Starting phenix.real_space_refine (version: dev) on Tue Dec 13 12:27:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/12_2022/5xlo_6729_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/12_2022/5xlo_6729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/12_2022/5xlo_6729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/12_2022/5xlo_6729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/12_2022/5xlo_6729_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/12_2022/5xlo_6729_neut.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D ARG 218": "NH1" <-> "NH2" Residue "D TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 218": "NH1" <-> "NH2" Residue "E TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 161": "NH1" <-> "NH2" Residue "F ARG 218": "NH1" <-> "NH2" Residue "F TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 75": "NH1" <-> "NH2" Residue "M ARG 75": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 15413 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2004 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 9, 'TRANS': 277} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'TRP:plan': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 180 Chain: "B" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 195 Chain: "C" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 195 Chain: "D" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 195 Chain: "E" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 195 Chain: "F" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 195 Chain: "K" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 809 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 17, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 29, 'rna3p': 8} Chain: "N" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 615 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 620 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Time building chain proxies: 8.98, per 1000 atoms: 0.58 Number of scatterers: 15413 At special positions: 0 Unit cell: (126.1, 143, 113.1, 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 18 16.00 P 38 15.00 O 3212 8.00 N 2690 7.00 C 9455 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.77 Conformation dependent library (CDL) restraints added in 2.7 seconds 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3830 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 21 sheets defined 30.1% alpha, 7.9% beta 0 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 121 through 138 Processing helix chain 'A' and resid 141 through 151 Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.719A pdb=" N GLU A 191 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 214 removed outlier: 3.683A pdb=" N VAL A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 275 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 293 through 297 removed outlier: 4.232A pdb=" N GLN A 297 " --> pdb=" O ALA A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.528A pdb=" N GLU A 316 " --> pdb=" O LEU A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 317 through 325 removed outlier: 5.201A pdb=" N GLN A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 340 removed outlier: 4.602A pdb=" N GLY A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 83 removed outlier: 4.039A pdb=" N GLN B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 78 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 138 Processing helix chain 'B' and resid 141 through 151 Processing helix chain 'B' and resid 187 through 191 removed outlier: 3.719A pdb=" N GLU B 191 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 214 removed outlier: 3.682A pdb=" N VAL B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 275 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 293 through 297 removed outlier: 4.232A pdb=" N GLN B 297 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 316 removed outlier: 3.528A pdb=" N GLU B 316 " --> pdb=" O LEU B 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 313 through 316' Processing helix chain 'B' and resid 317 through 325 removed outlier: 5.201A pdb=" N GLN B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 340 removed outlier: 4.602A pdb=" N GLY B 337 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU B 338 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 83 removed outlier: 4.166A pdb=" N VAL C 79 " --> pdb=" O ASN C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 138 Processing helix chain 'C' and resid 141 through 151 Processing helix chain 'C' and resid 187 through 191 removed outlier: 3.719A pdb=" N GLU C 191 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 214 removed outlier: 3.683A pdb=" N VAL C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 275 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 293 through 297 removed outlier: 4.231A pdb=" N GLN C 297 " --> pdb=" O ALA C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 316 removed outlier: 3.529A pdb=" N GLU C 316 " --> pdb=" O LEU C 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 313 through 316' Processing helix chain 'C' and resid 317 through 325 removed outlier: 5.201A pdb=" N GLN C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 340 removed outlier: 4.602A pdb=" N GLY C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU C 338 " --> pdb=" O GLY C 334 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU C 340 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 83 removed outlier: 4.420A pdb=" N THR D 78 " --> pdb=" O PRO D 74 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL D 79 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 138 Processing helix chain 'D' and resid 141 through 151 Processing helix chain 'D' and resid 187 through 191 removed outlier: 3.719A pdb=" N GLU D 191 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 214 removed outlier: 3.683A pdb=" N VAL D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 275 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 293 through 297 removed outlier: 4.232A pdb=" N GLN D 297 " --> pdb=" O ALA D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 316 removed outlier: 3.528A pdb=" N GLU D 316 " --> pdb=" O LEU D 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 313 through 316' Processing helix chain 'D' and resid 317 through 325 removed outlier: 5.200A pdb=" N GLN D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 340 removed outlier: 4.602A pdb=" N GLY D 337 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU D 338 " --> pdb=" O GLY D 334 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU D 340 " --> pdb=" O PHE D 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 81 removed outlier: 3.938A pdb=" N VAL E 79 " --> pdb=" O ASN E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 138 Processing helix chain 'E' and resid 141 through 151 Processing helix chain 'E' and resid 187 through 191 removed outlier: 3.720A pdb=" N GLU E 191 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 214 removed outlier: 3.683A pdb=" N VAL E 214 " --> pdb=" O LEU E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 275 Proline residue: E 272 - end of helix Processing helix chain 'E' and resid 293 through 297 removed outlier: 4.232A pdb=" N GLN E 297 " --> pdb=" O ALA E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 316 removed outlier: 3.527A pdb=" N GLU E 316 " --> pdb=" O LEU E 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 313 through 316' Processing helix chain 'E' and resid 317 through 325 removed outlier: 5.200A pdb=" N GLN E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 340 removed outlier: 4.602A pdb=" N GLY E 337 " --> pdb=" O GLY E 333 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU E 338 " --> pdb=" O GLY E 334 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU E 340 " --> pdb=" O PHE E 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 83 removed outlier: 4.524A pdb=" N VAL F 79 " --> pdb=" O ASN F 75 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN F 83 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 138 Processing helix chain 'F' and resid 141 through 151 Processing helix chain 'F' and resid 187 through 191 removed outlier: 3.720A pdb=" N GLU F 191 " --> pdb=" O ALA F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 214 removed outlier: 3.682A pdb=" N VAL F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 275 Proline residue: F 272 - end of helix Processing helix chain 'F' and resid 293 through 297 removed outlier: 4.232A pdb=" N GLN F 297 " --> pdb=" O ALA F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 316 removed outlier: 3.528A pdb=" N GLU F 316 " --> pdb=" O LEU F 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 313 through 316' Processing helix chain 'F' and resid 317 through 325 removed outlier: 5.200A pdb=" N GLN F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 340 removed outlier: 4.602A pdb=" N GLY F 337 " --> pdb=" O GLY F 333 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU F 338 " --> pdb=" O GLY F 334 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU F 340 " --> pdb=" O PHE F 336 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 56 removed outlier: 3.799A pdb=" N SER N 52 " --> pdb=" O GLU N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 74 removed outlier: 3.867A pdb=" N ILE N 65 " --> pdb=" O GLY N 61 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG N 74 " --> pdb=" O ASN N 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 56 removed outlier: 3.800A pdb=" N SER M 52 " --> pdb=" O GLU M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 74 removed outlier: 3.867A pdb=" N ILE M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG M 74 " --> pdb=" O ASN M 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 removed outlier: 4.056A pdb=" N ALA A 23 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 108 Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 23 removed outlier: 4.056A pdb=" N ALA B 23 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 60 removed outlier: 8.199A pdb=" N ALA B 252 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ALA B 88 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA B 254 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 108 Processing sheet with id=AA6, first strand: chain 'C' and resid 22 through 23 removed outlier: 4.055A pdb=" N ALA C 23 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 59 Processing sheet with id=AA8, first strand: chain 'C' and resid 104 through 108 Processing sheet with id=AA9, first strand: chain 'D' and resid 22 through 23 removed outlier: 4.057A pdb=" N ALA D 23 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 57 through 58 Processing sheet with id=AB2, first strand: chain 'D' and resid 104 through 108 Processing sheet with id=AB3, first strand: chain 'E' and resid 22 through 23 removed outlier: 4.055A pdb=" N ALA E 23 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 57 through 59 Processing sheet with id=AB5, first strand: chain 'E' and resid 104 through 108 Processing sheet with id=AB6, first strand: chain 'F' and resid 22 through 23 removed outlier: 4.056A pdb=" N ALA F 23 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 57 through 58 Processing sheet with id=AB8, first strand: chain 'F' and resid 104 through 108 Processing sheet with id=AB9, first strand: chain 'N' and resid 15 through 16 Processing sheet with id=AC1, first strand: chain 'N' and resid 19 through 21 Processing sheet with id=AC2, first strand: chain 'M' and resid 15 through 16 Processing sheet with id=AC3, first strand: chain 'M' and resid 19 through 21 415 hydrogen bonds defined for protein. 1161 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 4.28 Time building geometry restraints manager: 6.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4069 1.33 - 1.45: 2822 1.45 - 1.57: 8714 1.57 - 1.69: 75 1.69 - 1.81: 30 Bond restraints: 15710 Sorted by residual: bond pdb=" CB GLN A 37 " pdb=" CG GLN A 37 " ideal model delta sigma weight residual 1.520 1.436 0.084 3.00e-02 1.11e+03 7.85e+00 bond pdb=" CB GLN F 37 " pdb=" CG GLN F 37 " ideal model delta sigma weight residual 1.520 1.437 0.083 3.00e-02 1.11e+03 7.71e+00 bond pdb=" CB GLN C 37 " pdb=" CG GLN C 37 " ideal model delta sigma weight residual 1.520 1.437 0.083 3.00e-02 1.11e+03 7.68e+00 bond pdb=" CB GLN B 37 " pdb=" CG GLN B 37 " ideal model delta sigma weight residual 1.520 1.437 0.083 3.00e-02 1.11e+03 7.66e+00 bond pdb=" CB GLN D 37 " pdb=" CG GLN D 37 " ideal model delta sigma weight residual 1.520 1.437 0.083 3.00e-02 1.11e+03 7.64e+00 ... (remaining 15705 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.68: 735 106.68 - 113.71: 8669 113.71 - 120.74: 6633 120.74 - 127.77: 5387 127.77 - 134.81: 203 Bond angle restraints: 21627 Sorted by residual: angle pdb=" C4' A K 4 " pdb=" C3' A K 4 " pdb=" O3' A K 4 " ideal model delta sigma weight residual 109.40 117.56 -8.16 1.50e+00 4.44e-01 2.96e+01 angle pdb=" N GLY M 40 " pdb=" CA GLY M 40 " pdb=" C GLY M 40 " ideal model delta sigma weight residual 111.36 117.52 -6.16 1.17e+00 7.31e-01 2.77e+01 angle pdb=" N GLY N 40 " pdb=" CA GLY N 40 " pdb=" C GLY N 40 " ideal model delta sigma weight residual 111.36 117.51 -6.15 1.17e+00 7.31e-01 2.76e+01 angle pdb=" C HIS N 11 " pdb=" N LEU N 12 " pdb=" CA LEU N 12 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.59e+01 angle pdb=" C HIS M 11 " pdb=" N LEU M 12 " pdb=" CA LEU M 12 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.59e+01 ... (remaining 21622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.17: 9162 34.17 - 68.34: 111 68.34 - 102.51: 22 102.51 - 136.67: 3 136.67 - 170.84: 5 Dihedral angle restraints: 9303 sinusoidal: 3371 harmonic: 5932 Sorted by residual: dihedral pdb=" CA ALA M 10 " pdb=" C ALA M 10 " pdb=" N HIS M 11 " pdb=" CA HIS M 11 " ideal model delta harmonic sigma weight residual 180.00 45.61 134.39 0 5.00e+00 4.00e-02 7.22e+02 dihedral pdb=" CA ALA N 10 " pdb=" C ALA N 10 " pdb=" N HIS N 11 " pdb=" CA HIS N 11 " ideal model delta harmonic sigma weight residual 180.00 45.65 134.35 0 5.00e+00 4.00e-02 7.22e+02 dihedral pdb=" CA HIS M 11 " pdb=" C HIS M 11 " pdb=" N LEU M 12 " pdb=" CA LEU M 12 " ideal model delta harmonic sigma weight residual -180.00 -124.51 -55.49 0 5.00e+00 4.00e-02 1.23e+02 ... (remaining 9300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2247 0.086 - 0.172: 330 0.172 - 0.258: 28 0.258 - 0.344: 8 0.344 - 0.430: 2 Chirality restraints: 2615 Sorted by residual: chirality pdb=" C3' A K 4 " pdb=" C4' A K 4 " pdb=" O3' A K 4 " pdb=" C2' A K 4 " both_signs ideal model delta sigma weight residual False -2.74 -2.31 -0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" C3' G K 9 " pdb=" C4' G K 9 " pdb=" O3' G K 9 " pdb=" C2' G K 9 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" C3' A K 28 " pdb=" C4' A K 28 " pdb=" O3' A K 28 " pdb=" C2' A K 28 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 2612 not shown) Planarity restraints: 2759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS N 11 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C HIS N 11 " -0.052 2.00e-02 2.50e+03 pdb=" O HIS N 11 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU N 12 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS M 11 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.90e+00 pdb=" C HIS M 11 " -0.052 2.00e-02 2.50e+03 pdb=" O HIS M 11 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU M 12 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 317 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO F 318 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO F 318 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 318 " -0.038 5.00e-02 4.00e+02 ... (remaining 2756 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 268 2.62 - 3.19: 13712 3.19 - 3.76: 22598 3.76 - 4.33: 31434 4.33 - 4.90: 49707 Nonbonded interactions: 117719 Sorted by model distance: nonbonded pdb=" NZ LYS E 244 " pdb=" O SER F 248 " model vdw 2.050 2.520 nonbonded pdb=" N LYS C 60 " pdb=" OP2 U K 25 " model vdw 2.156 2.520 nonbonded pdb=" OD1 ASP F 80 " pdb=" OH TYR N 6 " model vdw 2.180 2.440 nonbonded pdb=" OG1 THR C 90 " pdb=" O ALA C 254 " model vdw 2.230 2.440 nonbonded pdb=" NZ LYS A 293 " pdb=" OP1 C K 30 " model vdw 2.233 2.520 ... (remaining 117714 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 'B' and (resid 15 through 53 or resid 93 through 340)) selection = (chain 'C' and (resid 15 through 53 or resid 93 through 340)) selection = (chain 'D' and (resid 15 through 53 or resid 93 through 340)) selection = (chain 'E' and (resid 15 through 53 or resid 93 through 340)) selection = (chain 'F' and (resid 15 through 53 or resid 93 through 340)) } ncs_group { reference = (chain 'M' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 78)) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 38 5.49 5 S 18 5.16 5 C 9455 2.51 5 N 2690 2.21 5 O 3212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.890 Check model and map are aligned: 0.220 Convert atoms to be neutral: 0.120 Process input model: 45.060 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 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 : 0.009 0.106 15710 Z= 0.618 Angle : 1.367 14.376 21627 Z= 0.701 Chirality : 0.064 0.430 2615 Planarity : 0.008 0.065 2759 Dihedral : 14.035 170.842 5473 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.78 % Allowed : 17.27 % Favored : 81.95 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.41 % 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: -6.02 (0.12), residues: 2055 helix: -4.14 (0.10), residues: 442 sheet: -3.84 (0.21), residues: 320 loop : -4.22 (0.12), residues: 1293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 452 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 454 average time/residue: 0.2786 time to fit residues: 180.3452 Evaluate side-chains 340 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 1.735 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 160 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 97 optimal weight: 0.0060 chunk 119 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN A 256 HIS B 83 ASN B 163 ASN B 310 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN E 72 GLN E 110 ASN E 323 GLN ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN F 258 GLN M 49 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 15710 Z= 0.212 Angle : 0.822 15.336 21627 Z= 0.419 Chirality : 0.043 0.278 2615 Planarity : 0.006 0.093 2759 Dihedral : 15.044 171.381 2626 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.97 % Favored : 87.49 % Rotamer Outliers : 3.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.14), residues: 2055 helix: -2.32 (0.20), residues: 462 sheet: -3.28 (0.24), residues: 292 loop : -3.80 (0.13), residues: 1301 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 368 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 21 residues processed: 397 average time/residue: 0.2860 time to fit residues: 162.7882 Evaluate side-chains 340 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 319 time to evaluate : 1.561 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1277 time to fit residues: 7.1543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 186 optimal weight: 0.0670 chunk 201 optimal weight: 0.7980 chunk 166 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 310 ASN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 GLN ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 GLN ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 49 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 15710 Z= 0.359 Angle : 0.890 11.810 21627 Z= 0.455 Chirality : 0.046 0.271 2615 Planarity : 0.006 0.079 2759 Dihedral : 15.096 173.342 2626 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.54 % Allowed : 17.18 % Favored : 82.29 % Rotamer Outliers : 5.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.68 (0.15), residues: 2055 helix: -2.02 (0.22), residues: 455 sheet: -3.31 (0.24), residues: 292 loop : -3.70 (0.14), residues: 1308 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 358 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 30 residues processed: 395 average time/residue: 0.2804 time to fit residues: 159.5740 Evaluate side-chains 358 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 328 time to evaluate : 1.659 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1488 time to fit residues: 10.3554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 198 optimal weight: 6.9990 chunk 97 optimal weight: 0.0010 chunk 177 optimal weight: 0.1980 chunk 53 optimal weight: 0.8980 overall best weight: 1.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 310 ASN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 GLN E 256 HIS E 324 HIS F 72 GLN F 151 ASN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 322 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 15710 Z= 0.272 Angle : 0.806 10.472 21627 Z= 0.411 Chirality : 0.044 0.272 2615 Planarity : 0.006 0.069 2759 Dihedral : 14.778 171.698 2626 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.54 % Allowed : 14.31 % Favored : 85.16 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.16), residues: 2055 helix: -1.69 (0.23), residues: 467 sheet: -3.35 (0.25), residues: 306 loop : -3.58 (0.14), residues: 1282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 330 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 21 residues processed: 350 average time/residue: 0.2819 time to fit residues: 142.5717 Evaluate side-chains 326 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 305 time to evaluate : 1.574 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1373 time to fit residues: 7.4037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 169 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 101 optimal weight: 0.8980 chunk 177 optimal weight: 0.0670 chunk 50 optimal weight: 9.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 310 ASN B 324 HIS ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 ASN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 322 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 15710 Z= 0.264 Angle : 0.797 10.484 21627 Z= 0.403 Chirality : 0.044 0.294 2615 Planarity : 0.006 0.075 2759 Dihedral : 14.677 171.805 2626 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.44 % Allowed : 16.01 % Favored : 83.55 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.16), residues: 2055 helix: -1.44 (0.24), residues: 467 sheet: -3.17 (0.26), residues: 301 loop : -3.55 (0.15), residues: 1287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 316 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 20 residues processed: 332 average time/residue: 0.2789 time to fit residues: 132.1574 Evaluate side-chains 317 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 297 time to evaluate : 1.521 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1522 time to fit residues: 7.2739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 310 ASN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN F 72 GLN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 15710 Z= 0.208 Angle : 0.749 8.155 21627 Z= 0.382 Chirality : 0.042 0.324 2615 Planarity : 0.005 0.074 2759 Dihedral : 14.414 171.335 2626 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.87 % Favored : 85.74 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.16), residues: 2055 helix: -1.17 (0.24), residues: 467 sheet: -3.24 (0.27), residues: 246 loop : -3.43 (0.14), residues: 1342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 303 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 319 average time/residue: 0.2915 time to fit residues: 133.6579 Evaluate side-chains 303 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 290 time to evaluate : 1.672 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1427 time to fit residues: 5.7591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 166 optimal weight: 0.0070 chunk 110 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.5646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 15710 Z= 0.227 Angle : 0.754 13.898 21627 Z= 0.382 Chirality : 0.043 0.350 2615 Planarity : 0.005 0.079 2759 Dihedral : 14.341 171.450 2626 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.29 % Allowed : 15.23 % Favored : 84.48 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.16), residues: 2055 helix: -1.12 (0.24), residues: 467 sheet: -3.25 (0.26), residues: 266 loop : -3.38 (0.15), residues: 1322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 303 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 13 residues processed: 318 average time/residue: 0.2994 time to fit residues: 136.9823 Evaluate side-chains 305 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 292 time to evaluate : 1.652 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1575 time to fit residues: 5.8268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 38 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 97 optimal weight: 0.0670 chunk 18 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 overall best weight: 2.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 310 ASN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 GLN D 329 ASN ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 HIS ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.5939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 15710 Z= 0.340 Angle : 0.850 16.525 21627 Z= 0.430 Chirality : 0.045 0.318 2615 Planarity : 0.006 0.083 2759 Dihedral : 14.636 171.995 2626 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 23.48 Ramachandran Plot: Outliers : 0.39 % Allowed : 17.27 % Favored : 82.34 % Rotamer Outliers : 2.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.16), residues: 2055 helix: -1.43 (0.24), residues: 475 sheet: -3.38 (0.24), residues: 296 loop : -3.48 (0.15), residues: 1284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 313 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 327 average time/residue: 0.2995 time to fit residues: 141.9495 Evaluate side-chains 318 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 300 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1404 time to fit residues: 6.7751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 chunk 183 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 HIS B 163 ASN B 310 ASN B 329 ASN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 15710 Z= 0.264 Angle : 0.821 15.618 21627 Z= 0.414 Chirality : 0.044 0.393 2615 Planarity : 0.006 0.086 2759 Dihedral : 14.458 170.554 2626 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.39 % Allowed : 16.01 % Favored : 83.60 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.16), residues: 2055 helix: -1.35 (0.24), residues: 474 sheet: -3.27 (0.26), residues: 266 loop : -3.45 (0.15), residues: 1315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 312 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 318 average time/residue: 0.2864 time to fit residues: 132.0823 Evaluate side-chains 313 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 302 time to evaluate : 1.761 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1682 time to fit residues: 5.4942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 10.0000 chunk 118 optimal weight: 0.0870 chunk 92 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 187 optimal weight: 0.0470 chunk 162 optimal weight: 0.0070 chunk 16 optimal weight: 0.4980 chunk 125 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN B 151 ASN B 163 ASN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN B 329 ASN C 151 ASN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS ** E 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 ASN F 151 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.6491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 15710 Z= 0.183 Angle : 0.765 14.061 21627 Z= 0.386 Chirality : 0.043 0.357 2615 Planarity : 0.005 0.090 2759 Dihedral : 13.936 173.050 2626 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.29 % Allowed : 13.33 % Favored : 86.37 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.17), residues: 2055 helix: -0.86 (0.25), residues: 469 sheet: -3.18 (0.26), residues: 268 loop : -3.32 (0.15), residues: 1318 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 327 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 328 average time/residue: 0.2861 time to fit residues: 135.3695 Evaluate side-chains 297 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 294 time to evaluate : 1.518 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1503 time to fit residues: 2.8751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 162 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN B 151 ASN B 163 ASN ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN B 310 ASN B 329 ASN C 151 ASN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.217794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.200058 restraints weight = 19169.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.199424 restraints weight = 26225.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.200608 restraints weight = 22697.381| |-----------------------------------------------------------------------------| r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 15710 Z= 0.334 Angle : 0.852 14.953 21627 Z= 0.433 Chirality : 0.045 0.365 2615 Planarity : 0.006 0.082 2759 Dihedral : 14.375 172.531 2626 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.44 % Allowed : 16.64 % Favored : 82.92 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.16), residues: 2055 helix: -1.15 (0.24), residues: 465 sheet: -3.24 (0.27), residues: 256 loop : -3.39 (0.14), residues: 1334 =============================================================================== Job complete usr+sys time: 3182.05 seconds wall clock time: 58 minutes 10.07 seconds (3490.07 seconds total)