Starting phenix.real_space_refine on Tue Mar 19 13:52:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i79_35212/03_2024/8i79_35212.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i79_35212/03_2024/8i79_35212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i79_35212/03_2024/8i79_35212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i79_35212/03_2024/8i79_35212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i79_35212/03_2024/8i79_35212.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i79_35212/03_2024/8i79_35212.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8126 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 10314 2.51 5 N 2918 2.21 5 O 2995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ASP 90": "OD1" <-> "OD2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "B ASP 26": "OD1" <-> "OD2" Residue "B ASP 127": "OD1" <-> "OD2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 120": "OE1" <-> "OE2" Residue "D PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 243": "OD1" <-> "OD2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "E TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "G ASP 106": "OD1" <-> "OD2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G ASP 165": "OD1" <-> "OD2" Residue "G ASP 240": "OD1" <-> "OD2" Residue "G TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 283": "OE1" <-> "OE2" Residue "H ASP 26": "OD1" <-> "OD2" Residue "H ASP 121": "OD1" <-> "OD2" Residue "H TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 92": "OE1" <-> "OE2" Residue "I ASP 98": "OD1" <-> "OD2" Residue "I ASP 100": "OD1" <-> "OD2" Residue "I ASP 165": "OD1" <-> "OD2" Residue "I ASP 251": "OD1" <-> "OD2" Residue "I GLU 283": "OE1" <-> "OE2" Residue "J PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 121": "OD1" <-> "OD2" Residue "J ASP 127": "OD1" <-> "OD2" Residue "J TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16293 Number of models: 1 Model: "" Number of chains: 10 Chain: "F" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1634 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain breaks: 2 Chain: "B" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1683 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 2, 'TRANS': 243} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 358 Unresolved non-hydrogen angles: 445 Unresolved non-hydrogen dihedrals: 291 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 19, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 207 Chain: "A" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1634 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain breaks: 2 Chain: "C" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1651 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 2, 'TRANS': 237} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 345 Unresolved non-hydrogen angles: 424 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 18, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 202 Chain: "D" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1631 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1660 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 2, 'TRANS': 239} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 436 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 19, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 207 Chain: "G" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1634 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain breaks: 2 Chain: "H" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1646 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 2, 'TRANS': 239} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 18, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 213 Chain: "I" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1634 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain breaks: 2 Chain: "J" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1486 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 520 Unresolved non-hydrogen dihedrals: 337 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 8, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 21, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 250 Time building chain proxies: 8.82, per 1000 atoms: 0.54 Number of scatterers: 16293 At special positions: 0 Unit cell: (179.355, 179.355, 93.482, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2995 8.00 N 2918 7.00 C 10314 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: 6.60 Conformation dependent library (CDL) restraints added in 3.1 seconds 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4178 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 10 sheets defined 71.8% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'F' and resid 66 through 70 Processing helix chain 'F' and resid 75 through 81 Processing helix chain 'F' and resid 103 through 113 removed outlier: 3.821A pdb=" N VAL F 107 " --> pdb=" O HIS F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 133 Processing helix chain 'F' and resid 134 through 143 Processing helix chain 'F' and resid 144 through 158 removed outlier: 4.366A pdb=" N GLU F 150 " --> pdb=" O PRO F 146 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE F 156 " --> pdb=" O VAL F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 182 Processing helix chain 'F' and resid 240 through 255 Processing helix chain 'B' and resid 27 through 46 Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 69 through 86 Processing helix chain 'B' and resid 88 through 96 Processing helix chain 'B' and resid 100 through 123 Processing helix chain 'B' and resid 123 through 129 Processing helix chain 'B' and resid 129 through 134 removed outlier: 3.548A pdb=" N ASN B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 152 Processing helix chain 'B' and resid 154 through 175 Processing helix chain 'B' and resid 179 through 194 removed outlier: 3.994A pdb=" N GLY B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 205 through 228 removed outlier: 3.554A pdb=" N GLN B 222 " --> pdb=" O GLN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 252 Processing helix chain 'B' and resid 256 through 270 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 75 through 81 Processing helix chain 'A' and resid 103 through 113 removed outlier: 3.781A pdb=" N VAL A 107 " --> pdb=" O HIS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 144 through 158 removed outlier: 4.277A pdb=" N GLU A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 156 " --> pdb=" O VAL A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 182 Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.641A pdb=" N LEU A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 46 Processing helix chain 'C' and resid 53 through 67 removed outlier: 3.542A pdb=" N LEU C 57 " --> pdb=" O SER C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 86 removed outlier: 3.598A pdb=" N LEU C 73 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 96 Processing helix chain 'C' and resid 100 through 123 Processing helix chain 'C' and resid 123 through 129 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 138 through 151 Processing helix chain 'C' and resid 154 through 175 Processing helix chain 'C' and resid 180 through 193 Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 205 through 228 Processing helix chain 'C' and resid 229 through 252 Processing helix chain 'C' and resid 256 through 267 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 75 through 81 Processing helix chain 'D' and resid 103 through 113 removed outlier: 3.718A pdb=" N VAL D 107 " --> pdb=" O HIS D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 133 Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 144 through 158 removed outlier: 4.008A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE D 156 " --> pdb=" O VAL D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 182 Processing helix chain 'D' and resid 240 through 255 removed outlier: 3.584A pdb=" N LEU D 244 " --> pdb=" O ASP D 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 46 Processing helix chain 'E' and resid 53 through 67 removed outlier: 3.537A pdb=" N LEU E 57 " --> pdb=" O SER E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 86 removed outlier: 3.619A pdb=" N LEU E 73 " --> pdb=" O HIS E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 96 Processing helix chain 'E' and resid 100 through 123 Processing helix chain 'E' and resid 123 through 129 removed outlier: 3.738A pdb=" N ASP E 127 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 138 through 152 Processing helix chain 'E' and resid 154 through 175 Processing helix chain 'E' and resid 179 through 194 removed outlier: 3.993A pdb=" N GLY E 194 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 205 through 228 Processing helix chain 'E' and resid 229 through 252 Processing helix chain 'E' and resid 256 through 267 removed outlier: 3.513A pdb=" N ILE E 260 " --> pdb=" O THR E 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 70 Processing helix chain 'G' and resid 75 through 81 Processing helix chain 'G' and resid 103 through 113 removed outlier: 3.746A pdb=" N VAL G 107 " --> pdb=" O HIS G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 133 Processing helix chain 'G' and resid 134 through 143 Processing helix chain 'G' and resid 144 through 158 removed outlier: 4.216A pdb=" N GLU G 150 " --> pdb=" O PRO G 146 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE G 156 " --> pdb=" O VAL G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 182 Processing helix chain 'G' and resid 240 through 255 Processing helix chain 'H' and resid 27 through 46 Processing helix chain 'H' and resid 53 through 67 removed outlier: 3.503A pdb=" N LEU H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 86 Processing helix chain 'H' and resid 88 through 95 Processing helix chain 'H' and resid 100 through 123 Processing helix chain 'H' and resid 123 through 129 removed outlier: 3.755A pdb=" N ASP H 127 " --> pdb=" O LEU H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 134 Processing helix chain 'H' and resid 138 through 152 Processing helix chain 'H' and resid 154 through 175 Processing helix chain 'H' and resid 179 through 194 removed outlier: 3.965A pdb=" N GLY H 194 " --> pdb=" O LEU H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 205 removed outlier: 3.598A pdb=" N ASP H 204 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 224 Processing helix chain 'H' and resid 230 through 252 Processing helix chain 'H' and resid 256 through 270 Processing helix chain 'I' and resid 66 through 70 Processing helix chain 'I' and resid 75 through 81 Processing helix chain 'I' and resid 103 through 113 removed outlier: 3.770A pdb=" N VAL I 107 " --> pdb=" O HIS I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 133 Processing helix chain 'I' and resid 134 through 143 Processing helix chain 'I' and resid 144 through 158 removed outlier: 4.146A pdb=" N GLU I 150 " --> pdb=" O PRO I 146 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE I 156 " --> pdb=" O VAL I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 182 Processing helix chain 'I' and resid 240 through 255 removed outlier: 3.524A pdb=" N LEU I 244 " --> pdb=" O ASP I 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 46 Processing helix chain 'J' and resid 53 through 67 Processing helix chain 'J' and resid 69 through 97 removed outlier: 3.643A pdb=" N LEU J 73 " --> pdb=" O HIS J 69 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 123 Processing helix chain 'J' and resid 123 through 129 removed outlier: 3.660A pdb=" N ASP J 127 " --> pdb=" O LEU J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 134 Processing helix chain 'J' and resid 138 through 152 Processing helix chain 'J' and resid 154 through 175 Processing helix chain 'J' and resid 179 through 194 removed outlier: 3.869A pdb=" N GLY J 194 " --> pdb=" O LEU J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 205 Processing helix chain 'J' and resid 205 through 220 Processing helix chain 'J' and resid 235 through 252 Processing helix chain 'J' and resid 256 through 268 Processing sheet with id=AA1, first strand: chain 'F' and resid 60 through 65 Processing sheet with id=AA2, first strand: chain 'F' and resid 230 through 232 removed outlier: 9.659A pdb=" N VAL F 230 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS F 189 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N PHE F 232 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS F 191 " --> pdb=" O PHE F 232 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR F 258 " --> pdb=" O THR F 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 65 Processing sheet with id=AA4, first strand: chain 'A' and resid 230 through 232 removed outlier: 9.702A pdb=" N VAL A 230 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS A 189 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N PHE A 232 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N CYS A 191 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR A 258 " --> pdb=" O THR A 287 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 60 through 65 Processing sheet with id=AA6, first strand: chain 'D' and resid 230 through 232 removed outlier: 9.702A pdb=" N VAL D 230 " --> pdb=" O LYS D 187 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS D 189 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N PHE D 232 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N CYS D 191 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR D 258 " --> pdb=" O THR D 287 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 60 through 65 Processing sheet with id=AA8, first strand: chain 'G' and resid 230 through 232 removed outlier: 9.720A pdb=" N VAL G 230 " --> pdb=" O LYS G 187 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS G 189 " --> pdb=" O VAL G 230 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N PHE G 232 " --> pdb=" O LYS G 189 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N CYS G 191 " --> pdb=" O PHE G 232 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR G 258 " --> pdb=" O THR G 287 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 60 through 65 Processing sheet with id=AB1, first strand: chain 'I' and resid 230 through 232 removed outlier: 9.724A pdb=" N VAL I 230 " --> pdb=" O LYS I 187 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS I 189 " --> pdb=" O VAL I 230 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N PHE I 232 " --> pdb=" O LYS I 189 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N CYS I 191 " --> pdb=" O PHE I 232 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR I 258 " --> pdb=" O THR I 287 " (cutoff:3.500A) 1204 hydrogen bonds defined for protein. 3582 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.98 Time building geometry restraints manager: 7.13 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: 5589 1.34 - 1.46: 2811 1.46 - 1.58: 8081 1.58 - 1.69: 0 1.69 - 1.81: 111 Bond restraints: 16592 Sorted by residual: bond pdb=" N PRO G 118 " pdb=" CA PRO G 118 " ideal model delta sigma weight residual 1.468 1.477 -0.009 7.90e-03 1.60e+04 1.41e+00 bond pdb=" CB GLN C 132 " pdb=" CG GLN C 132 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.40e+00 bond pdb=" CA VAL E 151 " pdb=" CB VAL E 151 " ideal model delta sigma weight residual 1.536 1.549 -0.013 1.24e-02 6.50e+03 1.16e+00 bond pdb=" CD GLU D 172 " pdb=" OE1 GLU D 172 " ideal model delta sigma weight residual 1.249 1.230 0.019 1.90e-02 2.77e+03 1.03e+00 bond pdb=" C ILE H 269 " pdb=" O ILE H 269 " ideal model delta sigma weight residual 1.231 1.242 -0.010 1.02e-02 9.61e+03 1.02e+00 ... (remaining 16587 not shown) Histogram of bond angle deviations from ideal: 98.79 - 105.84: 239 105.84 - 112.89: 8921 112.89 - 119.94: 5421 119.94 - 126.99: 7823 126.99 - 134.04: 165 Bond angle restraints: 22569 Sorted by residual: angle pdb=" C ARG C 128 " pdb=" N VAL C 129 " pdb=" CA VAL C 129 " ideal model delta sigma weight residual 123.16 118.38 4.78 1.06e+00 8.90e-01 2.03e+01 angle pdb=" C ARG J 128 " pdb=" N VAL J 129 " pdb=" CA VAL J 129 " ideal model delta sigma weight residual 123.16 118.50 4.66 1.06e+00 8.90e-01 1.93e+01 angle pdb=" N VAL J 152 " pdb=" CA VAL J 152 " pdb=" C VAL J 152 " ideal model delta sigma weight residual 111.90 108.79 3.11 8.10e-01 1.52e+00 1.48e+01 angle pdb=" C ARG E 128 " pdb=" N VAL E 129 " pdb=" CA VAL E 129 " ideal model delta sigma weight residual 123.16 119.09 4.07 1.06e+00 8.90e-01 1.47e+01 angle pdb=" N VAL B 152 " pdb=" CA VAL B 152 " pdb=" C VAL B 152 " ideal model delta sigma weight residual 112.12 109.02 3.10 8.40e-01 1.42e+00 1.36e+01 ... (remaining 22564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 9156 17.45 - 34.90: 565 34.90 - 52.35: 106 52.35 - 69.81: 9 69.81 - 87.26: 12 Dihedral angle restraints: 9848 sinusoidal: 3406 harmonic: 6442 Sorted by residual: dihedral pdb=" CA MET F 144 " pdb=" C MET F 144 " pdb=" N GLN F 145 " pdb=" CA GLN F 145 " ideal model delta harmonic sigma weight residual 180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA MET D 144 " pdb=" C MET D 144 " pdb=" N GLN D 145 " pdb=" CA GLN D 145 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA VAL B 129 " pdb=" C VAL B 129 " pdb=" N TYR B 130 " pdb=" CA TYR B 130 " ideal model delta harmonic sigma weight residual -180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 9845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1964 0.042 - 0.085: 502 0.085 - 0.127: 95 0.127 - 0.169: 14 0.169 - 0.212: 3 Chirality restraints: 2578 Sorted by residual: chirality pdb=" CA GLU D 172 " pdb=" N GLU D 172 " pdb=" C GLU D 172 " pdb=" CB GLU D 172 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB VAL E 151 " pdb=" CA VAL E 151 " pdb=" CG1 VAL E 151 " pdb=" CG2 VAL E 151 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLU A 172 " pdb=" N GLU A 172 " pdb=" C GLU A 172 " pdb=" CB GLU A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.77e-01 ... (remaining 2575 not shown) Planarity restraints: 2960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 34 " -0.034 2.00e-02 2.50e+03 2.52e-02 1.58e+01 pdb=" CG TRP H 34 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP H 34 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP H 34 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 34 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 34 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 34 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 34 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 34 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 34 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 34 " -0.029 2.00e-02 2.50e+03 2.27e-02 1.29e+01 pdb=" CG TRP E 34 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP E 34 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP E 34 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 34 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 34 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 34 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 34 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 34 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 34 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 85 " 0.012 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C LEU E 85 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU E 85 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE E 86 " 0.015 2.00e-02 2.50e+03 ... (remaining 2957 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1199 2.74 - 3.28: 16629 3.28 - 3.82: 28259 3.82 - 4.36: 30687 4.36 - 4.90: 55575 Nonbonded interactions: 132349 Sorted by model distance: nonbonded pdb=" OH TYR C 74 " pdb=" NH2 ARG C 78 " model vdw 2.195 2.520 nonbonded pdb=" NH2 ARG C 128 " pdb=" O ASP G 74 " model vdw 2.200 2.520 nonbonded pdb=" OH TYR J 74 " pdb=" NH2 ARG J 78 " model vdw 2.203 2.520 nonbonded pdb=" O PRO G 136 " pdb=" NE2 GLN G 140 " model vdw 2.207 2.520 nonbonded pdb=" ND2 ASN I 56 " pdb=" OD2 ASP I 90 " model vdw 2.208 2.520 ... (remaining 132344 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 45 and (name N or name CA or name C or name O or name CB \ )) or resid 46 through 289)) selection = chain 'D' selection = (chain 'F' and ((resid 45 and (name N or name CA or name C or name O or name CB \ )) or resid 46 through 289)) selection = (chain 'G' and ((resid 45 and (name N or name CA or name C or name O or name CB \ )) or resid 46 through 289)) selection = (chain 'I' and ((resid 45 and (name N or name CA or name C or name O or name CB \ )) or resid 46 through 289)) } ncs_group { reference = (chain 'B' and ((resid 26 and (name N or name CA or name C or name O or name CB \ )) or resid 27 or (resid 28 and (name N or name CA or name C or name O or name C \ B )) or resid 29 through 37 or (resid 38 and (name N or name CA or name C or nam \ e O or name CB )) or resid 39 through 41 or (resid 42 through 43 and (name N or \ name CA or name C or name O or name CB )) or resid 44 or (resid 45 through 49 an \ d (name N or name CA or name C or name O or name CB )) or resid 52 through 71 or \ (resid 72 and (name N or name CA or name C or name O or name CB )) or resid 73 \ through 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) \ or resid 80 through 86 or (resid 87 through 99 and (name N or name CA or name C \ or name O or name CB )) or resid 100 through 117 or (resid 118 and (name N or n \ ame CA or name C or name O or name CB )) or resid 119 through 156 or (resid 157 \ through 174 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 5 through 176 or resid 179 through 220 or resid 234 through 267)) selection = (chain 'C' and ((resid 26 and (name N or name CA or name C or name O or name CB \ )) or resid 27 through 41 or (resid 42 through 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 or (resid 45 through 49 and (name N or na \ me CA or name C or name O or name CB )) or resid 52 through 78 or (resid 79 and \ (name N or name CA or name C or name O or name CB )) or resid 80 through 86 or ( \ resid 87 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 117 or (resid 118 and (name N or name CA or name C or name O o \ r name CB )) or resid 119 through 157 or (resid 158 through 174 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 175 through 193 and (name N o \ r name CA or name C or name O or name CB )) or (resid 194 through 220 and (name \ N or name CA or name C or name O or name CB )) or resid 234 through 267)) selection = (chain 'E' and ((resid 26 and (name N or name CA or name C or name O or name CB \ )) or resid 27 or (resid 28 and (name N or name CA or name C or name O or name C \ B )) or resid 29 through 37 or (resid 38 and (name N or name CA or name C or nam \ e O or name CB )) or resid 39 through 41 or (resid 42 through 43 and (name N or \ name CA or name C or name O or name CB )) or resid 44 or (resid 45 through 49 an \ d (name N or name CA or name C or name O or name CB )) or resid 52 through 71 or \ (resid 72 and (name N or name CA or name C or name O or name CB )) or resid 73 \ through 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) \ or resid 80 through 86 or (resid 87 through 99 and (name N or name CA or name C \ or name O or name CB )) or resid 100 through 117 or (resid 118 and (name N or n \ ame CA or name C or name O or name CB )) or resid 119 through 156 or (resid 157 \ through 174 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 5 through 176 or resid 179 through 220 or resid 234 through 267)) selection = (chain 'H' and ((resid 26 and (name N or name CA or name C or name O or name CB \ )) or resid 27 or (resid 28 and (name N or name CA or name C or name O or name C \ B )) or resid 29 through 37 or (resid 38 and (name N or name CA or name C or nam \ e O or name CB )) or resid 39 through 41 or (resid 42 through 43 and (name N or \ name CA or name C or name O or name CB )) or resid 44 or (resid 45 through 49 an \ d (name N or name CA or name C or name O or name CB )) or resid 52 through 71 or \ (resid 72 and (name N or name CA or name C or name O or name CB )) or resid 73 \ through 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) \ or resid 80 through 86 or (resid 87 through 99 and (name N or name CA or name C \ or name O or name CB )) or resid 100 through 117 or (resid 118 and (name N or n \ ame CA or name C or name O or name CB )) or resid 119 through 156 or (resid 157 \ through 174 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 5 through 176 or resid 179 through 220 or resid 234 through 267)) selection = (chain 'J' and (resid 26 through 156 or (resid 157 through 174 and (name N or na \ me CA or name C or name O or name CB )) or resid 175 through 176 or resid 179 th \ rough 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 6.600 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 44.650 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 0.035 16592 Z= 0.216 Angle : 0.569 6.562 22569 Z= 0.335 Chirality : 0.039 0.212 2578 Planarity : 0.004 0.060 2960 Dihedral : 12.356 87.257 5670 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: 1.30 (0.18), residues: 2150 helix: 1.84 (0.14), residues: 1449 sheet: 0.45 (0.37), residues: 165 loop : -1.78 (0.22), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP H 34 HIS 0.004 0.001 HIS C 160 PHE 0.017 0.001 PHE D 185 TYR 0.017 0.002 TYR B 74 ARG 0.008 0.001 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 GLN cc_start: 0.8767 (mt0) cc_final: 0.8538 (mp10) REVERT: B 145 ILE cc_start: 0.8562 (mt) cc_final: 0.8356 (pp) REVERT: C 204 ASP cc_start: 0.7001 (m-30) cc_final: 0.6632 (m-30) REVERT: E 45 GLN cc_start: 0.8513 (mt0) cc_final: 0.7954 (pp30) REVERT: E 104 THR cc_start: 0.9454 (t) cc_final: 0.9245 (p) REVERT: E 113 GLN cc_start: 0.8781 (mt0) cc_final: 0.8511 (mp10) REVERT: E 150 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7935 (mp10) REVERT: H 113 GLN cc_start: 0.8711 (mt0) cc_final: 0.8496 (mt0) REVERT: H 145 ILE cc_start: 0.8571 (mt) cc_final: 0.8357 (pp) REVERT: H 150 GLN cc_start: 0.8268 (mm-40) cc_final: 0.8028 (mm110) REVERT: J 39 ASN cc_start: 0.8481 (t0) cc_final: 0.8280 (t0) REVERT: J 104 THR cc_start: 0.9235 (t) cc_final: 0.9011 (t) REVERT: J 138 ASN cc_start: 0.8336 (p0) cc_final: 0.7884 (p0) outliers start: 0 outliers final: 1 residues processed: 397 average time/residue: 1.3050 time to fit residues: 569.2644 Evaluate side-chains 246 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 66 optimal weight: 0.0000 chunk 103 optimal weight: 4.9990 chunk 127 optimal weight: 50.0000 chunk 197 optimal weight: 3.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 112 HIS ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 ASN ** J 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16592 Z= 0.350 Angle : 0.622 9.322 22569 Z= 0.327 Chirality : 0.041 0.149 2578 Planarity : 0.004 0.058 2960 Dihedral : 4.179 33.378 2381 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.60 % Allowed : 13.89 % Favored : 83.50 % 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: 1.53 (0.18), residues: 2150 helix: 1.99 (0.13), residues: 1478 sheet: 0.82 (0.46), residues: 115 loop : -1.71 (0.21), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 34 HIS 0.008 0.001 HIS B 84 PHE 0.014 0.001 PHE D 81 TYR 0.021 0.002 TYR B 154 ARG 0.010 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 255 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 GLN cc_start: 0.8632 (mt0) cc_final: 0.8307 (pp30) REVERT: B 46 ARG cc_start: 0.8401 (mpt180) cc_final: 0.8119 (mmt-90) REVERT: B 113 GLN cc_start: 0.8816 (mt0) cc_final: 0.8569 (mp10) REVERT: B 116 MET cc_start: 0.8975 (tpp) cc_final: 0.8292 (mmm) REVERT: B 146 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8122 (mm) REVERT: C 145 ILE cc_start: 0.8456 (pp) cc_final: 0.8183 (pp) REVERT: C 204 ASP cc_start: 0.6862 (m-30) cc_final: 0.6651 (m-30) REVERT: E 91 GLU cc_start: 0.7770 (mp0) cc_final: 0.6732 (pp20) REVERT: E 113 GLN cc_start: 0.8790 (mt0) cc_final: 0.8478 (mt0) REVERT: E 159 ASP cc_start: 0.8055 (p0) cc_final: 0.7834 (p0) REVERT: H 113 GLN cc_start: 0.8722 (mt0) cc_final: 0.8491 (mt0) REVERT: J 103 GLN cc_start: 0.8581 (pp30) cc_final: 0.8309 (pp30) REVERT: J 113 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8115 (mp10) REVERT: J 135 ASN cc_start: 0.8929 (m-40) cc_final: 0.8725 (m-40) REVERT: J 150 GLN cc_start: 0.6428 (OUTLIER) cc_final: 0.5751 (tm-30) outliers start: 38 outliers final: 9 residues processed: 273 average time/residue: 1.2218 time to fit residues: 370.3498 Evaluate side-chains 230 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 218 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain H residue 125 TYR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 113 GLN Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 150 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 214 optimal weight: 50.0000 chunk 176 optimal weight: 1.9990 chunk 196 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN ** D 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN ** G 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 ASN ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 16592 Z= 0.457 Angle : 0.641 11.051 22569 Z= 0.336 Chirality : 0.041 0.136 2578 Planarity : 0.004 0.055 2960 Dihedral : 4.169 24.692 2379 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.12 % Allowed : 16.22 % Favored : 81.66 % 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: 1.44 (0.18), residues: 2150 helix: 1.94 (0.13), residues: 1488 sheet: -0.50 (0.37), residues: 165 loop : -1.61 (0.23), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 34 HIS 0.007 0.001 HIS J 112 PHE 0.014 0.002 PHE J 101 TYR 0.019 0.002 TYR B 74 ARG 0.007 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 232 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 GLN cc_start: 0.8821 (mt0) cc_final: 0.8574 (mt0) REVERT: A 160 MET cc_start: 0.8694 (mtm) cc_final: 0.8452 (mtt) REVERT: C 159 ASP cc_start: 0.8574 (p0) cc_final: 0.8357 (p0) REVERT: E 113 GLN cc_start: 0.8802 (mt0) cc_final: 0.8471 (mt0) REVERT: E 159 ASP cc_start: 0.8018 (p0) cc_final: 0.7727 (p0) REVERT: H 75 THR cc_start: 0.8780 (p) cc_final: 0.8554 (p) REVERT: H 91 GLU cc_start: 0.8060 (mp0) cc_final: 0.7105 (pp20) REVERT: H 113 GLN cc_start: 0.8674 (mt0) cc_final: 0.8468 (mt0) REVERT: J 126 MET cc_start: 0.8229 (mtm) cc_final: 0.8024 (ttt) REVERT: J 135 ASN cc_start: 0.9030 (m-40) cc_final: 0.8793 (m-40) outliers start: 31 outliers final: 13 residues processed: 251 average time/residue: 1.1840 time to fit residues: 331.2288 Evaluate side-chains 217 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 204 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 147 PHE Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 131 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 199 optimal weight: 0.9980 chunk 210 optimal weight: 40.0000 chunk 103 optimal weight: 0.9980 chunk 188 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16592 Z= 0.192 Angle : 0.561 10.867 22569 Z= 0.292 Chirality : 0.039 0.147 2578 Planarity : 0.004 0.056 2960 Dihedral : 4.035 22.742 2379 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.85 % Allowed : 17.39 % Favored : 80.77 % 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: 1.64 (0.18), residues: 2150 helix: 2.04 (0.13), residues: 1496 sheet: 0.56 (0.46), residues: 115 loop : -1.62 (0.23), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 34 HIS 0.006 0.001 HIS B 84 PHE 0.015 0.001 PHE H 147 TYR 0.022 0.002 TYR I 126 ARG 0.006 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 242 time to evaluate : 2.118 Fit side-chains revert: symmetry clash REVERT: B 38 LYS cc_start: 0.8553 (tmmt) cc_final: 0.8094 (tmmt) REVERT: B 107 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8636 (tp-100) REVERT: B 111 ASP cc_start: 0.8516 (m-30) cc_final: 0.7619 (m-30) REVERT: B 113 GLN cc_start: 0.8800 (mt0) cc_final: 0.8542 (mp10) REVERT: C 116 MET cc_start: 0.9065 (tpp) cc_final: 0.8438 (mmm) REVERT: C 159 ASP cc_start: 0.8524 (p0) cc_final: 0.8298 (p0) REVERT: E 91 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: E 113 GLN cc_start: 0.8742 (mt0) cc_final: 0.8393 (mt0) REVERT: E 159 ASP cc_start: 0.7988 (p0) cc_final: 0.7695 (p0) REVERT: H 75 THR cc_start: 0.8671 (p) cc_final: 0.8461 (p) REVERT: H 91 GLU cc_start: 0.7941 (mp0) cc_final: 0.7072 (pp20) REVERT: H 113 GLN cc_start: 0.8638 (mt0) cc_final: 0.8398 (mt0) REVERT: H 149 ASP cc_start: 0.8897 (m-30) cc_final: 0.8586 (m-30) REVERT: J 135 ASN cc_start: 0.8941 (m-40) cc_final: 0.8685 (m-40) outliers start: 27 outliers final: 12 residues processed: 259 average time/residue: 1.1582 time to fit residues: 334.7523 Evaluate side-chains 222 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 209 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 154 TYR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 125 TYR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 131 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 40.0000 chunk 119 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 166 HIS ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 HIS ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 16592 Z= 0.481 Angle : 0.660 12.274 22569 Z= 0.341 Chirality : 0.042 0.154 2578 Planarity : 0.004 0.054 2960 Dihedral : 4.165 26.241 2379 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.46 % Allowed : 18.82 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.18), residues: 2150 helix: 1.98 (0.13), residues: 1486 sheet: -0.75 (0.37), residues: 165 loop : -1.52 (0.23), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 235 HIS 0.007 0.001 HIS B 84 PHE 0.017 0.002 PHE J 101 TYR 0.027 0.002 TYR I 126 ARG 0.007 0.001 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 216 time to evaluate : 2.196 Fit side-chains revert: symmetry clash REVERT: B 107 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8647 (tp-100) REVERT: B 113 GLN cc_start: 0.8828 (mt0) cc_final: 0.8506 (mt0) REVERT: C 159 ASP cc_start: 0.8514 (p0) cc_final: 0.8269 (p0) REVERT: E 91 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: E 113 GLN cc_start: 0.8802 (mt0) cc_final: 0.8454 (mt0) REVERT: E 159 ASP cc_start: 0.8016 (p0) cc_final: 0.7737 (p0) REVERT: H 113 GLN cc_start: 0.8686 (mt0) cc_final: 0.8445 (mt0) REVERT: J 135 ASN cc_start: 0.8980 (m-40) cc_final: 0.8676 (m-40) outliers start: 36 outliers final: 15 residues processed: 241 average time/residue: 1.1983 time to fit residues: 321.2197 Evaluate side-chains 208 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 150 GLN Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 141 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 41 optimal weight: 50.0000 chunk 123 optimal weight: 30.0000 chunk 52 optimal weight: 0.7980 chunk 210 optimal weight: 40.0000 chunk 175 optimal weight: 30.0000 chunk 97 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16592 Z= 0.222 Angle : 0.599 12.427 22569 Z= 0.308 Chirality : 0.039 0.154 2578 Planarity : 0.004 0.055 2960 Dihedral : 4.078 24.367 2379 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.16 % Allowed : 21.08 % Favored : 77.75 % 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: 1.58 (0.18), residues: 2150 helix: 2.00 (0.13), residues: 1495 sheet: 0.47 (0.45), residues: 115 loop : -1.62 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 34 HIS 0.006 0.001 HIS B 84 PHE 0.017 0.001 PHE H 147 TYR 0.030 0.002 TYR I 126 ARG 0.006 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 232 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 107 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8657 (tp-100) REVERT: B 113 GLN cc_start: 0.8823 (mt0) cc_final: 0.8573 (mt0) REVERT: C 116 MET cc_start: 0.9088 (tpp) cc_final: 0.8474 (mmm) REVERT: C 159 ASP cc_start: 0.8506 (p0) cc_final: 0.8241 (p0) REVERT: E 83 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8581 (tm-30) REVERT: E 90 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7244 (ttm-80) REVERT: E 113 GLN cc_start: 0.8733 (mt0) cc_final: 0.8379 (mt0) REVERT: E 159 ASP cc_start: 0.7985 (p0) cc_final: 0.7707 (p0) REVERT: H 91 GLU cc_start: 0.8012 (mp0) cc_final: 0.7217 (pp20) REVERT: J 135 ASN cc_start: 0.8931 (m-40) cc_final: 0.8610 (m-40) outliers start: 17 outliers final: 11 residues processed: 244 average time/residue: 1.2493 time to fit residues: 338.0648 Evaluate side-chains 215 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 203 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 150 GLN Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 131 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 177 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 210 optimal weight: 40.0000 chunk 131 optimal weight: 50.0000 chunk 128 optimal weight: 50.0000 chunk 97 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 HIS ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 16592 Z= 0.507 Angle : 0.717 13.289 22569 Z= 0.367 Chirality : 0.042 0.145 2578 Planarity : 0.004 0.053 2960 Dihedral : 4.263 26.272 2379 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.71 % Allowed : 21.42 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.18), residues: 2150 helix: 1.95 (0.13), residues: 1479 sheet: -0.89 (0.32), residues: 205 loop : -1.63 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 34 HIS 0.009 0.001 HIS B 84 PHE 0.022 0.002 PHE H 147 TYR 0.035 0.002 TYR I 126 ARG 0.010 0.001 ARG H 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 205 time to evaluate : 1.942 Fit side-chains revert: symmetry clash REVERT: B 107 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8765 (tp-100) REVERT: B 113 GLN cc_start: 0.8844 (mt0) cc_final: 0.8493 (mt0) REVERT: B 146 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8113 (mp) REVERT: C 159 ASP cc_start: 0.8401 (p0) cc_final: 0.8159 (p0) REVERT: D 140 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8387 (mp10) REVERT: E 113 GLN cc_start: 0.8800 (mt0) cc_final: 0.8339 (mt0) REVERT: E 116 MET cc_start: 0.9150 (tpp) cc_final: 0.8864 (mmm) REVERT: E 159 ASP cc_start: 0.8066 (p0) cc_final: 0.7825 (p0) REVERT: H 91 GLU cc_start: 0.8146 (mp0) cc_final: 0.7252 (pp20) REVERT: H 107 GLN cc_start: 0.9270 (mm-40) cc_final: 0.8743 (tp-100) REVERT: J 135 ASN cc_start: 0.9004 (m-40) cc_final: 0.8714 (m-40) outliers start: 25 outliers final: 15 residues processed: 225 average time/residue: 1.2324 time to fit residues: 307.7533 Evaluate side-chains 207 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 190 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 124 MET Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 150 GLN Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 141 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 50.0000 chunk 83 optimal weight: 50.0000 chunk 125 optimal weight: 30.0000 chunk 63 optimal weight: 0.5980 chunk 41 optimal weight: 50.0000 chunk 40 optimal weight: 50.0000 chunk 133 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16592 Z= 0.207 Angle : 0.636 13.027 22569 Z= 0.325 Chirality : 0.039 0.186 2578 Planarity : 0.004 0.055 2960 Dihedral : 4.094 24.348 2379 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.37 % Allowed : 22.18 % Favored : 76.45 % 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: 1.59 (0.18), residues: 2150 helix: 2.02 (0.13), residues: 1489 sheet: 0.41 (0.46), residues: 115 loop : -1.57 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 109 HIS 0.006 0.001 HIS B 84 PHE 0.033 0.001 PHE H 147 TYR 0.036 0.002 TYR I 126 ARG 0.007 0.001 ARG H 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 228 time to evaluate : 2.121 Fit side-chains revert: symmetry clash REVERT: B 107 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8671 (tp-100) REVERT: B 111 ASP cc_start: 0.8500 (m-30) cc_final: 0.7401 (m-30) REVERT: B 113 GLN cc_start: 0.8830 (mt0) cc_final: 0.8586 (mt0) REVERT: C 116 MET cc_start: 0.9016 (tpp) cc_final: 0.8713 (tpp) REVERT: C 159 ASP cc_start: 0.8329 (p0) cc_final: 0.8054 (p0) REVERT: E 90 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7289 (ttm-80) REVERT: E 113 GLN cc_start: 0.8737 (mt0) cc_final: 0.8276 (mt0) REVERT: E 116 MET cc_start: 0.9059 (tpp) cc_final: 0.8776 (mmm) REVERT: E 124 MET cc_start: 0.8495 (ttm) cc_final: 0.8287 (tpp) REVERT: E 159 ASP cc_start: 0.8032 (p0) cc_final: 0.7739 (p0) REVERT: H 91 GLU cc_start: 0.8052 (mp0) cc_final: 0.7235 (pp20) REVERT: H 107 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8664 (tp-100) REVERT: J 135 ASN cc_start: 0.8951 (m-40) cc_final: 0.8612 (m-40) outliers start: 20 outliers final: 8 residues processed: 243 average time/residue: 1.2756 time to fit residues: 344.3984 Evaluate side-chains 212 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 203 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 131 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.1657 > 50: distance: 12 - 13: 22.704 distance: 13 - 14: 41.018 distance: 13 - 16: 22.195 distance: 14 - 15: 28.433 distance: 14 - 20: 28.720 distance: 16 - 17: 33.760 distance: 17 - 18: 29.123 distance: 17 - 19: 14.638 distance: 20 - 21: 54.785 distance: 21 - 22: 18.081 distance: 21 - 24: 16.552 distance: 22 - 23: 23.998 distance: 22 - 27: 5.071 distance: 24 - 25: 30.636 distance: 25 - 26: 28.836 distance: 27 - 28: 29.273 distance: 29 - 36: 14.710 distance: 36 - 37: 39.033 distance: 37 - 38: 10.391 distance: 37 - 40: 32.934 distance: 38 - 39: 14.422 distance: 38 - 45: 58.904 distance: 40 - 41: 22.975 distance: 41 - 42: 54.138 distance: 42 - 44: 39.851 distance: 45 - 46: 14.992 distance: 46 - 47: 4.232 distance: 46 - 49: 24.229 distance: 47 - 56: 17.508 distance: 49 - 50: 46.301 distance: 50 - 51: 6.858 distance: 50 - 52: 4.904 distance: 51 - 53: 5.503 distance: 52 - 54: 10.382 distance: 53 - 55: 5.959 distance: 54 - 55: 9.166 distance: 56 - 57: 14.959 distance: 56 - 62: 10.641 distance: 57 - 58: 17.878 distance: 57 - 60: 4.247 distance: 58 - 59: 24.680 distance: 58 - 63: 9.250 distance: 60 - 61: 10.650 distance: 61 - 62: 34.107 distance: 63 - 64: 13.327 distance: 64 - 65: 14.754 distance: 65 - 66: 39.774 distance: 65 - 72: 14.176 distance: 68 - 69: 3.126 distance: 69 - 70: 5.922 distance: 69 - 71: 3.225 distance: 73 - 74: 15.066 distance: 73 - 76: 16.811 distance: 74 - 75: 27.608 distance: 74 - 79: 41.144 distance: 76 - 77: 24.832 distance: 76 - 78: 17.114 distance: 79 - 80: 34.348 distance: 79 - 111: 31.967 distance: 80 - 81: 41.210 distance: 80 - 83: 39.882 distance: 81 - 82: 13.896 distance: 81 - 86: 19.162 distance: 82 - 108: 10.563 distance: 83 - 84: 18.984 distance: 83 - 85: 6.360