Starting phenix.real_space_refine on Sun Dec 10 19:39:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/12_2023/5xlo_6729_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/12_2023/5xlo_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_2023/5xlo_6729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/12_2023/5xlo_6729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/12_2023/5xlo_6729_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/12_2023/5xlo_6729_neut.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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-1.21rc1-5172/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: 9.16, per 1000 atoms: 0.59 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: 6.21 Conformation dependent library (CDL) restraints added in 3.1 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: 4.66 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: 4.17 Time building geometry restraints manager: 6.60 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: 9219 34.17 - 68.34: 150 68.34 - 102.51: 32 102.51 - 136.67: 3 136.67 - 170.84: 5 Dihedral angle restraints: 9409 sinusoidal: 3477 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 9406 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 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: 0.490 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: 2.080 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 44.990 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 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 : 15.082 170.842 5579 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 % Allowed : 2.87 % Favored : 96.83 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP F 270 HIS 0.012 0.003 HIS C 208 PHE 0.027 0.004 PHE E 336 TYR 0.020 0.002 TYR M 20 ARG 0.006 0.001 ARG B 172 *********************** 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 : 1.605 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: 0.3069 time to fit residues: 197.0366 Evaluate side-chains 340 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 1.471 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0280 ------------------------------------------------------------------------------- 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: 0.6235 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15710 Z= 0.209 Angle : 0.826 15.341 21627 Z= 0.421 Chirality : 0.044 0.288 2615 Planarity : 0.006 0.086 2759 Dihedral : 16.959 171.041 2732 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.54 % Allowed : 12.21 % Favored : 87.25 % Rotamer: Outliers : 3.83 % Allowed : 11.50 % Favored : 84.67 % 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: 456 sheet: -3.29 (0.24), residues: 292 loop : -3.78 (0.13), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 53 HIS 0.019 0.002 HIS M 11 PHE 0.033 0.002 PHE E 131 TYR 0.017 0.001 TYR E 125 ARG 0.005 0.001 ARG B 265 *********************** 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 423 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 371 time to evaluate : 1.725 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: 52 outliers final: 21 residues processed: 400 average time/residue: 0.3074 time to fit residues: 175.5230 Evaluate side-chains 341 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 320 time to evaluate : 1.572 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1390 time to fit residues: 7.5114 ------------------------------------------------------------------------------- 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: 0.7980 chunk 154 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 186 optimal weight: 0.5980 chunk 201 optimal weight: 0.7980 chunk 166 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 324 HIS ** 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: 0.6456 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15710 Z= 0.282 Angle : 0.822 11.533 21627 Z= 0.420 Chirality : 0.044 0.269 2615 Planarity : 0.006 0.077 2759 Dihedral : 16.827 174.012 2732 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.58 % Allowed : 15.33 % Favored : 84.09 % Rotamer: Outliers : 4.35 % Allowed : 13.26 % Favored : 82.39 % 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: -4.51 (0.15), residues: 2055 helix: -1.81 (0.22), residues: 460 sheet: -3.22 (0.25), residues: 292 loop : -3.61 (0.14), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 270 HIS 0.012 0.001 HIS C 208 PHE 0.035 0.002 PHE E 131 TYR 0.033 0.002 TYR E 125 ARG 0.012 0.001 ARG A 314 *********************** 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 407 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 348 time to evaluate : 1.447 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 outliers start: 59 outliers final: 22 residues processed: 378 average time/residue: 0.3002 time to fit residues: 163.7192 Evaluate side-chains 344 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 322 time to evaluate : 1.593 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1562 time to fit residues: 8.4623 ------------------------------------------------------------------------------- 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: 10.0000 chunk 140 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 20 optimal weight: 0.0050 chunk 89 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 198 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 177 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15710 Z= 0.282 Angle : 0.814 11.357 21627 Z= 0.413 Chirality : 0.044 0.285 2615 Planarity : 0.006 0.068 2759 Dihedral : 16.730 171.911 2732 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.49 % Allowed : 14.40 % Favored : 85.11 % Rotamer: Outliers : 3.54 % Allowed : 15.55 % Favored : 80.91 % Cbeta Deviations : 0.00 % 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: -4.42 (0.16), residues: 2055 helix: -1.62 (0.23), residues: 467 sheet: -3.34 (0.25), residues: 306 loop : -3.54 (0.15), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP C 270 HIS 0.005 0.001 HIS C 208 PHE 0.036 0.002 PHE E 131 TYR 0.022 0.002 TYR E 125 ARG 0.008 0.001 ARG A 314 *********************** 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 377 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 329 time to evaluate : 1.580 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: 48 outliers final: 24 residues processed: 355 average time/residue: 0.3026 time to fit residues: 153.5525 Evaluate side-chains 326 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 302 time to evaluate : 1.771 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1428 time to fit residues: 8.6974 ------------------------------------------------------------------------------- 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: 9.9990 chunk 112 optimal weight: 0.4980 chunk 2 optimal weight: 6.9990 chunk 147 optimal weight: 0.0010 chunk 81 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 101 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 ASN M 49 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15710 Z= 0.210 Angle : 0.751 8.758 21627 Z= 0.382 Chirality : 0.042 0.297 2615 Planarity : 0.005 0.074 2759 Dihedral : 16.484 172.565 2732 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.72 % Favored : 85.84 % Rotamer: Outliers : 2.21 % Allowed : 18.87 % Favored : 78.92 % Cbeta Deviations : 0.00 % 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: -4.08 (0.16), residues: 2055 helix: -1.17 (0.24), residues: 467 sheet: -3.19 (0.25), residues: 306 loop : -3.38 (0.15), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 270 HIS 0.003 0.001 HIS D 208 PHE 0.038 0.002 PHE E 131 TYR 0.029 0.001 TYR E 125 ARG 0.009 0.001 ARG A 314 *********************** 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 347 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 317 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 328 average time/residue: 0.2976 time to fit residues: 140.8847 Evaluate side-chains 308 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 293 time to evaluate : 1.534 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1415 time to fit residues: 6.0618 ------------------------------------------------------------------------------- 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: 0.9980 chunk 178 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 48 optimal weight: 0.2980 chunk 198 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 91 optimal weight: 0.0980 chunk 16 optimal weight: 10.0000 chunk 65 optimal weight: 0.1980 chunk 104 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN C 110 ASN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN F 32 GLN F 72 GLN F 144 ASN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 ASN M 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15710 Z= 0.198 Angle : 0.725 8.011 21627 Z= 0.370 Chirality : 0.042 0.317 2615 Planarity : 0.005 0.077 2759 Dihedral : 16.327 173.183 2732 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.33 % Favored : 86.33 % Rotamer: Outliers : 2.65 % Allowed : 18.57 % Favored : 78.78 % 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: -3.92 (0.17), residues: 2055 helix: -0.87 (0.25), residues: 462 sheet: -3.08 (0.27), residues: 248 loop : -3.38 (0.14), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 270 HIS 0.006 0.001 HIS D 208 PHE 0.039 0.002 PHE E 131 TYR 0.023 0.001 TYR E 125 ARG 0.007 0.001 ARG B 94 *********************** 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 345 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 309 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 328 average time/residue: 0.3063 time to fit residues: 143.8708 Evaluate side-chains 314 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 294 time to evaluate : 1.641 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1915 time to fit residues: 8.4612 ------------------------------------------------------------------------------- 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: 9.9990 chunk 22 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 144 optimal weight: 0.0770 chunk 112 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 110 optimal weight: 0.0470 chunk 197 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- 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 32 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** C 329 ASN ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN F 32 GLN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15710 Z= 0.201 Angle : 0.717 7.942 21627 Z= 0.367 Chirality : 0.042 0.342 2615 Planarity : 0.005 0.078 2759 Dihedral : 16.220 173.015 2732 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.72 % Favored : 85.89 % Rotamer: Outliers : 1.33 % Allowed : 21.00 % Favored : 77.67 % 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: -3.78 (0.17), residues: 2055 helix: -0.75 (0.25), residues: 464 sheet: -3.02 (0.27), residues: 243 loop : -3.28 (0.14), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP B 270 HIS 0.004 0.001 HIS D 208 PHE 0.041 0.002 PHE E 131 TYR 0.023 0.001 TYR E 125 ARG 0.005 0.001 ARG E 56 *********************** 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 322 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 304 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 311 average time/residue: 0.3141 time to fit residues: 138.8954 Evaluate side-chains 294 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 287 time to evaluate : 1.592 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1438 time to fit residues: 4.1506 ------------------------------------------------------------------------------- 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: 0.9990 chunk 78 optimal weight: 20.0000 chunk 118 optimal weight: 0.0870 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- 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 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 GLN ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 15710 Z= 0.287 Angle : 0.796 16.867 21627 Z= 0.403 Chirality : 0.044 0.313 2615 Planarity : 0.006 0.086 2759 Dihedral : 16.360 172.324 2732 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.39 % Allowed : 15.96 % Favored : 83.65 % Rotamer: Outliers : 1.77 % Allowed : 21.52 % Favored : 76.71 % 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: -3.88 (0.16), residues: 2055 helix: -0.92 (0.25), residues: 459 sheet: -3.08 (0.27), residues: 256 loop : -3.29 (0.15), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 270 HIS 0.007 0.002 HIS M 11 PHE 0.040 0.002 PHE E 131 TYR 0.027 0.002 TYR E 125 ARG 0.010 0.001 ARG A 314 *********************** 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 323 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 299 time to evaluate : 1.820 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: 24 outliers final: 18 residues processed: 308 average time/residue: 0.3199 time to fit residues: 140.0669 Evaluate side-chains 306 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 288 time to evaluate : 1.602 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1402 time to fit residues: 6.8789 ------------------------------------------------------------------------------- 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: 4.9990 chunk 184 optimal weight: 0.0170 chunk 110 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 183 optimal weight: 0.0870 chunk 120 optimal weight: 3.9990 overall best weight: 2.2202 ------------------------------------------------------------------------------- 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 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN E 256 HIS ** E 310 ASN ** 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 151 ASN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6604 moved from start: 0.6143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 15710 Z= 0.325 Angle : 0.849 16.575 21627 Z= 0.429 Chirality : 0.045 0.295 2615 Planarity : 0.006 0.089 2759 Dihedral : 16.489 172.175 2732 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 22.90 Ramachandran Plot: Outliers : 0.49 % Allowed : 17.13 % Favored : 82.38 % Rotamer: Outliers : 1.18 % Allowed : 21.96 % Favored : 76.86 % 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: -4.05 (0.17), residues: 2055 helix: -1.22 (0.24), residues: 465 sheet: -3.12 (0.24), residues: 346 loop : -3.32 (0.15), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 270 HIS 0.008 0.002 HIS M 11 PHE 0.044 0.002 PHE E 131 TYR 0.027 0.002 TYR E 125 ARG 0.009 0.001 ARG D 56 *********************** 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 330 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 314 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 321 average time/residue: 0.3143 time to fit residues: 143.6983 Evaluate side-chains 306 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 300 time to evaluate : 1.613 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1985 time to fit residues: 4.2259 ------------------------------------------------------------------------------- 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: 8.9990 chunk 92 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 204 optimal weight: 0.6980 chunk 187 optimal weight: 8.9990 chunk 162 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 129 GLN B 163 ASN ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN 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 256 HIS D 323 GLN D 324 HIS D 329 ASN 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 ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.6362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 15710 Z= 0.282 Angle : 0.826 16.558 21627 Z= 0.418 Chirality : 0.044 0.276 2615 Planarity : 0.006 0.092 2759 Dihedral : 16.461 173.242 2732 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.49 % Allowed : 16.40 % Favored : 83.11 % Rotamer: Outliers : 1.25 % Allowed : 23.80 % Favored : 74.94 % 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: -4.15 (0.16), residues: 2055 helix: -1.17 (0.24), residues: 465 sheet: -3.25 (0.23), residues: 361 loop : -3.40 (0.15), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 270 HIS 0.008 0.001 HIS D 324 PHE 0.044 0.002 PHE E 131 TYR 0.024 0.002 TYR E 125 ARG 0.007 0.001 ARG C 56 ********************** 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 327 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 310 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 315 average time/residue: 0.3217 time to fit residues: 143.8764 Evaluate side-chains 303 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 295 time to evaluate : 1.768 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1519 time to fit residues: 4.5753 ------------------------------------------------------------------------------- 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: 9.9990 chunk 49 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 24 optimal weight: 0.0470 chunk 45 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.7482 ------------------------------------------------------------------------------- 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 163 ASN ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN B 310 ASN B 323 GLN B 329 ASN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN ** E 32 GLN ** 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 256 HIS F 324 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.218870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.202287 restraints weight = 19007.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.201602 restraints weight = 23904.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.202704 restraints weight = 21076.789| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.6547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 15710 Z= 0.284 Angle : 0.829 16.361 21627 Z= 0.418 Chirality : 0.044 0.271 2615 Planarity : 0.006 0.087 2759 Dihedral : 16.426 172.594 2732 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.49 % Allowed : 17.03 % Favored : 82.48 % Rotamer: Outliers : 0.81 % Allowed : 23.95 % Favored : 75.24 % 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: -4.05 (0.17), residues: 2055 helix: -1.11 (0.24), residues: 465 sheet: -3.14 (0.24), residues: 356 loop : -3.35 (0.15), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 270 HIS 0.008 0.002 HIS D 256 PHE 0.039 0.002 PHE E 131 TYR 0.031 0.002 TYR B 125 ARG 0.012 0.001 ARG D 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3401.88 seconds wall clock time: 62 minutes 22.60 seconds (3742.60 seconds total)