Starting phenix.real_space_refine on Tue Mar 19 02:27:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwu_32873/03_2024/7wwu_32873.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwu_32873/03_2024/7wwu_32873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwu_32873/03_2024/7wwu_32873.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwu_32873/03_2024/7wwu_32873.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwu_32873/03_2024/7wwu_32873.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwu_32873/03_2024/7wwu_32873.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4092 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: 5 Type Number sf(0) Gaussians P 49 5.49 5 S 67 5.16 5 C 11635 2.51 5 N 3241 2.21 5 O 3872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 60": "OE1" <-> "OE2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 75": "OD1" <-> "OD2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B ASP 227": "OD1" <-> "OD2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 287": "OD1" <-> "OD2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 217": "OD1" <-> "OD2" Residue "F ASP 287": "OD1" <-> "OD2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "H PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 93": "OE1" <-> "OE2" Residue "H TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 161": "OD1" <-> "OD2" Residue "H PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 250": "OE1" <-> "OE2" Residue "H ASP 287": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18864 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1431 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain: "B" Number of atoms: 1924 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1919 Classifications: {'peptide': 248} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 237} Conformer: "B" Number of residues, atoms: 248, 1919 Classifications: {'peptide': 248} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 237} bond proxies already assigned to first conformer: 1950 Chain: "C" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2302 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 657 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 656 Classifications: {'peptide': 167} Incomplete info: {'backbone_only': 143, 'n_c_alpha_c_only': 10} Link IDs: {'PTRANS': 3, 'TRANS': 163} Unresolved chain links: 1 Unresolved chain link angles: 18 Unresolved chain link dihedrals: 8 Unresolved non-hydrogen bonds: 668 Unresolved non-hydrogen angles: 953 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 208 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 7, 'TYR:plan': 6, 'ASN:plan1': 10, 'HIS:plan': 2, 'PHE:plan': 8, 'GLU:plan': 9, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 267 Conformer: "B" Number of residues, atoms: 167, 656 Classifications: {'peptide': 167} Incomplete info: {'backbone_only': 143, 'n_c_alpha_c_only': 10} Link IDs: {'PTRANS': 3, 'TRANS': 163} Unresolved chain links: 1 Unresolved chain link angles: 18 Unresolved chain link dihedrals: 8 Unresolved non-hydrogen bonds: 668 Unresolved non-hydrogen angles: 953 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 208 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 7, 'TYR:plan': 6, 'ASN:plan1': 10, 'HIS:plan': 2, 'PHE:plan': 8, 'GLU:plan': 9, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 267 bond proxies already assigned to first conformer: 651 Chain: "M" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1015 Classifications: {'DNA': 1, 'RNA': 49} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 10, 'rna3p_pur': 10, 'rna3p_pyr': 20} Link IDs: {'rna2p': 18, 'rna3p': 31} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' G%rna3p_pur:plan': 1, ' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 11.44, per 1000 atoms: 0.61 Number of scatterers: 18864 At special positions: 0 Unit cell: (147.66, 144.9, 118.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 P 49 15.00 O 3872 8.00 N 3241 7.00 C 11635 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: 7.64 Conformation dependent library (CDL) restraints added in 4.2 seconds 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4074 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 37 sheets defined 25.1% alpha, 18.0% beta 0 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 5.61 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.970A pdb=" N ALA A 52 " --> pdb=" O PRO A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 68 removed outlier: 4.062A pdb=" N VAL A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN A 67 " --> pdb=" O TRP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 82 through 90 removed outlier: 4.014A pdb=" N TYR A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.751A pdb=" N LEU A 124 " --> pdb=" O ASN A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 44 removed outlier: 4.117A pdb=" N PHE B 32 " --> pdb=" O PRO B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 148 through 153 removed outlier: 4.020A pdb=" N LYS B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 removed outlier: 3.957A pdb=" N ASP B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.782A pdb=" N GLN B 228 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 removed outlier: 4.094A pdb=" N ASP C 56 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 53 through 57' Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 112 through 125 removed outlier: 4.215A pdb=" N ALA C 116 " --> pdb=" O PHE C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 178 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 270 through 279 Processing helix chain 'C' and resid 284 through 297 removed outlier: 3.620A pdb=" N ARG C 297 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 removed outlier: 3.680A pdb=" N ASP D 56 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA D 57 " --> pdb=" O PRO D 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 57' Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.932A pdb=" N LEU D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D 123 " --> pdb=" O TYR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 178 removed outlier: 3.959A pdb=" N ALA D 167 " --> pdb=" O ASP D 163 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D 168 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 169 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 270 through 279 Processing helix chain 'D' and resid 284 through 295 Processing helix chain 'E' and resid 98 through 107 removed outlier: 3.570A pdb=" N THR E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.750A pdb=" N LEU E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE E 123 " --> pdb=" O TYR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 178 removed outlier: 4.703A pdb=" N MET E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 234 removed outlier: 3.937A pdb=" N ILE E 229 " --> pdb=" O HIS E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 284 through 297 removed outlier: 3.752A pdb=" N ARG E 297 " --> pdb=" O ALA E 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 107 Processing helix chain 'F' and resid 111 through 126 removed outlier: 4.367A pdb=" N LEU F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE F 123 " --> pdb=" O TYR F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 134 Processing helix chain 'F' and resid 166 through 177 removed outlier: 4.712A pdb=" N MET F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL F 173 " --> pdb=" O ILE F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 269 through 279 removed outlier: 3.581A pdb=" N LEU F 273 " --> pdb=" O ASP F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 4.355A pdb=" N MET F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 107 Processing helix chain 'G' and resid 111 through 125 removed outlier: 4.316A pdb=" N LEU G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 178 Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'G' and resid 269 through 279 Processing helix chain 'G' and resid 284 through 297 removed outlier: 3.507A pdb=" N MET G 289 " --> pdb=" O GLU G 285 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG G 297 " --> pdb=" O ALA G 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 59 removed outlier: 3.571A pdb=" N ALA H 57 " --> pdb=" O PRO H 54 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP H 58 " --> pdb=" O ASN H 55 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS H 59 " --> pdb=" O ASP H 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 54 through 59' Processing helix chain 'H' and resid 99 through 105 Processing helix chain 'H' and resid 111 through 126 removed outlier: 3.914A pdb=" N LEU H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY H 126 " --> pdb=" O ASN H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 178 Processing helix chain 'H' and resid 225 through 234 removed outlier: 3.666A pdb=" N ILE H 229 " --> pdb=" O HIS H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 279 removed outlier: 4.448A pdb=" N ASP H 275 " --> pdb=" O PHE H 271 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY H 276 " --> pdb=" O THR H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 297 removed outlier: 4.135A pdb=" N GLN H 288 " --> pdb=" O THR H 284 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET H 289 " --> pdb=" O GLU H 285 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE H 290 " --> pdb=" O GLU H 286 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU H 295 " --> pdb=" O VAL H 291 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG H 297 " --> pdb=" O ALA H 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 49 Processing helix chain 'I' and resid 50 through 53 removed outlier: 3.720A pdb=" N GLY I 53 " --> pdb=" O HIS I 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 50 through 53' Processing helix chain 'I' and resid 83 through 91 WARNING: missing atoms! removed outlier: 3.742A pdb=" N LEU I 91 " --> pdb=" O LEU I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 131 Processing helix chain 'I' and resid 134 through 142 removed outlier: 3.910A pdb=" N ALA I 138 " --> pdb=" O SER I 134 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 107 Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 140 removed outlier: 3.614A pdb=" N PHE A 140 " --> pdb=" O GLN A 165 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN A 165 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL B 24 " --> pdb=" O PHE A 166 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 59 removed outlier: 7.695A pdb=" N VAL B 50 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N GLU B 103 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TYR B 52 " --> pdb=" O CYS B 101 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N CYS B 101 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N SER B 54 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR B 99 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU B 100 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 8 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N PHE B 102 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE B 6 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 104 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE B 4 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 59 removed outlier: 7.695A pdb=" N VAL B 50 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N GLU B 103 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TYR B 52 " --> pdb=" O CYS B 101 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N CYS B 101 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N SER B 54 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR B 99 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU B 100 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 8 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N PHE B 102 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE B 6 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 104 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE B 4 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 163 removed outlier: 7.210A pdb=" N LEU B 207 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS B 188 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N THR B 209 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR B 186 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR B 211 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 215 " --> pdb=" O GLN B 180 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN B 180 " --> pdb=" O ILE B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.545A pdb=" N LYS B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 18 Processing sheet with id=AB1, first strand: chain 'C' and resid 16 through 18 Processing sheet with id=AB2, first strand: chain 'C' and resid 42 through 46 Processing sheet with id=AB3, first strand: chain 'C' and resid 254 through 255 Processing sheet with id=AB4, first strand: chain 'D' and resid 16 through 18 Processing sheet with id=AB5, first strand: chain 'D' and resid 42 through 47 Processing sheet with id=AB6, first strand: chain 'D' and resid 203 through 204 removed outlier: 3.556A pdb=" N GLU D 204 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLN D 214 " --> pdb=" O GLU D 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.710A pdb=" N GLY E 299 " --> pdb=" O TYR E 12 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 21 through 25 current: chain 'E' and resid 140 through 144 Processing sheet with id=AB9, first strand: chain 'E' and resid 35 through 36 removed outlier: 3.692A pdb=" N THR E 35 " --> pdb=" O ALA E 25 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 42 through 46 Processing sheet with id=AC2, first strand: chain 'E' and resid 203 through 204 removed outlier: 4.323A pdb=" N GLN E 214 " --> pdb=" O GLU E 204 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 235 through 237 removed outlier: 3.549A pdb=" N ILE E 247 " --> pdb=" O ASP E 237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 254 through 255 removed outlier: 3.618A pdb=" N VAL E 260 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 11 through 12 removed outlier: 4.496A pdb=" N GLY F 299 " --> pdb=" O TYR F 12 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 21 through 25 current: chain 'F' and resid 141 through 144 Processing sheet with id=AC7, first strand: chain 'F' and resid 35 through 36 removed outlier: 3.627A pdb=" N THR F 35 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 42 through 47 removed outlier: 8.344A pdb=" N SER F 212 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR F 64 " --> pdb=" O SER F 212 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AD1, first strand: chain 'G' and resid 16 through 18 Processing sheet with id=AD2, first strand: chain 'G' and resid 16 through 18 removed outlier: 3.505A pdb=" N LYS G 186 " --> pdb=" O THR G 144 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL G 142 " --> pdb=" O GLU G 188 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 42 through 47 Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AD5, first strand: chain 'H' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 21 through 26 current: chain 'H' and resid 139 through 145 Processing sheet with id=AD6, first strand: chain 'H' and resid 34 through 36 Processing sheet with id=AD7, first strand: chain 'H' and resid 42 through 45 Processing sheet with id=AD8, first strand: chain 'I' and resid 59 through 61 Processing sheet with id=AD9, first strand: chain 'I' and resid 112 through 113 Processing sheet with id=AE1, first strand: chain 'I' and resid 155 through 159 560 hydrogen bonds defined for protein. 1545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 5.35 Time building geometry restraints manager: 8.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5651 1.33 - 1.45: 3255 1.45 - 1.57: 10159 1.57 - 1.69: 97 1.69 - 1.81: 123 Bond restraints: 19285 Sorted by residual: bond pdb=" CA VAL G 206 " pdb=" CB VAL G 206 " ideal model delta sigma weight residual 1.542 1.560 -0.018 1.55e-02 4.16e+03 1.34e+00 bond pdb=" CB ASP F 226 " pdb=" CG ASP F 226 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.26e+00 bond pdb=" CA GLU C 108 " pdb=" CB GLU C 108 " ideal model delta sigma weight residual 1.529 1.545 -0.016 1.62e-02 3.81e+03 9.94e-01 bond pdb=" CA MET A 1 " pdb=" C MET A 1 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.10e-02 2.27e+03 8.88e-01 bond pdb=" CG LEU D 270 " pdb=" CD1 LEU D 270 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.87e-01 ... (remaining 19280 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.62: 449 105.62 - 112.72: 10011 112.72 - 119.81: 6153 119.81 - 126.90: 9469 126.90 - 134.00: 216 Bond angle restraints: 26298 Sorted by residual: angle pdb=" C LEU D 107 " pdb=" N GLU D 108 " pdb=" CA GLU D 108 " ideal model delta sigma weight residual 125.66 132.04 -6.38 1.85e+00 2.92e-01 1.19e+01 angle pdb=" N ILE A 75 " pdb=" CA ILE A 75 " pdb=" C ILE A 75 " ideal model delta sigma weight residual 113.16 108.09 5.07 1.49e+00 4.50e-01 1.16e+01 angle pdb=" C LEU E 107 " pdb=" N GLU E 108 " pdb=" CA GLU E 108 " ideal model delta sigma weight residual 125.66 131.41 -5.75 1.85e+00 2.92e-01 9.66e+00 angle pdb=" CA GLU C 108 " pdb=" CB GLU C 108 " pdb=" CG GLU C 108 " ideal model delta sigma weight residual 114.10 119.95 -5.85 2.00e+00 2.50e-01 8.57e+00 angle pdb=" C ASN E 73 " pdb=" N LYS E 74 " pdb=" CA LYS E 74 " ideal model delta sigma weight residual 121.87 128.15 -6.28 2.24e+00 1.99e-01 7.87e+00 ... (remaining 26293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.79: 10630 26.79 - 53.57: 513 53.57 - 80.36: 97 80.36 - 107.14: 11 107.14 - 133.93: 1 Dihedral angle restraints: 11252 sinusoidal: 4707 harmonic: 6545 Sorted by residual: dihedral pdb=" O4' U M 27 " pdb=" C1' U M 27 " pdb=" N1 U M 27 " pdb=" C2 U M 27 " ideal model delta sinusoidal sigma weight residual 200.00 66.07 133.93 1 1.50e+01 4.44e-03 7.23e+01 dihedral pdb=" CA ARG G 131 " pdb=" C ARG G 131 " pdb=" N ASN G 132 " pdb=" CA ASN G 132 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA TRP G 130 " pdb=" C TRP G 130 " pdb=" N ARG G 131 " pdb=" CA ARG G 131 " ideal model delta harmonic sigma weight residual 180.00 -157.75 -22.25 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 11249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2431 0.054 - 0.108: 429 0.108 - 0.162: 70 0.162 - 0.216: 3 0.216 - 0.270: 1 Chirality restraints: 2934 Sorted by residual: chirality pdb=" CB ILE A 2 " pdb=" CA ILE A 2 " pdb=" CG1 ILE A 2 " pdb=" CG2 ILE A 2 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB THR H 268 " pdb=" CA THR H 268 " pdb=" OG1 THR H 268 " pdb=" CG2 THR H 268 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB THR G 235 " pdb=" CA THR G 235 " pdb=" OG1 THR G 235 " pdb=" CG2 THR G 235 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.90e-01 ... (remaining 2931 not shown) Planarity restraints: 3316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA G 6 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO G 7 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO G 7 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 7 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 116 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 117 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 226 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" C ASP F 226 " -0.027 2.00e-02 2.50e+03 pdb=" O ASP F 226 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN F 227 " 0.009 2.00e-02 2.50e+03 ... (remaining 3313 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 749 2.71 - 3.26: 18518 3.26 - 3.80: 27265 3.80 - 4.35: 34396 4.35 - 4.90: 58053 Nonbonded interactions: 138981 Sorted by model distance: nonbonded pdb=" OH TYR G 117 " pdb=" O ASP G 161 " model vdw 2.159 2.440 nonbonded pdb=" OG SER D 13 " pdb=" OE1 GLU D 93 " model vdw 2.185 2.440 nonbonded pdb=" OD1 ASN B 184 " pdb=" OG1 THR B 211 " model vdw 2.193 2.440 nonbonded pdb=" O TRP D 130 " pdb=" N ASN D 132 " model vdw 2.214 2.520 nonbonded pdb=" N MET A 1 " pdb=" OE2 GLU A 4 " model vdw 2.220 2.520 ... (remaining 138976 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 'C' selection = (chain 'D' and (resid 3 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 303)) selection = (chain 'E' and (resid 3 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 303)) selection = (chain 'F' and (resid 3 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 303)) selection = (chain 'G' and (resid 3 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 303)) selection = (chain 'H' and (resid 3 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 303)) } 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=0.06 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 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: 0.020 Extract box with map and model: 2.900 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 55.480 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 0.034 19285 Z= 0.181 Angle : 0.604 8.573 26298 Z= 0.336 Chirality : 0.042 0.270 2934 Planarity : 0.004 0.055 3316 Dihedral : 15.511 133.927 7178 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.11 % Allowed : 0.54 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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 (0.17), residues: 2380 helix: 0.47 (0.23), residues: 526 sheet: -0.17 (0.25), residues: 474 loop : -2.25 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 130 HIS 0.003 0.001 HIS E 189 PHE 0.015 0.001 PHE H 150 TYR 0.026 0.001 TYR D 240 ARG 0.006 0.000 ARG H 257 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 307 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.5183 (OUTLIER) cc_final: 0.4865 (p0) REVERT: A 142 GLN cc_start: 0.7915 (pp30) cc_final: 0.7506 (pp30) REVERT: A 150 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8214 (tm-30) REVERT: D 198 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8205 (tm-30) REVERT: E 289 MET cc_start: 0.8255 (ttm) cc_final: 0.8043 (ttm) REVERT: F 88 ASP cc_start: 0.7984 (t70) cc_final: 0.7578 (t70) outliers start: 2 outliers final: 1 residues processed: 308 average time/residue: 0.2791 time to fit residues: 133.3188 Evaluate side-chains 250 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 248 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain G residue 19 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 101 optimal weight: 0.0670 chunk 62 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 115 optimal weight: 0.0470 chunk 141 optimal weight: 3.9990 chunk 219 optimal weight: 0.9980 overall best weight: 0.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN D 158 ASN ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN G 63 GLN H 66 ASN H 288 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 19285 Z= 0.149 Angle : 0.545 10.449 26298 Z= 0.290 Chirality : 0.041 0.197 2934 Planarity : 0.003 0.045 3316 Dihedral : 13.042 132.876 3293 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 1.31 % Allowed : 8.65 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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 (0.17), residues: 2380 helix: 0.57 (0.23), residues: 537 sheet: -0.34 (0.24), residues: 503 loop : -2.12 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 130 HIS 0.002 0.001 HIS F 189 PHE 0.032 0.001 PHE B 226 TYR 0.023 0.001 TYR D 240 ARG 0.003 0.000 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 272 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7071 (t80) cc_final: 0.6138 (t80) REVERT: A 112 TYR cc_start: 0.5167 (OUTLIER) cc_final: 0.4047 (t80) REVERT: A 128 THR cc_start: 0.6307 (p) cc_final: 0.6078 (p) REVERT: A 142 GLN cc_start: 0.7753 (pp30) cc_final: 0.7284 (pp30) REVERT: A 150 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 165 GLN cc_start: 0.4786 (mp10) cc_final: 0.4352 (mp10) REVERT: C 103 LEU cc_start: 0.9017 (tp) cc_final: 0.8780 (tp) REVERT: D 292 THR cc_start: 0.9052 (t) cc_final: 0.8816 (t) REVERT: E 289 MET cc_start: 0.8188 (ttm) cc_final: 0.7894 (ttm) REVERT: F 88 ASP cc_start: 0.8005 (t70) cc_final: 0.7745 (t70) REVERT: H 191 MET cc_start: 0.7985 (ttm) cc_final: 0.7681 (ttp) outliers start: 24 outliers final: 17 residues processed: 280 average time/residue: 0.2691 time to fit residues: 118.3032 Evaluate side-chains 267 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 249 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 258 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 182 optimal weight: 0.0980 chunk 149 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 220 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 chunk 196 optimal weight: 0.1980 chunk 218 optimal weight: 0.0870 chunk 75 optimal weight: 0.8980 chunk 176 optimal weight: 8.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 GLN F 227 GLN ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 288 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19285 Z= 0.128 Angle : 0.519 10.923 26298 Z= 0.273 Chirality : 0.040 0.179 2934 Planarity : 0.003 0.040 3316 Dihedral : 12.864 132.348 3290 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 1.31 % Allowed : 11.64 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.39 (0.17), residues: 2380 helix: 0.85 (0.23), residues: 531 sheet: -0.24 (0.25), residues: 500 loop : -2.02 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 231 HIS 0.002 0.001 HIS E 189 PHE 0.018 0.001 PHE B 120 TYR 0.021 0.001 TYR B 159 ARG 0.002 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 269 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.5152 (mp) cc_final: 0.3917 (mt) REVERT: A 112 TYR cc_start: 0.4907 (OUTLIER) cc_final: 0.4497 (t80) REVERT: A 142 GLN cc_start: 0.7810 (pp30) cc_final: 0.7260 (pp30) REVERT: A 150 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7954 (tm-30) REVERT: A 165 GLN cc_start: 0.4831 (mp10) cc_final: 0.4379 (mp10) REVERT: B 35 LEU cc_start: 0.7905 (pp) cc_final: 0.7052 (mt) REVERT: B 63 ARG cc_start: 0.7871 (mmp-170) cc_final: 0.7631 (mmp-170) REVERT: B 207 LEU cc_start: 0.4618 (tt) cc_final: 0.4344 (tt) REVERT: C 103 LEU cc_start: 0.8997 (tp) cc_final: 0.8783 (tp) REVERT: D 292 THR cc_start: 0.9070 (t) cc_final: 0.8843 (t) REVERT: E 289 MET cc_start: 0.8198 (ttm) cc_final: 0.7741 (ttm) REVERT: F 88 ASP cc_start: 0.7982 (t70) cc_final: 0.7708 (t70) outliers start: 24 outliers final: 21 residues processed: 283 average time/residue: 0.2807 time to fit residues: 124.0982 Evaluate side-chains 275 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 253 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 258 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 217 optimal weight: 0.0370 chunk 165 optimal weight: 10.0000 chunk 114 optimal weight: 0.0670 chunk 24 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 chunk 209 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 227 GLN ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19285 Z= 0.193 Angle : 0.540 11.492 26298 Z= 0.284 Chirality : 0.041 0.170 2934 Planarity : 0.003 0.042 3316 Dihedral : 12.952 131.801 3290 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.80 % Favored : 90.16 % Rotamer: Outliers : 2.18 % Allowed : 14.31 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.40 (0.17), residues: 2380 helix: 0.97 (0.24), residues: 528 sheet: -0.38 (0.24), residues: 509 loop : -2.04 (0.16), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 231 HIS 0.002 0.001 HIS H 225 PHE 0.018 0.001 PHE D 67 TYR 0.023 0.001 TYR B 159 ARG 0.005 0.000 ARG H 257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 267 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.4242 (p0) cc_final: 0.3602 (p0) REVERT: A 66 LEU cc_start: 0.5184 (mp) cc_final: 0.3907 (mt) REVERT: A 112 TYR cc_start: 0.4701 (OUTLIER) cc_final: 0.3893 (t80) REVERT: A 142 GLN cc_start: 0.7728 (pp30) cc_final: 0.7075 (pp30) REVERT: A 150 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8009 (tm-30) REVERT: A 165 GLN cc_start: 0.4889 (mp10) cc_final: 0.4367 (mp10) REVERT: B 207 LEU cc_start: 0.4629 (tt) cc_final: 0.4354 (tt) REVERT: D 292 THR cc_start: 0.9092 (t) cc_final: 0.8871 (t) REVERT: E 289 MET cc_start: 0.8160 (ttm) cc_final: 0.7656 (ttm) REVERT: F 88 ASP cc_start: 0.8009 (t70) cc_final: 0.7703 (t70) REVERT: H 14 ARG cc_start: 0.3286 (mpt90) cc_final: 0.2107 (mmt180) outliers start: 40 outliers final: 28 residues processed: 295 average time/residue: 0.2759 time to fit residues: 126.6174 Evaluate side-chains 286 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 257 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 258 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 194 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 174 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 161 optimal weight: 0.0050 chunk 0 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 209 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 GLN F 227 GLN ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19285 Z= 0.290 Angle : 0.596 11.661 26298 Z= 0.315 Chirality : 0.042 0.171 2934 Planarity : 0.004 0.040 3316 Dihedral : 13.107 130.389 3290 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.51 % Favored : 89.40 % Rotamer: Outliers : 2.39 % Allowed : 16.32 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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 (0.17), residues: 2380 helix: 0.85 (0.24), residues: 528 sheet: -0.38 (0.25), residues: 484 loop : -2.19 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 130 HIS 0.004 0.001 HIS H 225 PHE 0.019 0.002 PHE D 67 TYR 0.023 0.002 TYR C 99 ARG 0.004 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 252 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.5193 (mp) cc_final: 0.4075 (tp) REVERT: A 106 PHE cc_start: 0.7043 (t80) cc_final: 0.6176 (t80) REVERT: A 112 TYR cc_start: 0.4616 (OUTLIER) cc_final: 0.3599 (t80) REVERT: A 142 GLN cc_start: 0.7802 (pp30) cc_final: 0.7104 (pp30) REVERT: A 150 GLN cc_start: 0.8446 (tm-30) cc_final: 0.7994 (tm-30) REVERT: A 165 GLN cc_start: 0.4983 (mp10) cc_final: 0.4454 (mp10) REVERT: C 130 TRP cc_start: 0.6814 (m100) cc_final: 0.6535 (m100) REVERT: D 191 MET cc_start: 0.7661 (mtm) cc_final: 0.7456 (mtt) REVERT: F 88 ASP cc_start: 0.8003 (t70) cc_final: 0.7693 (t70) REVERT: G 139 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7780 (pt) REVERT: H 14 ARG cc_start: 0.3590 (mpt90) cc_final: 0.3085 (mmt180) outliers start: 44 outliers final: 35 residues processed: 279 average time/residue: 0.2767 time to fit residues: 120.0000 Evaluate side-chains 287 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 250 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 258 ASN Chi-restraints excluded: chain H residue 268 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 78 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 46 optimal weight: 0.0770 chunk 137 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 19 optimal weight: 0.0870 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.1920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN C 203 GLN D 146 ASN F 227 GLN ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19285 Z= 0.190 Angle : 0.557 12.176 26298 Z= 0.292 Chirality : 0.041 0.184 2934 Planarity : 0.003 0.068 3316 Dihedral : 12.956 129.126 3290 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.55 % Favored : 90.41 % Rotamer: Outliers : 2.39 % Allowed : 17.30 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.50 (0.17), residues: 2380 helix: 0.95 (0.24), residues: 529 sheet: -0.35 (0.25), residues: 484 loop : -2.15 (0.16), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 130 HIS 0.003 0.001 HIS E 189 PHE 0.019 0.001 PHE B 202 TYR 0.018 0.001 TYR D 240 ARG 0.010 0.000 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 267 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.5158 (mp) cc_final: 0.4079 (tp) REVERT: A 112 TYR cc_start: 0.4571 (OUTLIER) cc_final: 0.4106 (t80) REVERT: A 142 GLN cc_start: 0.7707 (pp30) cc_final: 0.6993 (pp30) REVERT: A 150 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 165 GLN cc_start: 0.5066 (mp10) cc_final: 0.4567 (mp10) REVERT: D 108 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6604 (pt0) REVERT: D 292 THR cc_start: 0.9094 (t) cc_final: 0.8879 (t) REVERT: F 88 ASP cc_start: 0.8018 (t70) cc_final: 0.7698 (t70) REVERT: H 14 ARG cc_start: 0.3550 (mpt90) cc_final: 0.2967 (mmt180) outliers start: 44 outliers final: 32 residues processed: 297 average time/residue: 0.2850 time to fit residues: 130.3570 Evaluate side-chains 292 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 258 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 258 ASN Chi-restraints excluded: chain H residue 268 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 225 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 197 optimal weight: 0.0670 chunk 130 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19285 Z= 0.315 Angle : 0.625 12.253 26298 Z= 0.328 Chirality : 0.043 0.172 2934 Planarity : 0.004 0.052 3316 Dihedral : 13.144 129.148 3290 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.82 % Favored : 88.10 % Rotamer: Outliers : 2.56 % Allowed : 18.17 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.70 (0.17), residues: 2380 helix: 0.80 (0.24), residues: 529 sheet: -0.55 (0.24), residues: 484 loop : -2.25 (0.16), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 130 HIS 0.004 0.001 HIS H 225 PHE 0.022 0.002 PHE A 106 TYR 0.025 0.002 TYR C 99 ARG 0.012 0.001 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 250 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.5207 (mp) cc_final: 0.4162 (tp) REVERT: A 112 TYR cc_start: 0.4693 (OUTLIER) cc_final: 0.3697 (t80) REVERT: A 142 GLN cc_start: 0.7797 (pp30) cc_final: 0.7068 (pp30) REVERT: A 165 GLN cc_start: 0.5121 (mp10) cc_final: 0.4604 (mp10) REVERT: C 130 TRP cc_start: 0.6911 (m100) cc_final: 0.6664 (m100) REVERT: C 158 ASN cc_start: 0.6906 (t0) cc_final: 0.6625 (t0) REVERT: D 108 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6668 (pt0) REVERT: D 289 MET cc_start: 0.7711 (mtm) cc_final: 0.7427 (mtm) REVERT: F 88 ASP cc_start: 0.8031 (t70) cc_final: 0.7717 (t70) outliers start: 47 outliers final: 36 residues processed: 283 average time/residue: 0.2838 time to fit residues: 123.6841 Evaluate side-chains 286 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 248 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 258 ASN Chi-restraints excluded: chain H residue 268 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 144 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 212 optimal weight: 0.0570 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN D 48 GLN F 227 GLN ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19285 Z= 0.174 Angle : 0.570 12.334 26298 Z= 0.295 Chirality : 0.041 0.194 2934 Planarity : 0.003 0.066 3316 Dihedral : 12.921 128.271 3290 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.50 % Favored : 90.45 % Rotamer: Outliers : 2.39 % Allowed : 18.93 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.51 (0.17), residues: 2380 helix: 0.97 (0.24), residues: 528 sheet: -0.39 (0.24), residues: 494 loop : -2.17 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 130 HIS 0.003 0.001 HIS E 189 PHE 0.018 0.001 PHE B 202 TYR 0.018 0.001 TYR B 52 ARG 0.005 0.000 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 259 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.5038 (mp) cc_final: 0.3978 (mt) REVERT: A 112 TYR cc_start: 0.5077 (OUTLIER) cc_final: 0.4582 (t80) REVERT: A 142 GLN cc_start: 0.7797 (pp30) cc_final: 0.7100 (pp30) REVERT: A 165 GLN cc_start: 0.5000 (mp10) cc_final: 0.4485 (mp10) REVERT: D 108 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6662 (pt0) REVERT: D 289 MET cc_start: 0.7793 (mtm) cc_final: 0.7588 (mtm) REVERT: D 292 THR cc_start: 0.9138 (t) cc_final: 0.8923 (t) REVERT: F 88 ASP cc_start: 0.8029 (t70) cc_final: 0.7722 (t70) outliers start: 44 outliers final: 35 residues processed: 288 average time/residue: 0.2821 time to fit residues: 125.9987 Evaluate side-chains 291 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 254 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 258 ASN Chi-restraints excluded: chain H residue 268 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 223 optimal weight: 0.2980 chunk 203 optimal weight: 0.8980 chunk 217 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 94 optimal weight: 0.0370 chunk 170 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 196 optimal weight: 0.4980 chunk 205 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.1460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN D 48 GLN D 294 ASN F 227 GLN ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN ** H 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19285 Z= 0.188 Angle : 0.578 12.380 26298 Z= 0.296 Chirality : 0.041 0.191 2934 Planarity : 0.003 0.044 3316 Dihedral : 12.916 128.659 3290 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.05 % Favored : 89.91 % Rotamer: Outliers : 2.18 % Allowed : 19.42 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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 (0.17), residues: 2380 helix: 1.01 (0.24), residues: 528 sheet: -0.36 (0.24), residues: 494 loop : -2.15 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 130 HIS 0.003 0.001 HIS F 225 PHE 0.017 0.001 PHE B 202 TYR 0.018 0.001 TYR B 52 ARG 0.004 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 248 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.5122 (mp) cc_final: 0.4027 (mt) REVERT: A 112 TYR cc_start: 0.4583 (OUTLIER) cc_final: 0.3764 (t80) REVERT: A 142 GLN cc_start: 0.7792 (pp30) cc_final: 0.7093 (pp30) REVERT: A 165 GLN cc_start: 0.4980 (mp10) cc_final: 0.4438 (mp10) REVERT: C 270 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7580 (tt) REVERT: D 108 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6630 (pt0) REVERT: D 289 MET cc_start: 0.7820 (mtm) cc_final: 0.7595 (mtm) REVERT: D 292 THR cc_start: 0.9162 (t) cc_final: 0.8941 (t) REVERT: F 88 ASP cc_start: 0.8036 (t70) cc_final: 0.7525 (t70) outliers start: 40 outliers final: 36 residues processed: 277 average time/residue: 0.2820 time to fit residues: 122.1739 Evaluate side-chains 286 residues out of total 1998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 247 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 258 ASN Chi-restraints excluded: chain H residue 268 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 55.3126 > 50: distance: 48 - 55: 16.887 distance: 55 - 56: 18.063 distance: 56 - 57: 10.293 distance: 56 - 59: 14.239 distance: 57 - 58: 17.368 distance: 57 - 60: 8.038 distance: 60 - 61: 14.114 distance: 61 - 62: 12.217 distance: 61 - 64: 12.721 distance: 62 - 63: 16.689 distance: 62 - 69: 15.236 distance: 64 - 65: 16.990 distance: 65 - 66: 7.979 distance: 66 - 67: 10.276 distance: 66 - 68: 10.056 distance: 69 - 70: 9.469 distance: 70 - 71: 16.401 distance: 70 - 73: 24.982 distance: 71 - 72: 15.793 distance: 71 - 77: 15.433 distance: 73 - 74: 11.528 distance: 74 - 75: 19.545 distance: 74 - 76: 20.922 distance: 77 - 78: 21.418 distance: 78 - 79: 17.533 distance: 79 - 80: 12.332 distance: 79 - 81: 16.588 distance: 81 - 82: 11.666 distance: 82 - 83: 29.173 distance: 83 - 84: 27.286 distance: 83 - 85: 13.131 distance: 85 - 86: 15.421 distance: 86 - 87: 15.212 distance: 87 - 88: 11.765 distance: 87 - 89: 3.818 distance: 89 - 90: 6.310 distance: 90 - 91: 7.327 distance: 91 - 92: 7.852 distance: 91 - 98: 5.300 distance: 92 - 124: 6.432 distance: 93 - 94: 3.109 distance: 95 - 96: 6.265 distance: 95 - 97: 4.342 distance: 98 - 99: 8.542 distance: 99 - 100: 3.733 distance: 99 - 102: 11.632 distance: 100 - 101: 4.794 distance: 100 - 110: 8.307 distance: 101 - 131: 11.073 distance: 103 - 104: 9.111 distance: 103 - 105: 3.628 distance: 104 - 106: 4.494 distance: 105 - 107: 4.259 distance: 106 - 108: 6.319 distance: 107 - 108: 7.667 distance: 108 - 109: 4.243 distance: 110 - 111: 3.388 distance: 111 - 112: 7.134 distance: 111 - 114: 5.729 distance: 112 - 113: 3.156 distance: 112 - 116: 6.477 distance: 113 - 139: 11.534 distance: 114 - 115: 5.495 distance: 116 - 117: 11.542 distance: 117 - 118: 6.937 distance: 117 - 120: 5.756 distance: 118 - 119: 5.056 distance: 118 - 124: 3.447 distance: 119 - 146: 5.906 distance: 120 - 121: 7.316 distance: 121 - 122: 8.280 distance: 121 - 123: 3.752