \ CA or name C or name O or name CB )) or resid 52 through 98)) } ncs_group { reference = (chain 'D' and (resid 37 through 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB )) or resid 71 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 88 or (resid 89 and ( \ name N or name CA or name C or name O or name CB )) or resid 90 through 94 or (r \ esid 95 and (name N or name CA or name C or name O or name CB )) or resid 96 thr \ ough 106 or (resid 107 and (name N or name CA or name C or name O or name CB )) \ or resid 108 through 117 or (resid 129 and (name N or name CA or name C or name \ O or name CB )) or resid 130 through 152)) selection = (chain 'K' and (resid 37 through 91 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 117 or resid 129 through 152)) } ncs_group { reference = chain 'E' selection = (chain 'H' and (resid 1 through 193 or (resid 194 and (name N or name CA or name \ C or name O or name CB )) or resid 195 through 259)) } ncs_group { reference = (chain 'F' and (resid 6 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 63 or (resid 64 and (name N or name \ CA or name C or name O or name CB )) or resid 65 through 134 or (resid 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 through 267 or \ resid 301 through 302)) selection = (chain 'G' and (resid 6 through 248 or (resid 249 and (name N or name CA or name \ C or name O or name CB )) or resid 250 through 267 or resid 301 through 302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 69 5.16 5 C 9597 2.51 5 N 2504 2.21 5 O 2726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 5.120 Check model and map are aligned: 0.240 Process input model: 38.310 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.130 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 0.044 15161 Z= 0.190 Angle : 0.797 15.605 20629 Z= 0.393 Chirality : 0.049 0.253 2521 Planarity : 0.005 0.057 2568 Dihedral : 13.498 159.710 5397 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 0.00 % 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: -5.91 (0.13), residues: 1934 helix: -5.17 (0.04), residues: 649 sheet: -3.13 (0.27), residues: 233 loop : -3.32 (0.15), residues: 1052 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 634 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 634 average time/residue: 0.3070 time to fit residues: 270.8964 Evaluate side-chains 376 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 1.871 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 0.9980 chunk 144 optimal weight: 0.0270 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 173 optimal weight: 0.3980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 88 GLN I 115 ASN J 2 GLN L 135 GLN B 75 GLN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN C 70 ASN C 75 GLN ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 GLN G 235 ASN E 29 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 15161 Z= 0.164 Angle : 0.637 10.567 20629 Z= 0.302 Chirality : 0.043 0.237 2521 Planarity : 0.005 0.056 2568 Dihedral : 8.071 153.857 2121 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.19 % 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: -4.77 (0.15), residues: 1934 helix: -3.83 (0.12), residues: 616 sheet: -2.90 (0.28), residues: 246 loop : -2.85 (0.16), residues: 1072 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 465 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 466 average time/residue: 0.2678 time to fit residues: 181.4545 Evaluate side-chains 335 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 1.957 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 144 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 154 optimal weight: 0.0970 chunk 172 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 92 GLN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN G 235 ASN E 47 GLN H 220 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 15161 Z= 0.145 Angle : 0.605 9.850 20629 Z= 0.282 Chirality : 0.042 0.168 2521 Planarity : 0.004 0.043 2568 Dihedral : 7.651 147.883 2121 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 0.19 % 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: -3.92 (0.16), residues: 1934 helix: -2.59 (0.17), residues: 632 sheet: -2.61 (0.29), residues: 251 loop : -2.63 (0.17), residues: 1051 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 435 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 436 average time/residue: 0.2740 time to fit residues: 176.8168 Evaluate side-chains 326 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.858 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 0.5980 chunk 130 optimal weight: 0.0570 chunk 90 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 184 optimal weight: 0.5980 chunk 91 optimal weight: 0.0370 chunk 165 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 92 GLN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS G 235 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 15161 Z= 0.136 Angle : 0.597 9.042 20629 Z= 0.274 Chirality : 0.042 0.181 2521 Planarity : 0.003 0.057 2568 Dihedral : 7.360 153.092 2121 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.25 % 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: -3.44 (0.17), residues: 1934 helix: -1.98 (0.19), residues: 643 sheet: -2.35 (0.29), residues: 263 loop : -2.48 (0.18), residues: 1028 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 434 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 435 average time/residue: 0.2603 time to fit residues: 166.3854 Evaluate side-chains 323 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 1.912 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 0.5980 chunk 104 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 157 optimal weight: 0.1980 chunk 127 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 HIS G 7 ASN G 235 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 15161 Z= 0.227 Angle : 0.671 10.961 20629 Z= 0.318 Chirality : 0.043 0.142 2521 Planarity : 0.004 0.061 2568 Dihedral : 7.141 176.112 2121 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.13 % 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: -2.74 (0.18), residues: 1934 helix: -1.22 (0.20), residues: 668 sheet: -2.16 (0.30), residues: 252 loop : -2.14 (0.19), residues: 1014 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 408 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 409 average time/residue: 0.2496 time to fit residues: 151.3751 Evaluate side-chains 308 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 1.703 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 61 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 135 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 15161 Z= 0.171 Angle : 0.634 8.666 20629 Z= 0.295 Chirality : 0.043 0.190 2521 Planarity : 0.003 0.057 2568 Dihedral : 6.801 177.182 2121 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 0.06 % 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: -2.43 (0.19), residues: 1934 helix: -0.87 (0.21), residues: 670 sheet: -1.92 (0.30), residues: 258 loop : -2.04 (0.19), residues: 1006 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 421 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 422 average time/residue: 0.2595 time to fit residues: 162.2980 Evaluate side-chains 326 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.888 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 112 optimal weight: 0.3980 chunk 84 optimal weight: 40.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 GLN H 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.6254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 15161 Z= 0.204 Angle : 0.655 8.535 20629 Z= 0.308 Chirality : 0.043 0.158 2521 Planarity : 0.004 0.056 2568 Dihedral : 6.606 171.654 2121 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer Outliers : 0.00 % 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: -2.21 (0.19), residues: 1934 helix: -0.61 (0.21), residues: 682 sheet: -1.91 (0.30), residues: 256 loop : -1.96 (0.19), residues: 996 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.2652 time to fit residues: 151.7650 Evaluate side-chains 304 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.831 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 0.3980 chunk 73 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 55 optimal weight: 0.0670 chunk 36 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 117 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.6339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 15161 Z= 0.146 Angle : 0.637 11.692 20629 Z= 0.290 Chirality : 0.042 0.158 2521 Planarity : 0.003 0.055 2568 Dihedral : 6.188 164.155 2121 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 0.00 % 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: -2.08 (0.19), residues: 1934 helix: -0.52 (0.21), residues: 667 sheet: -1.64 (0.32), residues: 245 loop : -1.92 (0.19), residues: 1022 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.2735 time to fit residues: 166.5929 Evaluate side-chains 321 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.831 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 171 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 52 optimal weight: 30.0000 chunk 155 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.6495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 15161 Z= 0.156 Angle : 0.649 11.234 20629 Z= 0.298 Chirality : 0.043 0.150 2521 Planarity : 0.003 0.055 2568 Dihedral : 5.911 151.948 2121 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 0.00 % 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: -1.94 (0.19), residues: 1934 helix: -0.35 (0.21), residues: 670 sheet: -1.47 (0.32), residues: 241 loop : -1.91 (0.19), residues: 1023 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.2750 time to fit residues: 161.6066 Evaluate side-chains 313 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 1.859 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.4980 chunk 181 optimal weight: 0.0470 chunk 110 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.6607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 15161 Z= 0.151 Angle : 0.643 10.788 20629 Z= 0.293 Chirality : 0.043 0.144 2521 Planarity : 0.003 0.052 2568 Dihedral : 5.706 142.845 2121 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 0.00 % 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: -1.85 (0.19), residues: 1934 helix: -0.29 (0.21), residues: 664 sheet: -1.42 (0.33), residues: 241 loop : -1.83 (0.19), residues: 1029 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.2730 time to fit residues: 162.4676 Evaluate side-chains 313 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 1.987 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 10.0000 chunk 161 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 139 optimal weight: 0.0670 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 151 optimal weight: 0.4980 chunk 63 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS F 226 HIS ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 HIS ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.086847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.064585 restraints weight = 64677.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.066398 restraints weight = 41394.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.067658 restraints weight = 29560.701| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.6722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 15161 Z= 0.153 Angle : 0.656 10.523 20629 Z= 0.298 Chirality : 0.042 0.144 2521 Planarity : 0.003 0.051 2568 Dihedral : 5.600 135.265 2121 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.00 % 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: -1.71 (0.19), residues: 1934 helix: -0.18 (0.22), residues: 663 sheet: -1.36 (0.33), residues: 241 loop : -1.74 (0.19), residues: 1030 =============================================================================== Job complete usr+sys time: 3610.68 seconds wall clock time: 65 minutes 38.39 seconds (3938.39 seconds total)