Starting phenix.real_space_refine (version: dev) on Tue Apr 5 19:29:23 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/04_2022/5xlo_6729_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/04_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_6729/04_2022/5xlo_6729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/04_2022/5xlo_6729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/04_2022/5xlo_6729_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/04_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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'rna3p_pyr': 2, 'rna2p_pur': 13, 'rna3p_pur': 6, 'rna2p_pyr': 17} Link IDs: {'rna3p': 8, 'rna2p': 29} 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: 9.85, per 1000 atoms: 0.64 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: 7.50 Conformation dependent library (CDL) restraints added in 2.8 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: 4.33 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: 4.84 Time building geometry restraints manager: 7.96 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: 0.450 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: 2.800 Check model and map are aligned: 0.240 Convert atoms to be neutral: 0.140 Process input model: 48.600 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.070 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.300 ------------------------------------------------------------------------------- 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 : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 454 average time/residue: 0.3046 time to fit residues: 198.8325 Evaluate side-chains 336 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 2.077 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5016 ------------------------------------------------------------------------------- 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: 8.9990 chunk 62 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6367 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.104 15710 Z= 0.254 Angle : 0.882 16.090 21627 Z= 0.448 Chirality : 0.044 0.280 2615 Planarity : 0.007 0.122 2759 Dihedral : 15.195 171.286 2626 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.49 % Allowed : 12.46 % Favored : 87.06 % Rotamer Outliers : 4.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -4.89 (0.14), residues: 2055 helix: -2.43 (0.19), residues: 462 sheet: -3.27 (0.28), residues: 232 loop : -3.80 (0.13), residues: 1361 *********************** 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 417 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 361 time to evaluate : 1.521 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: 56 outliers final: 23 residues processed: 389 average time/residue: 0.2937 time to fit residues: 163.4479 Evaluate side-chains 336 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 313 time to evaluate : 1.530 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1294 time to fit residues: 7.6598 ------------------------------------------------------------------------------- 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: 8.9990 chunk 57 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 GLN ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.099 15710 Z= 0.317 Angle : 0.880 14.331 21627 Z= 0.448 Chirality : 0.045 0.262 2615 Planarity : 0.006 0.083 2759 Dihedral : 14.941 173.381 2626 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.49 % Allowed : 15.77 % Favored : 83.75 % Rotamer Outliers : 4.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -4.53 (0.15), residues: 2055 helix: -1.80 (0.22), residues: 451 sheet: -3.38 (0.26), residues: 247 loop : -3.62 (0.14), residues: 1357 *********************** 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 393 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 337 time to evaluate : 1.697 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: 56 outliers final: 23 residues processed: 368 average time/residue: 0.2947 time to fit residues: 156.3832 Evaluate side-chains 324 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 301 time to evaluate : 1.789 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1582 time to fit residues: 8.9925 ------------------------------------------------------------------------------- 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: 4.9990 chunk 140 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 198 optimal weight: 0.0570 chunk 97 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 310 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 GLN E 256 HIS E 324 HIS F 72 GLN F 110 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: 0.6458 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.103 15710 Z= 0.269 Angle : 0.893 17.171 21627 Z= 0.455 Chirality : 0.043 0.288 2615 Planarity : 0.006 0.091 2759 Dihedral : 14.591 172.305 2626 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.49 % Allowed : 12.70 % Favored : 86.81 % Rotamer Outliers : 3.68 % 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: -1.45 (0.23), residues: 468 sheet: -3.32 (0.27), residues: 242 loop : -3.54 (0.14), residues: 1345 *********************** 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 372 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 322 time to evaluate : 1.818 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 outliers start: 50 outliers final: 23 residues processed: 348 average time/residue: 0.2889 time to fit residues: 145.8098 Evaluate side-chains 316 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 293 time to evaluate : 1.718 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1379 time to fit residues: 8.2441 ------------------------------------------------------------------------------- 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: 9.9990 chunk 147 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 101 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 310 ASN B 324 HIS ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 GLN ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 GLN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN F 144 ASN F 151 ASN F 241 GLN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 322 GLN M 49 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.112 15710 Z= 0.498 Angle : 1.083 15.680 21627 Z= 0.554 Chirality : 0.049 0.310 2615 Planarity : 0.008 0.123 2759 Dihedral : 15.198 171.813 2626 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 26.69 Ramachandran Plot: Outliers : 0.44 % Allowed : 19.51 % Favored : 80.05 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -4.72 (0.16), residues: 2055 helix: -1.98 (0.22), residues: 474 sheet: -3.53 (0.23), residues: 351 loop : -3.67 (0.15), residues: 1230 *********************** 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 389 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 339 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 30 residues processed: 362 average time/residue: 0.2888 time to fit residues: 157.7719 Evaluate side-chains 326 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 296 time to evaluate : 1.575 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1436 time to fit residues: 10.1214 ------------------------------------------------------------------------------- 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: 6.9990 chunk 178 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 198 optimal weight: 0.1980 chunk 164 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 chunk 16 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 258 GLN B 310 ASN B 329 ASN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS F 241 GLN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 322 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 1.016 15710 Z= 0.933 Angle : 1.479 106.065 21627 Z= 0.649 Chirality : 0.047 0.317 2615 Planarity : 0.009 0.145 2759 Dihedral : 15.132 170.921 2626 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 26.04 Ramachandran Plot: Outliers : 0.54 % Allowed : 17.03 % Favored : 82.43 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -4.65 (0.16), residues: 2055 helix: -1.91 (0.22), residues: 474 sheet: -3.62 (0.25), residues: 261 loop : -3.65 (0.14), residues: 1320 *********************** 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 359 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 320 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 21 residues processed: 339 average time/residue: 0.3030 time to fit residues: 146.8382 Evaluate side-chains 327 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 306 time to evaluate : 1.678 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2022 time to fit residues: 9.1043 ------------------------------------------------------------------------------- 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: 0.5980 chunk 22 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 120 optimal weight: 0.0670 chunk 91 optimal weight: 2.9990 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 310 ASN B 329 ASN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 GLN ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 ASN F 241 GLN F 256 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 1.021 15710 Z= 0.956 Angle : 1.446 106.082 21627 Z= 0.642 Chirality : 0.047 0.346 2615 Planarity : 0.009 0.140 2759 Dihedral : 15.050 170.578 2626 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.54 % Allowed : 17.57 % Favored : 81.90 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -4.62 (0.15), residues: 2055 helix: -1.91 (0.22), residues: 474 sheet: -3.53 (0.26), residues: 241 loop : -3.66 (0.14), residues: 1340 *********************** 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 338 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 301 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 23 residues processed: 314 average time/residue: 0.2937 time to fit residues: 132.7440 Evaluate side-chains 319 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 296 time to evaluate : 1.695 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1664 time to fit residues: 8.9115 ------------------------------------------------------------------------------- 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: 2.9990 chunk 78 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN B 329 ASN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 1.016 15710 Z= 0.990 Angle : 1.380 84.080 21627 Z= 0.675 Chirality : 0.048 0.351 2615 Planarity : 0.009 0.150 2759 Dihedral : 15.042 170.631 2626 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 26.55 Ramachandran Plot: Outliers : 0.49 % Allowed : 17.66 % Favored : 81.85 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -4.62 (0.15), residues: 2055 helix: -1.90 (0.22), residues: 474 sheet: -3.54 (0.26), residues: 236 loop : -3.66 (0.14), residues: 1345 *********************** 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 325 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 303 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 309 average time/residue: 0.3073 time to fit residues: 136.3132 Evaluate side-chains 310 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 295 time to evaluate : 1.580 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1676 time to fit residues: 6.7177 ------------------------------------------------------------------------------- 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: 0.9980 chunk 172 optimal weight: 0.1980 chunk 184 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 174 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN B 329 ASN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.016 1.056 15710 Z= 1.188 Angle : 1.530 93.566 21627 Z= 0.717 Chirality : 0.047 0.363 2615 Planarity : 0.009 0.142 2759 Dihedral : 15.046 170.519 2626 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 26.82 Ramachandran Plot: Outliers : 0.49 % Allowed : 17.18 % Favored : 82.34 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.20 % 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: -4.60 (0.15), residues: 2055 helix: -1.89 (0.22), residues: 474 sheet: -3.53 (0.26), residues: 236 loop : -3.65 (0.14), residues: 1345 *********************** 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 316 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 299 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 305 average time/residue: 0.3007 time to fit residues: 132.1177 Evaluate side-chains 302 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 292 time to evaluate : 1.669 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1659 time to fit residues: 5.2175 ------------------------------------------------------------------------------- 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: 3.9990 chunk 118 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 204 optimal weight: 0.0570 chunk 187 optimal weight: 10.0000 chunk 162 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.020 1.247 15710 Z= 1.409 Angle : 1.676 93.566 21627 Z= 0.847 Chirality : 0.047 0.363 2615 Planarity : 0.011 0.193 2759 Dihedral : 15.046 170.519 2626 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 29.93 Ramachandran Plot: Outliers : 0.49 % Allowed : 17.18 % Favored : 82.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.20 % 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: -4.60 (0.15), residues: 2055 helix: -1.89 (0.22), residues: 474 sheet: -3.53 (0.26), residues: 236 loop : -3.65 (0.14), residues: 1345 ********************** 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 294 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.3330 time to fit residues: 140.7522 Evaluate side-chains 292 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.549 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4152 ------------------------------------------------------------------------------- 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: 6.9990 chunk 49 optimal weight: 0.1980 chunk 149 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 45 optimal weight: 0.5980 chunk 162 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 20 optimal weight: 0.0020 chunk 30 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.215093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.191759 restraints weight = 19248.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.192424 restraints weight = 22239.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.193808 restraints weight = 16877.070| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.020 1.247 15710 Z= 1.408 Angle : 1.675 93.566 21627 Z= 0.847 Chirality : 0.047 0.363 2615 Planarity : 0.011 0.193 2759 Dihedral : 15.046 170.519 2626 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 29.86 Ramachandran Plot: Outliers : 0.49 % Allowed : 17.18 % Favored : 82.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.20 % 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: -4.60 (0.15), residues: 2055 helix: -1.89 (0.22), residues: 474 sheet: -3.53 (0.26), residues: 236 loop : -3.65 (0.14), residues: 1345 =============================================================================== Job complete usr+sys time: 3212.66 seconds wall clock time: 58 minutes 51.72 seconds (3531.72 seconds total)