Starting phenix.real_space_refine on Wed Feb 14 17:55:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egk_31135/02_2024/7egk_31135_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egk_31135/02_2024/7egk_31135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egk_31135/02_2024/7egk_31135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egk_31135/02_2024/7egk_31135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egk_31135/02_2024/7egk_31135_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egk_31135/02_2024/7egk_31135_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 51 5.16 5 Na 3 4.78 5 C 6444 2.51 5 N 1602 2.21 5 O 1791 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E GLU 240": "OE1" <-> "OE2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9894 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2443 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "C" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2443 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "E" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2443 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 5.69, per 1000 atoms: 0.58 Number of scatterers: 9894 At special positions: 0 Unit cell: (98.0343, 100.189, 88.3386, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 3 15.00 Na 3 11.00 O 1791 8.00 N 1602 7.00 C 6444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 105 " - pdb=" SG CYS D 110 " distance=2.02 Simple disulfide: pdb=" SG CYS F 105 " - pdb=" SG CYS F 110 " distance=2.02 Simple disulfide: pdb=" SG CYS B 105 " - pdb=" SG CYS B 110 " distance=2.02 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: 3.86 Conformation dependent library (CDL) restraints added in 1.9 seconds 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 3 sheets defined 63.1% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 3.600A pdb=" N LEU A 8 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 31 Processing helix chain 'A' and resid 40 through 60 removed outlier: 4.041A pdb=" N GLY A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 90 removed outlier: 4.074A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 111 removed outlier: 3.594A pdb=" N ALA A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 127 Processing helix chain 'A' and resid 134 through 163 removed outlier: 4.193A pdb=" N GLY A 137 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Proline residue: A 141 - end of helix removed outlier: 3.704A pdb=" N ASP A 144 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE A 145 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Proline residue: A 146 - end of helix removed outlier: 3.944A pdb=" N VAL A 149 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 151 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 153 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 154 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 155 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A 162 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 163 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 219 Processing helix chain 'A' and resid 222 through 236 removed outlier: 3.615A pdb=" N ALA A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 251 through 269 removed outlier: 3.560A pdb=" N ILE A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY A 263 " --> pdb=" O MET A 259 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ALA A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.597A pdb=" N ARG A 274 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 271 through 275' Processing helix chain 'A' and resid 279 through 303 removed outlier: 3.537A pdb=" N ILE A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Proline residue: A 288 - end of helix removed outlier: 3.520A pdb=" N ILE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 removed outlier: 3.504A pdb=" N VAL A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 335 removed outlier: 3.542A pdb=" N ALA A 334 " --> pdb=" O PRO A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 350 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 360 through 370 removed outlier: 3.773A pdb=" N THR A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 26 removed outlier: 4.458A pdb=" N LYS D 18 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS D 19 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE D 20 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA D 21 " --> pdb=" O LYS D 18 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE D 24 " --> pdb=" O ALA D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 83 Processing helix chain 'D' and resid 102 through 105 No H-bonds generated for 'chain 'D' and resid 102 through 105' Processing helix chain 'C' and resid 4 through 15 removed outlier: 3.600A pdb=" N LEU C 8 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 31 Processing helix chain 'C' and resid 40 through 60 removed outlier: 4.041A pdb=" N GLY C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 90 removed outlier: 4.074A pdb=" N VAL C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 90 " --> pdb=" O PHE C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 111 removed outlier: 3.594A pdb=" N ALA C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 134 through 163 removed outlier: 4.193A pdb=" N GLY C 137 " --> pdb=" O ALA C 134 " (cutoff:3.500A) Proline residue: C 141 - end of helix removed outlier: 3.705A pdb=" N ASP C 144 " --> pdb=" O PRO C 141 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE C 145 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Proline residue: C 146 - end of helix removed outlier: 3.944A pdb=" N VAL C 149 " --> pdb=" O PRO C 146 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C 151 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 153 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 154 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C 155 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 159 " --> pdb=" O ASN C 156 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG C 162 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 163 " --> pdb=" O ASN C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 Processing helix chain 'C' and resid 222 through 236 removed outlier: 3.615A pdb=" N ALA C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 251 through 269 removed outlier: 3.559A pdb=" N ILE C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY C 263 " --> pdb=" O MET C 259 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ALA C 266 " --> pdb=" O MET C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.596A pdb=" N ARG C 274 " --> pdb=" O GLY C 271 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS C 275 " --> pdb=" O GLU C 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 271 through 275' Processing helix chain 'C' and resid 279 through 303 removed outlier: 3.538A pdb=" N ILE C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Proline residue: C 288 - end of helix removed outlier: 3.521A pdb=" N ILE C 301 " --> pdb=" O GLY C 297 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 321 removed outlier: 3.505A pdb=" N VAL C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 335 removed outlier: 3.541A pdb=" N ALA C 334 " --> pdb=" O PRO C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 350 Processing helix chain 'C' and resid 352 through 358 Processing helix chain 'C' and resid 360 through 370 removed outlier: 3.773A pdb=" N THR C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 26 removed outlier: 4.456A pdb=" N LYS F 18 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS F 19 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE F 20 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA F 21 " --> pdb=" O LYS F 18 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE F 24 " --> pdb=" O ALA F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 83 Processing helix chain 'F' and resid 102 through 105 No H-bonds generated for 'chain 'F' and resid 102 through 105' Processing helix chain 'E' and resid 4 through 15 removed outlier: 3.601A pdb=" N LEU E 8 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR E 9 " --> pdb=" O SER E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 31 Processing helix chain 'E' and resid 40 through 60 removed outlier: 4.040A pdb=" N GLY E 59 " --> pdb=" O GLY E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 90 removed outlier: 4.073A pdb=" N VAL E 85 " --> pdb=" O GLY E 81 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE E 90 " --> pdb=" O PHE E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 111 removed outlier: 3.593A pdb=" N ALA E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 127 Processing helix chain 'E' and resid 134 through 163 removed outlier: 4.193A pdb=" N GLY E 137 " --> pdb=" O ALA E 134 " (cutoff:3.500A) Proline residue: E 141 - end of helix removed outlier: 3.705A pdb=" N ASP E 144 " --> pdb=" O PRO E 141 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE E 145 " --> pdb=" O PHE E 142 " (cutoff:3.500A) Proline residue: E 146 - end of helix removed outlier: 3.944A pdb=" N VAL E 149 " --> pdb=" O PRO E 146 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA E 151 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 153 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL E 154 " --> pdb=" O ALA E 151 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA E 155 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU E 159 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG E 162 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS E 163 " --> pdb=" O ASN E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 219 Processing helix chain 'E' and resid 222 through 236 removed outlier: 3.615A pdb=" N ALA E 226 " --> pdb=" O PRO E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 245 Processing helix chain 'E' and resid 251 through 269 removed outlier: 3.558A pdb=" N ILE E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY E 263 " --> pdb=" O MET E 259 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ALA E 266 " --> pdb=" O MET E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 275 removed outlier: 3.596A pdb=" N ARG E 274 " --> pdb=" O GLY E 271 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS E 275 " --> pdb=" O GLU E 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 271 through 275' Processing helix chain 'E' and resid 279 through 303 removed outlier: 3.538A pdb=" N ILE E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Proline residue: E 288 - end of helix removed outlier: 3.521A pdb=" N ILE E 301 " --> pdb=" O GLY E 297 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 321 removed outlier: 3.504A pdb=" N VAL E 314 " --> pdb=" O LEU E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 335 removed outlier: 4.024A pdb=" N THR E 331 " --> pdb=" O SER E 327 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA E 334 " --> pdb=" O PRO E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 350 Processing helix chain 'E' and resid 352 through 358 Processing helix chain 'E' and resid 360 through 370 removed outlier: 3.772A pdb=" N THR E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 26 removed outlier: 4.458A pdb=" N LYS B 18 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS B 19 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE B 20 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA B 21 " --> pdb=" O LYS B 18 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 24 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 83 Processing helix chain 'B' and resid 102 through 105 No H-bonds generated for 'chain 'B' and resid 102 through 105' Processing sheet with id= A, first strand: chain 'D' and resid 89 through 98 Processing sheet with id= B, first strand: chain 'F' and resid 89 through 98 Processing sheet with id= C, first strand: chain 'B' and resid 89 through 98 530 hydrogen bonds defined for protein. 1428 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: 2.51 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3044 1.34 - 1.45: 1492 1.45 - 1.57: 5454 1.57 - 1.69: 3 1.69 - 1.80: 90 Bond restraints: 10083 Sorted by residual: bond pdb=" N ILE C 326 " pdb=" CA ILE C 326 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.20e+00 bond pdb=" N ILE E 326 " pdb=" CA ILE E 326 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.15e+00 bond pdb=" N ILE A 326 " pdb=" CA ILE A 326 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.57e+00 bond pdb=" N SER A 322 " pdb=" CA SER A 322 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.31e-02 5.83e+03 6.26e+00 bond pdb=" N SER E 322 " pdb=" CA SER E 322 " ideal model delta sigma weight residual 1.453 1.485 -0.032 1.31e-02 5.83e+03 6.07e+00 ... (remaining 10078 not shown) Histogram of bond angle deviations from ideal: 98.51 - 105.98: 280 105.98 - 113.44: 5643 113.44 - 120.91: 5107 120.91 - 128.38: 2598 128.38 - 135.85: 79 Bond angle restraints: 13707 Sorted by residual: angle pdb=" N LEU A 20 " pdb=" CA LEU A 20 " pdb=" C LEU A 20 " ideal model delta sigma weight residual 114.04 107.61 6.43 1.24e+00 6.50e-01 2.69e+01 angle pdb=" N LEU C 20 " pdb=" CA LEU C 20 " pdb=" C LEU C 20 " ideal model delta sigma weight residual 114.04 107.62 6.42 1.24e+00 6.50e-01 2.68e+01 angle pdb=" N LEU E 20 " pdb=" CA LEU E 20 " pdb=" C LEU E 20 " ideal model delta sigma weight residual 114.04 107.62 6.42 1.24e+00 6.50e-01 2.68e+01 angle pdb=" C PRO A 18 " pdb=" N THR A 19 " pdb=" CA THR A 19 " ideal model delta sigma weight residual 121.54 129.50 -7.96 1.91e+00 2.74e-01 1.74e+01 angle pdb=" C PRO E 18 " pdb=" N THR E 19 " pdb=" CA THR E 19 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.71e+01 ... (remaining 13702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.75: 5255 15.75 - 31.50: 499 31.50 - 47.25: 159 47.25 - 63.00: 39 63.00 - 78.75: 15 Dihedral angle restraints: 5967 sinusoidal: 2247 harmonic: 3720 Sorted by residual: dihedral pdb=" CA SER C 323 " pdb=" C SER C 323 " pdb=" N SER C 324 " pdb=" CA SER C 324 " ideal model delta harmonic sigma weight residual -180.00 -151.83 -28.17 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA SER A 323 " pdb=" C SER A 323 " pdb=" N SER A 324 " pdb=" CA SER A 324 " ideal model delta harmonic sigma weight residual -180.00 -151.92 -28.08 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA GLY E 263 " pdb=" C GLY E 263 " pdb=" N MET E 264 " pdb=" CA MET E 264 " ideal model delta harmonic sigma weight residual 180.00 155.38 24.62 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 5964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1010 0.042 - 0.085: 489 0.085 - 0.127: 123 0.127 - 0.170: 34 0.170 - 0.212: 6 Chirality restraints: 1662 Sorted by residual: chirality pdb=" CA PRO C 96 " pdb=" N PRO C 96 " pdb=" C PRO C 96 " pdb=" CB PRO C 96 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO A 96 " pdb=" N PRO A 96 " pdb=" C PRO A 96 " pdb=" CB PRO A 96 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA PRO E 96 " pdb=" N PRO E 96 " pdb=" C PRO E 96 " pdb=" CB PRO E 96 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1659 not shown) Planarity restraints: 1686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 323 " -0.020 2.00e-02 2.50e+03 4.17e-02 1.74e+01 pdb=" C SER E 323 " 0.072 2.00e-02 2.50e+03 pdb=" O SER E 323 " -0.028 2.00e-02 2.50e+03 pdb=" N SER E 324 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 329 " 0.044 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO E 330 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO E 330 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 330 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 329 " 0.044 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO A 330 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " 0.037 5.00e-02 4.00e+02 ... (remaining 1683 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2263 2.77 - 3.30: 8621 3.30 - 3.84: 16495 3.84 - 4.37: 20343 4.37 - 4.90: 34821 Nonbonded interactions: 82543 Sorted by model distance: nonbonded pdb=" OD2 ASP E 325 " pdb=" OG1 THR E 353 " model vdw 2.240 2.440 nonbonded pdb=" OD2 ASP A 325 " pdb=" OG1 THR A 353 " model vdw 2.267 2.440 nonbonded pdb=" OD1 ASP A 325 " pdb=" OG SER A 348 " model vdw 2.279 2.440 nonbonded pdb=" O THR A 124 " pdb=" OG SER A 128 " model vdw 2.285 2.440 nonbonded pdb=" O THR E 124 " pdb=" OG SER E 128 " model vdw 2.286 2.440 ... (remaining 82538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.300 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 29.010 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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:10.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 10083 Z= 0.488 Angle : 0.969 7.965 13707 Z= 0.544 Chirality : 0.053 0.212 1662 Planarity : 0.008 0.066 1686 Dihedral : 14.756 78.745 3588 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.23 % Favored : 96.54 % Rotamer: Outliers : 8.02 % Allowed : 5.41 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.67 (0.14), residues: 1299 helix: -4.31 (0.07), residues: 861 sheet: -1.54 (0.48), residues: 99 loop : -1.97 (0.24), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 212 HIS 0.003 0.001 HIS E 291 PHE 0.016 0.003 PHE E 296 TYR 0.016 0.002 TYR E 344 ARG 0.002 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 223 time to evaluate : 1.081 Fit side-chains REVERT: A 10 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6766 (t0) REVERT: A 70 MET cc_start: 0.8566 (ptm) cc_final: 0.8129 (ptt) REVERT: A 133 GLU cc_start: 0.8460 (mp0) cc_final: 0.8259 (mp0) REVERT: A 161 LYS cc_start: 0.7767 (mtmt) cc_final: 0.7334 (mmtm) REVERT: D 40 LYS cc_start: 0.8630 (ttmm) cc_final: 0.8359 (ttpm) REVERT: D 50 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: D 78 ARG cc_start: 0.7830 (mtp180) cc_final: 0.7522 (mtp85) REVERT: C 70 MET cc_start: 0.8490 (ptm) cc_final: 0.8056 (ptp) REVERT: C 133 GLU cc_start: 0.8481 (mp0) cc_final: 0.8105 (mp0) REVERT: C 300 MET cc_start: 0.8911 (mmm) cc_final: 0.8689 (mmm) REVERT: C 323 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8634 (p) REVERT: F 40 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8380 (ttpm) REVERT: F 43 ARG cc_start: 0.8478 (mtt90) cc_final: 0.8139 (mtt180) REVERT: F 50 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: F 78 ARG cc_start: 0.7806 (mtp180) cc_final: 0.7603 (mtp85) REVERT: E 10 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6897 (t0) REVERT: E 70 MET cc_start: 0.8456 (ptm) cc_final: 0.7986 (ptt) REVERT: E 133 GLU cc_start: 0.8255 (mp0) cc_final: 0.7893 (mp0) REVERT: E 161 LYS cc_start: 0.7682 (mtmt) cc_final: 0.7430 (mptt) REVERT: E 300 MET cc_start: 0.8965 (mmm) cc_final: 0.8585 (mmm) REVERT: B 40 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8500 (tttm) REVERT: B 78 ARG cc_start: 0.7829 (mtp180) cc_final: 0.7508 (mtp180) outliers start: 83 outliers final: 14 residues processed: 275 average time/residue: 1.4395 time to fit residues: 419.5056 Evaluate side-chains 198 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 179 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 94 CYS Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 348 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 101 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 156 ASN A 291 HIS A 303 HIS D 36 ASN C 14 GLN C 156 ASN C 291 HIS C 303 HIS E 14 GLN E 97 ASN E 156 ASN E 291 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10083 Z= 0.189 Angle : 0.645 7.111 13707 Z= 0.322 Chirality : 0.042 0.135 1662 Planarity : 0.006 0.041 1686 Dihedral : 7.568 62.929 1444 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.67 % Allowed : 14.40 % Favored : 81.93 % 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: -2.55 (0.19), residues: 1299 helix: -1.70 (0.15), residues: 843 sheet: -0.85 (0.47), residues: 99 loop : -1.33 (0.26), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 212 HIS 0.001 0.001 HIS C 303 PHE 0.012 0.001 PHE B 62 TYR 0.014 0.001 TYR A 344 ARG 0.002 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 192 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 10 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6814 (t70) REVERT: A 161 LYS cc_start: 0.7541 (mtmt) cc_final: 0.6973 (mmtm) REVERT: D 40 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8347 (ttpm) REVERT: D 45 VAL cc_start: 0.9303 (OUTLIER) cc_final: 0.9054 (t) REVERT: D 63 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7628 (mt-10) REVERT: D 78 ARG cc_start: 0.7656 (mtp180) cc_final: 0.7346 (mtp85) REVERT: C 40 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6830 (pp20) REVERT: C 129 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8040 (mttp) REVERT: F 50 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8033 (pt0) REVERT: F 67 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: F 78 ARG cc_start: 0.7720 (mtp180) cc_final: 0.7474 (mtp85) REVERT: E 10 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.7011 (t0) REVERT: E 70 MET cc_start: 0.8451 (ptm) cc_final: 0.7878 (ptt) REVERT: E 300 MET cc_start: 0.8972 (mmm) cc_final: 0.8659 (mmm) REVERT: B 40 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8472 (mptt) REVERT: B 78 ARG cc_start: 0.7624 (mtp180) cc_final: 0.7306 (mtp180) outliers start: 38 outliers final: 9 residues processed: 210 average time/residue: 1.6577 time to fit residues: 366.7601 Evaluate side-chains 190 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain F residue 22 LYS Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 323 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN B 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10083 Z= 0.299 Angle : 0.664 6.964 13707 Z= 0.329 Chirality : 0.044 0.142 1662 Planarity : 0.005 0.038 1686 Dihedral : 7.099 80.941 1428 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.64 % Allowed : 14.69 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.22), residues: 1299 helix: -0.32 (0.17), residues: 852 sheet: -0.53 (0.48), residues: 99 loop : -1.04 (0.28), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 267 HIS 0.003 0.001 HIS C 291 PHE 0.014 0.002 PHE C 246 TYR 0.015 0.002 TYR E 140 ARG 0.002 0.000 ARG D 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 184 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 161 LYS cc_start: 0.7319 (mtmt) cc_final: 0.6882 (mmtm) REVERT: A 210 LYS cc_start: 0.8068 (mmmt) cc_final: 0.7700 (mmmt) REVERT: A 224 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8471 (tt) REVERT: D 40 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8335 (ttpm) REVERT: D 78 ARG cc_start: 0.7657 (mtp180) cc_final: 0.7371 (mtp85) REVERT: C 40 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: C 367 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9071 (tt) REVERT: F 67 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: F 78 ARG cc_start: 0.7750 (mtp180) cc_final: 0.7473 (mtp85) REVERT: E 300 MET cc_start: 0.9010 (mmm) cc_final: 0.8678 (mmm) REVERT: B 35 MET cc_start: 0.8319 (mtm) cc_final: 0.8007 (mtm) REVERT: B 40 LYS cc_start: 0.8663 (ttmm) cc_final: 0.8434 (mptt) outliers start: 48 outliers final: 20 residues processed: 211 average time/residue: 1.6009 time to fit residues: 356.0500 Evaluate side-chains 208 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 85 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 4.9990 chunk 88 optimal weight: 0.1980 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 0.0070 chunk 56 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN B 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10083 Z= 0.165 Angle : 0.594 6.525 13707 Z= 0.289 Chirality : 0.041 0.133 1662 Planarity : 0.004 0.035 1686 Dihedral : 6.010 55.621 1421 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.90 % Allowed : 16.52 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.23), residues: 1299 helix: 0.44 (0.18), residues: 840 sheet: -0.26 (0.49), residues: 99 loop : -0.68 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 267 HIS 0.001 0.000 HIS C 291 PHE 0.013 0.001 PHE B 62 TYR 0.015 0.001 TYR E 344 ARG 0.002 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 186 time to evaluate : 1.167 Fit side-chains revert: symmetry clash REVERT: A 161 LYS cc_start: 0.7252 (mtmt) cc_final: 0.6840 (mmtm) REVERT: A 224 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8491 (tt) REVERT: D 40 LYS cc_start: 0.8590 (ttmm) cc_final: 0.8340 (ttpm) REVERT: D 67 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: F 78 ARG cc_start: 0.7652 (mtp180) cc_final: 0.7309 (mtp85) REVERT: E 300 MET cc_start: 0.8961 (mmm) cc_final: 0.8595 (mmm) outliers start: 30 outliers final: 13 residues processed: 201 average time/residue: 1.6198 time to fit residues: 343.0183 Evaluate side-chains 195 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 180 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 85 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 0.0040 chunk 1 optimal weight: 5.9990 chunk 92 optimal weight: 0.0270 chunk 51 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 0.4650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN B 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10083 Z= 0.152 Angle : 0.580 6.240 13707 Z= 0.279 Chirality : 0.041 0.132 1662 Planarity : 0.004 0.034 1686 Dihedral : 5.684 55.374 1420 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.90 % Allowed : 17.39 % Favored : 79.71 % 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: 0.44 (0.23), residues: 1299 helix: 0.70 (0.18), residues: 858 sheet: -0.10 (0.49), residues: 99 loop : -0.35 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 267 HIS 0.001 0.000 HIS C 291 PHE 0.012 0.001 PHE B 62 TYR 0.015 0.001 TYR E 344 ARG 0.002 0.000 ARG E 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 182 time to evaluate : 1.161 Fit side-chains REVERT: A 161 LYS cc_start: 0.7228 (mtmt) cc_final: 0.6814 (mmtm) REVERT: A 224 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8473 (tt) REVERT: D 40 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8350 (ttpm) REVERT: D 67 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7474 (mt-10) REVERT: E 300 MET cc_start: 0.8953 (mmm) cc_final: 0.8638 (mmm) REVERT: B 14 LYS cc_start: 0.8770 (tttt) cc_final: 0.8561 (tttt) outliers start: 30 outliers final: 9 residues processed: 201 average time/residue: 1.6057 time to fit residues: 340.5919 Evaluate side-chains 189 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 178 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain B residue 48 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN B 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10083 Z= 0.237 Angle : 0.624 7.008 13707 Z= 0.304 Chirality : 0.043 0.141 1662 Planarity : 0.004 0.037 1686 Dihedral : 5.911 55.862 1419 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.90 % Allowed : 17.87 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.23), residues: 1299 helix: 0.77 (0.18), residues: 855 sheet: -0.11 (0.50), residues: 99 loop : -0.35 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 267 HIS 0.002 0.000 HIS C 291 PHE 0.013 0.001 PHE C 246 TYR 0.014 0.001 TYR E 140 ARG 0.002 0.000 ARG E 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 161 LYS cc_start: 0.7273 (mtmt) cc_final: 0.6850 (mmtm) REVERT: A 224 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8470 (tt) REVERT: D 40 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8334 (ttpm) REVERT: D 67 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: C 367 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9084 (tt) REVERT: E 300 MET cc_start: 0.8983 (mmm) cc_final: 0.8712 (mmm) outliers start: 30 outliers final: 12 residues processed: 201 average time/residue: 1.5789 time to fit residues: 334.8547 Evaluate side-chains 194 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN B 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10083 Z= 0.189 Angle : 0.601 6.965 13707 Z= 0.289 Chirality : 0.042 0.137 1662 Planarity : 0.004 0.035 1686 Dihedral : 5.814 55.808 1419 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.93 % Allowed : 19.23 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1299 helix: 0.92 (0.19), residues: 846 sheet: -0.05 (0.50), residues: 99 loop : -0.20 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 267 HIS 0.001 0.000 HIS C 291 PHE 0.012 0.001 PHE B 62 TYR 0.014 0.001 TYR A 344 ARG 0.001 0.000 ARG E 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 161 LYS cc_start: 0.7262 (mtmt) cc_final: 0.6839 (mmtm) REVERT: A 224 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8517 (tt) REVERT: D 40 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8344 (ttpm) REVERT: D 67 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: E 300 MET cc_start: 0.8980 (mmm) cc_final: 0.8626 (mmm) outliers start: 20 outliers final: 10 residues processed: 194 average time/residue: 1.6705 time to fit residues: 341.4258 Evaluate side-chains 191 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 179 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10083 Z= 0.188 Angle : 0.604 7.361 13707 Z= 0.290 Chirality : 0.042 0.137 1662 Planarity : 0.004 0.035 1686 Dihedral : 5.783 55.769 1419 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.71 % Allowed : 18.74 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.24), residues: 1299 helix: 0.97 (0.19), residues: 846 sheet: -0.07 (0.50), residues: 99 loop : -0.15 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 267 HIS 0.001 0.000 HIS C 291 PHE 0.012 0.001 PHE B 62 TYR 0.014 0.001 TYR A 344 ARG 0.001 0.000 ARG D 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 176 time to evaluate : 1.184 Fit side-chains REVERT: A 40 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7076 (pp20) REVERT: A 161 LYS cc_start: 0.7240 (mtmt) cc_final: 0.6862 (mmtm) REVERT: A 224 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8490 (tt) REVERT: A 259 MET cc_start: 0.8847 (mmp) cc_final: 0.8553 (mmm) REVERT: D 40 LYS cc_start: 0.8610 (ttmm) cc_final: 0.8344 (ttpm) REVERT: D 67 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: E 300 MET cc_start: 0.8981 (mmm) cc_final: 0.8631 (mmm) outliers start: 28 outliers final: 15 residues processed: 195 average time/residue: 1.6274 time to fit residues: 334.3379 Evaluate side-chains 195 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN C 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10083 Z= 0.194 Angle : 0.609 6.710 13707 Z= 0.292 Chirality : 0.042 0.138 1662 Planarity : 0.004 0.036 1686 Dihedral : 5.788 55.781 1419 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.80 % Allowed : 18.36 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.24), residues: 1299 helix: 0.98 (0.19), residues: 846 sheet: -0.08 (0.50), residues: 99 loop : -0.12 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 267 HIS 0.001 0.000 HIS C 291 PHE 0.012 0.001 PHE B 62 TYR 0.014 0.001 TYR A 344 ARG 0.001 0.000 ARG D 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 1.090 Fit side-chains REVERT: A 40 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7085 (pp20) REVERT: A 161 LYS cc_start: 0.7236 (mtmt) cc_final: 0.6863 (mmtm) REVERT: A 224 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8497 (tt) REVERT: A 259 MET cc_start: 0.8848 (mmp) cc_final: 0.8579 (mmp) REVERT: D 40 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8344 (ttpm) REVERT: D 67 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: E 300 MET cc_start: 0.8980 (mmm) cc_final: 0.8632 (mmm) outliers start: 29 outliers final: 17 residues processed: 202 average time/residue: 1.6282 time to fit residues: 346.4481 Evaluate side-chains 200 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN C 97 ASN F 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10083 Z= 0.201 Angle : 0.619 8.914 13707 Z= 0.296 Chirality : 0.042 0.138 1662 Planarity : 0.004 0.036 1686 Dihedral : 5.824 55.790 1419 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.84 % Allowed : 19.23 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.24), residues: 1299 helix: 0.95 (0.19), residues: 849 sheet: -0.08 (0.50), residues: 99 loop : -0.04 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 267 HIS 0.001 0.000 HIS C 291 PHE 0.013 0.001 PHE C 246 TYR 0.014 0.001 TYR A 344 ARG 0.001 0.000 ARG D 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 180 time to evaluate : 1.144 Fit side-chains REVERT: A 161 LYS cc_start: 0.7240 (mtmt) cc_final: 0.6854 (mmtm) REVERT: A 224 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8469 (tt) REVERT: A 259 MET cc_start: 0.8862 (mmp) cc_final: 0.8620 (mmp) REVERT: D 40 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8343 (ttpm) REVERT: D 67 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7500 (mt-10) REVERT: E 300 MET cc_start: 0.8990 (mmm) cc_final: 0.8644 (mmm) outliers start: 19 outliers final: 15 residues processed: 194 average time/residue: 1.6482 time to fit residues: 336.7256 Evaluate side-chains 197 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain B residue 48 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 chunk 102 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN C 97 ASN F 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.090235 restraints weight = 12118.879| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.75 r_work: 0.2832 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10083 Z= 0.160 Angle : 0.596 8.424 13707 Z= 0.283 Chirality : 0.041 0.132 1662 Planarity : 0.004 0.035 1686 Dihedral : 5.666 55.646 1419 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.74 % Allowed : 19.13 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.24), residues: 1299 helix: 0.99 (0.19), residues: 858 sheet: -0.03 (0.50), residues: 99 loop : -0.08 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 267 HIS 0.001 0.000 HIS B 102 PHE 0.013 0.001 PHE B 62 TYR 0.016 0.001 TYR E 344 ARG 0.001 0.000 ARG D 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5172.42 seconds wall clock time: 92 minutes 0.12 seconds (5520.12 seconds total)