Starting phenix.real_space_refine on Sat Mar 16 18:52:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/03_2024/5xlo_6729_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/03_2024/5xlo_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_6729/03_2024/5xlo_6729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/03_2024/5xlo_6729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/03_2024/5xlo_6729_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlo_6729/03_2024/5xlo_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-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15413 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2004 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 9, 'TRANS': 277} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'TRP:plan': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 180 Chain: "B" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 195 Chain: "C" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 195 Chain: "D" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 195 Chain: "E" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 195 Chain: "F" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 195 Chain: "K" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 809 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 17, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 29, 'rna3p': 8} Chain: "N" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 615 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 620 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Time building chain proxies: 8.87, per 1000 atoms: 0.58 Number of scatterers: 15413 At special positions: 0 Unit cell: (126.1, 143, 113.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 38 15.00 O 3212 8.00 N 2690 7.00 C 9455 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.30 Conformation dependent library (CDL) restraints added in 3.2 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: 4.31 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: 3.75 Time building geometry restraints manager: 6.79 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: 9238 34.17 - 68.34: 167 68.34 - 102.51: 32 102.51 - 136.67: 3 136.67 - 170.84: 5 Dihedral angle restraints: 9445 sinusoidal: 3513 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 9442 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: 0.350 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: 2.260 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 44.190 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.910 ------------------------------------------------------------------------------- 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 : 15.312 170.842 5615 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 : 1.631 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: A 119 LEU cc_start: 0.6661 (mp) cc_final: 0.6402 (tt) REVERT: A 270 TRP cc_start: 0.6527 (t-100) cc_final: 0.6034 (t-100) REVERT: B 24 LEU cc_start: 0.8048 (mp) cc_final: 0.7611 (mp) REVERT: B 214 VAL cc_start: 0.7705 (t) cc_final: 0.7378 (p) REVERT: B 332 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7655 (mtt180) REVERT: C 46 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6321 (tt0) REVERT: C 58 LYS cc_start: 0.7297 (mttt) cc_final: 0.6647 (mttt) REVERT: C 91 LEU cc_start: 0.7295 (mt) cc_final: 0.6497 (mt) REVERT: D 58 LYS cc_start: 0.7634 (mttt) cc_final: 0.7418 (mttt) REVERT: D 91 LEU cc_start: 0.7289 (mt) cc_final: 0.7039 (mt) REVERT: D 127 ASN cc_start: 0.8169 (m-40) cc_final: 0.7900 (m-40) REVERT: D 131 PHE cc_start: 0.7596 (m-80) cc_final: 0.7335 (m-80) REVERT: D 234 ASP cc_start: 0.6790 (m-30) cc_final: 0.6395 (t0) REVERT: D 267 ILE cc_start: 0.8047 (mt) cc_final: 0.7812 (mt) REVERT: E 25 MET cc_start: 0.4921 (mmm) cc_final: 0.4522 (mmm) REVERT: E 125 TYR cc_start: 0.6944 (t80) cc_final: 0.6289 (t80) REVERT: E 131 PHE cc_start: 0.6337 (m-80) cc_final: 0.6091 (m-80) REVERT: E 275 ASP cc_start: 0.6848 (t70) cc_final: 0.6538 (t0) REVERT: F 116 ASP cc_start: 0.8191 (m-30) cc_final: 0.7223 (p0) REVERT: F 144 ASN cc_start: 0.5234 (m-40) cc_final: 0.4879 (m110) REVERT: F 163 ASN cc_start: 0.7872 (m-40) cc_final: 0.7504 (m-40) REVERT: F 172 ARG cc_start: 0.6061 (mtt-85) cc_final: 0.5684 (mtt90) REVERT: F 308 LEU cc_start: 0.5927 (mt) cc_final: 0.5429 (tp) REVERT: N 50 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6243 (tm) REVERT: M 29 ARG cc_start: 0.7177 (ttp-170) cc_final: 0.6909 (ptm160) outliers start: 4 outliers final: 0 residues processed: 454 average time/residue: 0.2944 time to fit residues: 188.7824 Evaluate side-chains 346 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 345 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 50 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 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: 0.0370 chunk 97 optimal weight: 0.0060 chunk 119 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 overall best weight: 0.4074 ------------------------------------------------------------------------------- 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 110 ASN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 HIS ** 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 241 GLN F 258 GLN M 49 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15710 Z= 0.198 Angle : 0.812 15.725 21627 Z= 0.414 Chirality : 0.043 0.181 2615 Planarity : 0.006 0.082 2759 Dihedral : 17.274 171.157 2770 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.68 % Favored : 87.79 % Rotamer: Outliers : 3.61 % Allowed : 11.50 % Favored : 84.89 % 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: -4.81 (0.15), residues: 2055 helix: -2.28 (0.20), residues: 465 sheet: -3.26 (0.24), residues: 292 loop : -3.76 (0.13), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP N 53 HIS 0.020 0.002 HIS M 11 PHE 0.022 0.002 PHE A 131 TYR 0.015 0.001 TYR D 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 419 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 370 time to evaluate : 1.528 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: A 270 TRP cc_start: 0.5991 (t-100) cc_final: 0.5758 (t-100) REVERT: A 332 ARG cc_start: 0.7802 (mtp85) cc_final: 0.5557 (ttp80) REVERT: B 37 GLN cc_start: 0.5330 (mt0) cc_final: 0.4951 (mt0) REVERT: B 169 GLU cc_start: 0.6009 (tt0) cc_final: 0.5370 (pt0) REVERT: B 239 LYS cc_start: 0.8072 (mtmt) cc_final: 0.7527 (mttt) REVERT: B 314 ARG cc_start: 0.7704 (mmm160) cc_final: 0.7120 (tpt90) REVERT: C 58 LYS cc_start: 0.7128 (mttt) cc_final: 0.6689 (mttt) REVERT: C 295 TYR cc_start: 0.7944 (m-80) cc_final: 0.7744 (m-80) REVERT: D 46 GLU cc_start: 0.6274 (tm-30) cc_final: 0.5876 (tm-30) REVERT: D 234 ASP cc_start: 0.6994 (m-30) cc_final: 0.6532 (t0) REVERT: D 235 LYS cc_start: 0.6687 (mmtp) cc_final: 0.6388 (mmtp) REVERT: E 42 VAL cc_start: 0.7445 (OUTLIER) cc_final: 0.7099 (t) REVERT: E 125 TYR cc_start: 0.7260 (t80) cc_final: 0.6807 (t80) REVERT: F 46 GLU cc_start: 0.7511 (tt0) cc_final: 0.7252 (tt0) REVERT: F 163 ASN cc_start: 0.8183 (m-40) cc_final: 0.7943 (m-40) REVERT: F 336 PHE cc_start: 0.6269 (m-10) cc_final: 0.5807 (m-80) REVERT: N 49 GLN cc_start: 0.6556 (OUTLIER) cc_final: 0.6337 (mp10) REVERT: N 53 TRP cc_start: 0.6399 (p-90) cc_final: 0.6158 (t60) REVERT: N 65 ILE cc_start: 0.8361 (mp) cc_final: 0.8120 (mt) outliers start: 49 outliers final: 20 residues processed: 398 average time/residue: 0.3211 time to fit residues: 182.2127 Evaluate side-chains 343 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 321 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 53 TRP 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: 7.9990 chunk 154 optimal weight: 0.2980 chunk 126 optimal weight: 0.0870 chunk 51 optimal weight: 7.9990 chunk 186 optimal weight: 0.0040 chunk 201 optimal weight: 5.9990 chunk 166 optimal weight: 0.0050 chunk 184 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.2184 ------------------------------------------------------------------------------- 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 163 ASN B 258 GLN B 310 ASN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 GLN D 241 GLN E 256 HIS ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 HIS ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN M 32 ASN M 49 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15710 Z= 0.177 Angle : 0.736 13.002 21627 Z= 0.373 Chirality : 0.041 0.179 2615 Planarity : 0.005 0.069 2759 Dihedral : 16.833 175.487 2770 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.87 % Favored : 87.64 % Rotamer: Outliers : 4.20 % Allowed : 14.15 % Favored : 81.65 % 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: -4.00 (0.16), residues: 2055 helix: -0.74 (0.26), residues: 393 sheet: -3.08 (0.25), residues: 299 loop : -3.38 (0.14), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 270 HIS 0.006 0.001 HIS C 324 PHE 0.033 0.002 PHE E 131 TYR 0.016 0.001 TYR D 125 ARG 0.009 0.001 ARG A 94 *********************** 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: 57 poor density : 336 time to evaluate : 1.676 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: A 46 GLU cc_start: 0.5422 (tm-30) cc_final: 0.5184 (mm-30) REVERT: A 270 TRP cc_start: 0.5880 (t-100) cc_final: 0.5604 (t-100) REVERT: A 332 ARG cc_start: 0.7795 (mtp85) cc_final: 0.5549 (ttt180) REVERT: B 37 GLN cc_start: 0.5044 (mt0) cc_final: 0.4715 (mt0) REVERT: B 169 GLU cc_start: 0.5812 (tt0) cc_final: 0.5257 (pt0) REVERT: B 239 LYS cc_start: 0.8010 (mtmt) cc_final: 0.7584 (mtpt) REVERT: B 293 LYS cc_start: 0.7799 (mmtt) cc_final: 0.7496 (mmtt) REVERT: B 314 ARG cc_start: 0.7462 (mmm160) cc_final: 0.7219 (mmm160) REVERT: B 332 ARG cc_start: 0.8023 (mtt180) cc_final: 0.7559 (mtt180) REVERT: C 34 ASP cc_start: 0.7364 (m-30) cc_final: 0.6230 (p0) REVERT: C 58 LYS cc_start: 0.6918 (mttt) cc_final: 0.6575 (mttt) REVERT: D 46 GLU cc_start: 0.6533 (tm-30) cc_final: 0.5948 (tm-30) REVERT: D 179 LEU cc_start: 0.7431 (mt) cc_final: 0.6846 (tp) REVERT: D 218 ARG cc_start: 0.5162 (tmm-80) cc_final: 0.4926 (tmm-80) REVERT: E 42 VAL cc_start: 0.7368 (OUTLIER) cc_final: 0.7040 (t) REVERT: E 125 TYR cc_start: 0.7230 (t80) cc_final: 0.6728 (t80) REVERT: E 127 ASN cc_start: 0.7418 (t0) cc_final: 0.7202 (t0) REVERT: E 131 PHE cc_start: 0.6276 (m-80) cc_final: 0.5641 (m-80) REVERT: E 148 LEU cc_start: 0.6358 (tp) cc_final: 0.5381 (tt) REVERT: E 210 LEU cc_start: 0.5534 (OUTLIER) cc_final: 0.5296 (mt) REVERT: E 340 GLU cc_start: 0.6555 (mp0) cc_final: 0.6245 (mt-10) REVERT: F 46 GLU cc_start: 0.7332 (tt0) cc_final: 0.7028 (tt0) REVERT: F 116 ASP cc_start: 0.8161 (m-30) cc_final: 0.7745 (p0) REVERT: F 223 GLN cc_start: 0.5061 (mt0) cc_final: 0.4740 (mt0) REVERT: F 234 ASP cc_start: 0.6363 (t0) cc_final: 0.6078 (t0) REVERT: F 308 LEU cc_start: 0.5729 (mt) cc_final: 0.5339 (tp) REVERT: M 29 ARG cc_start: 0.6718 (ptm160) cc_final: 0.6460 (ptp-110) outliers start: 57 outliers final: 31 residues processed: 370 average time/residue: 0.2974 time to fit residues: 156.8129 Evaluate side-chains 337 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 304 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 147 PHE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 53 TRP Chi-restraints excluded: chain M residue 73 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 177 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 258 GLN 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 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN F 241 GLN F 310 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.4391 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= 0.236 Angle : 0.762 11.375 21627 Z= 0.386 Chirality : 0.043 0.207 2615 Planarity : 0.005 0.068 2759 Dihedral : 16.802 173.406 2768 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.28 % Favored : 86.28 % Rotamer: Outliers : 5.53 % Allowed : 14.74 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.16), residues: 2055 helix: -1.10 (0.24), residues: 462 sheet: -2.94 (0.26), residues: 294 loop : -3.42 (0.15), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 270 HIS 0.006 0.001 HIS C 208 PHE 0.040 0.002 PHE F 131 TYR 0.020 0.002 TYR M 6 ARG 0.006 0.001 ARG D 56 *********************** 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 411 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 336 time to evaluate : 1.615 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: A 46 GLU cc_start: 0.5403 (tm-30) cc_final: 0.4996 (mm-30) REVERT: A 270 TRP cc_start: 0.6106 (t-100) cc_final: 0.5336 (t-100) REVERT: A 332 ARG cc_start: 0.8064 (mtp85) cc_final: 0.5746 (ttp80) REVERT: B 91 LEU cc_start: 0.7742 (mt) cc_final: 0.7470 (mt) REVERT: B 169 GLU cc_start: 0.5623 (tt0) cc_final: 0.5156 (pt0) REVERT: B 239 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7466 (mttt) REVERT: B 293 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7617 (mmtt) REVERT: B 314 ARG cc_start: 0.7822 (mmm160) cc_final: 0.7205 (tpt90) REVERT: C 58 LYS cc_start: 0.6947 (mttt) cc_final: 0.6599 (mttt) REVERT: C 131 PHE cc_start: 0.7420 (m-80) cc_final: 0.7143 (m-10) REVERT: D 46 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6533 (tm-30) REVERT: D 125 TYR cc_start: 0.8269 (t80) cc_final: 0.7949 (t80) REVERT: D 179 LEU cc_start: 0.7518 (mt) cc_final: 0.6989 (tp) REVERT: D 234 ASP cc_start: 0.7132 (m-30) cc_final: 0.6911 (m-30) REVERT: E 42 VAL cc_start: 0.7706 (OUTLIER) cc_final: 0.7277 (t) REVERT: E 125 TYR cc_start: 0.7597 (t80) cc_final: 0.7127 (t80) REVERT: E 131 PHE cc_start: 0.6297 (m-80) cc_final: 0.5738 (m-80) REVERT: E 210 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5555 (mt) REVERT: E 331 ILE cc_start: 0.4759 (OUTLIER) cc_final: 0.4538 (mp) REVERT: F 46 GLU cc_start: 0.7516 (tt0) cc_final: 0.7190 (tt0) REVERT: F 58 LYS cc_start: 0.7462 (mttt) cc_final: 0.7061 (mttt) REVERT: F 116 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7529 (p0) REVERT: F 308 LEU cc_start: 0.5730 (mt) cc_final: 0.5344 (tp) REVERT: F 332 ARG cc_start: 0.7031 (mtp85) cc_final: 0.6772 (mtp85) REVERT: N 50 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6673 (tm) REVERT: M 29 ARG cc_start: 0.6415 (ptm160) cc_final: 0.6168 (ptp-110) outliers start: 75 outliers final: 48 residues processed: 377 average time/residue: 0.2929 time to fit residues: 157.1196 Evaluate side-chains 359 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 306 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 53 TRP Chi-restraints excluded: chain M residue 73 SER 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: 2.9990 chunk 2 optimal weight: 20.0000 chunk 147 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN C 129 GLN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 GLN D 258 GLN E 256 HIS ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.114 15710 Z= 0.520 Angle : 1.023 15.417 21627 Z= 0.520 Chirality : 0.050 0.327 2615 Planarity : 0.007 0.084 2759 Dihedral : 17.500 172.558 2768 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 27.95 Ramachandran Plot: Outliers : 0.49 % Allowed : 18.49 % Favored : 81.02 % Rotamer: Outliers : 6.85 % Allowed : 15.18 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % 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: -4.64 (0.16), residues: 2055 helix: -2.06 (0.22), residues: 486 sheet: -3.53 (0.22), residues: 358 loop : -3.53 (0.15), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP C 270 HIS 0.015 0.002 HIS M 11 PHE 0.026 0.004 PHE F 131 TYR 0.022 0.003 TYR B 125 ARG 0.011 0.001 ARG E 94 *********************** 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 437 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 344 time to evaluate : 1.611 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: A 100 LEU cc_start: 0.2585 (mt) cc_final: 0.2365 (mt) REVERT: A 270 TRP cc_start: 0.6662 (t-100) cc_final: 0.5762 (t-100) REVERT: A 336 PHE cc_start: 0.6633 (m-80) cc_final: 0.5425 (m-80) REVERT: B 44 VAL cc_start: 0.8907 (t) cc_final: 0.8692 (m) REVERT: B 239 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7619 (mttt) REVERT: B 336 PHE cc_start: 0.6893 (m-80) cc_final: 0.6262 (m-80) REVERT: C 58 LYS cc_start: 0.7096 (mttt) cc_final: 0.6539 (mttt) REVERT: C 332 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7476 (mtp180) REVERT: C 336 PHE cc_start: 0.6741 (m-80) cc_final: 0.6256 (m-80) REVERT: D 46 GLU cc_start: 0.7628 (tm-30) cc_final: 0.6981 (tm-30) REVERT: D 179 LEU cc_start: 0.8111 (mt) cc_final: 0.7684 (tp) REVERT: E 42 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7822 (t) REVERT: E 125 TYR cc_start: 0.8107 (t80) cc_final: 0.7777 (t80) REVERT: E 131 PHE cc_start: 0.6541 (m-80) cc_final: 0.5997 (m-80) REVERT: E 176 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.6197 (m-80) REVERT: E 210 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6308 (mt) REVERT: E 280 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6810 (pt) REVERT: F 148 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6886 (mm) REVERT: F 336 PHE cc_start: 0.6509 (m-10) cc_final: 0.6124 (m-80) REVERT: N 51 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7753 (mm-30) REVERT: M 7 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7906 (mp) REVERT: M 29 ARG cc_start: 0.6594 (ptm160) cc_final: 0.6228 (ptp-170) REVERT: M 32 ASN cc_start: 0.6294 (m110) cc_final: 0.5695 (p0) outliers start: 93 outliers final: 57 residues processed: 394 average time/residue: 0.2929 time to fit residues: 165.9895 Evaluate side-chains 378 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 315 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 300 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 241 GLN Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 53 TRP Chi-restraints excluded: chain M residue 73 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 9.9990 chunk 178 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 91 optimal weight: 0.0030 chunk 16 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 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 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 GLN D 323 GLN D 324 HIS F 32 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15710 Z= 0.206 Angle : 0.772 14.529 21627 Z= 0.392 Chirality : 0.043 0.268 2615 Planarity : 0.005 0.079 2759 Dihedral : 16.845 172.936 2768 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.49 % Allowed : 12.94 % Favored : 86.57 % Rotamer: Outliers : 4.72 % Allowed : 20.12 % Favored : 75.17 % 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: -4.08 (0.16), residues: 2055 helix: -1.25 (0.24), residues: 463 sheet: -2.93 (0.26), residues: 286 loop : -3.43 (0.15), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 270 HIS 0.006 0.001 HIS D 324 PHE 0.025 0.002 PHE F 131 TYR 0.015 0.001 TYR N 20 ARG 0.006 0.001 ARG B 161 *********************** 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 386 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 322 time to evaluate : 1.676 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: A 270 TRP cc_start: 0.6128 (t-100) cc_final: 0.5217 (t-100) REVERT: A 332 ARG cc_start: 0.7933 (mtp85) cc_final: 0.5955 (ttp80) REVERT: B 239 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7615 (mttt) REVERT: B 258 GLN cc_start: 0.6026 (mt0) cc_final: 0.5757 (mt0) REVERT: B 314 ARG cc_start: 0.7911 (mmm160) cc_final: 0.7446 (tpt90) REVERT: C 58 LYS cc_start: 0.6949 (mttt) cc_final: 0.6576 (mttt) REVERT: C 265 ARG cc_start: 0.7166 (ttp-110) cc_final: 0.6674 (mtt90) REVERT: D 46 GLU cc_start: 0.7519 (tm-30) cc_final: 0.6605 (tm-30) REVERT: D 179 LEU cc_start: 0.7911 (mt) cc_final: 0.7568 (tp) REVERT: D 234 ASP cc_start: 0.6876 (m-30) cc_final: 0.6375 (t0) REVERT: D 270 TRP cc_start: 0.6197 (t-100) cc_final: 0.5875 (t-100) REVERT: E 125 TYR cc_start: 0.7775 (t80) cc_final: 0.7343 (t80) REVERT: E 129 GLN cc_start: 0.8003 (tp-100) cc_final: 0.7707 (tp40) REVERT: E 131 PHE cc_start: 0.6176 (m-80) cc_final: 0.5486 (m-80) REVERT: E 210 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.6064 (mt) REVERT: F 46 GLU cc_start: 0.7326 (tt0) cc_final: 0.7034 (tt0) REVERT: F 148 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6650 (mm) REVERT: F 308 LEU cc_start: 0.5840 (mt) cc_final: 0.5462 (tp) REVERT: N 51 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7703 (mm-30) outliers start: 64 outliers final: 42 residues processed: 360 average time/residue: 0.2938 time to fit residues: 151.0748 Evaluate side-chains 348 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 304 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 300 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 53 TRP Chi-restraints excluded: chain M residue 73 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 144 optimal weight: 0.1980 chunk 112 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 197 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 120 optimal weight: 0.0980 chunk 91 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN B 329 ASN C 129 GLN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN ** 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15710 Z= 0.223 Angle : 0.754 13.948 21627 Z= 0.383 Chirality : 0.042 0.234 2615 Planarity : 0.005 0.081 2759 Dihedral : 16.556 170.861 2768 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.39 % Allowed : 15.86 % Favored : 83.75 % Rotamer: Outliers : 5.01 % Allowed : 19.82 % Favored : 75.17 % 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: -4.04 (0.17), residues: 2055 helix: -1.15 (0.24), residues: 484 sheet: -3.14 (0.23), residues: 351 loop : -3.35 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 270 HIS 0.007 0.001 HIS M 11 PHE 0.023 0.002 PHE F 131 TYR 0.016 0.001 TYR M 20 ARG 0.005 0.001 ARG D 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 386 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 318 time to evaluate : 1.638 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: A 270 TRP cc_start: 0.6140 (t-100) cc_final: 0.5424 (t-100) REVERT: A 332 ARG cc_start: 0.7969 (mtp85) cc_final: 0.5960 (ttp80) REVERT: B 176 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7463 (m-10) REVERT: B 239 LYS cc_start: 0.8221 (mtmt) cc_final: 0.7620 (mttt) REVERT: B 314 ARG cc_start: 0.7936 (mmm160) cc_final: 0.7474 (tpt90) REVERT: C 58 LYS cc_start: 0.6903 (mttt) cc_final: 0.6501 (mttt) REVERT: D 234 ASP cc_start: 0.7146 (m-30) cc_final: 0.6497 (t0) REVERT: D 270 TRP cc_start: 0.6299 (t-100) cc_final: 0.5974 (t-100) REVERT: E 125 TYR cc_start: 0.7821 (t80) cc_final: 0.7402 (t80) REVERT: E 131 PHE cc_start: 0.6233 (m-80) cc_final: 0.5740 (m-80) REVERT: E 210 LEU cc_start: 0.6377 (OUTLIER) cc_final: 0.6087 (mt) REVERT: E 280 ILE cc_start: 0.7817 (pt) cc_final: 0.7594 (mt) REVERT: F 46 GLU cc_start: 0.7222 (tt0) cc_final: 0.6706 (tt0) REVERT: N 15 MET cc_start: 0.6033 (mtm) cc_final: 0.5720 (mtt) REVERT: N 51 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7705 (mm-30) REVERT: M 15 MET cc_start: 0.5184 (OUTLIER) cc_final: 0.4646 (mmt) outliers start: 68 outliers final: 48 residues processed: 359 average time/residue: 0.3035 time to fit residues: 154.5172 Evaluate side-chains 358 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 307 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 300 GLN Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 125 TYR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 53 TRP Chi-restraints excluded: chain M residue 73 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 97 optimal weight: 0.0770 chunk 18 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 179 optimal weight: 10.0000 overall best weight: 2.4146 ------------------------------------------------------------------------------- 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 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 310 ASN B 324 HIS B 329 ASN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN ** E 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN F 144 ASN F 151 ASN F 256 HIS ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 15710 Z= 0.342 Angle : 0.870 20.204 21627 Z= 0.438 Chirality : 0.045 0.269 2615 Planarity : 0.006 0.097 2759 Dihedral : 16.777 172.280 2768 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 24.71 Ramachandran Plot: Outliers : 0.34 % Allowed : 18.10 % Favored : 81.56 % Rotamer: Outliers : 5.08 % Allowed : 20.49 % Favored : 74.43 % 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: -4.14 (0.17), residues: 2055 helix: -1.14 (0.26), residues: 445 sheet: -3.24 (0.23), residues: 364 loop : -3.38 (0.15), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 270 HIS 0.010 0.002 HIS M 11 PHE 0.025 0.002 PHE F 131 TYR 0.018 0.002 TYR M 20 ARG 0.007 0.001 ARG D 56 *********************** 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 386 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 317 time to evaluate : 1.691 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: A 94 ARG cc_start: 0.5740 (OUTLIER) cc_final: 0.5307 (mmp80) REVERT: A 270 TRP cc_start: 0.6498 (t-100) cc_final: 0.5802 (t-100) REVERT: A 332 ARG cc_start: 0.7862 (mtp85) cc_final: 0.5778 (ttp80) REVERT: B 239 LYS cc_start: 0.8370 (mtmt) cc_final: 0.7617 (mttt) REVERT: B 258 GLN cc_start: 0.5886 (mt0) cc_final: 0.5624 (mt0) REVERT: B 314 ARG cc_start: 0.8118 (mmm160) cc_final: 0.7707 (tpt90) REVERT: C 58 LYS cc_start: 0.6984 (mttt) cc_final: 0.6487 (mttt) REVERT: D 179 LEU cc_start: 0.7767 (mp) cc_final: 0.7112 (tp) REVERT: D 234 ASP cc_start: 0.7205 (m-30) cc_final: 0.6630 (t0) REVERT: D 270 TRP cc_start: 0.6587 (t-100) cc_final: 0.6327 (t-100) REVERT: E 125 TYR cc_start: 0.8013 (t80) cc_final: 0.7549 (t80) REVERT: E 131 PHE cc_start: 0.6597 (m-80) cc_final: 0.6076 (m-80) REVERT: E 210 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6422 (mt) REVERT: N 51 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7755 (mm-30) REVERT: M 15 MET cc_start: 0.5910 (OUTLIER) cc_final: 0.5440 (mmt) outliers start: 69 outliers final: 52 residues processed: 353 average time/residue: 0.2997 time to fit residues: 150.1736 Evaluate side-chains 366 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 311 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 241 GLN Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 53 TRP Chi-restraints excluded: chain M residue 73 SER 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: 1.9990 chunk 110 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 174 optimal weight: 20.0000 chunk 183 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 324 HIS ** A 329 ASN ** 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 329 ASN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 GLN D 329 ASN ** E 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.6544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 15710 Z= 0.500 Angle : 1.036 20.477 21627 Z= 0.524 Chirality : 0.051 0.442 2615 Planarity : 0.007 0.089 2759 Dihedral : 17.277 173.001 2768 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 28.32 Ramachandran Plot: Outliers : 0.54 % Allowed : 20.68 % Favored : 78.78 % Rotamer: Outliers : 5.45 % Allowed : 21.08 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.16), residues: 2055 helix: -1.76 (0.24), residues: 447 sheet: -3.50 (0.22), residues: 364 loop : -3.50 (0.15), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP B 270 HIS 0.017 0.003 HIS M 11 PHE 0.028 0.004 PHE B 95 TYR 0.024 0.003 TYR B 125 ARG 0.013 0.001 ARG C 332 *********************** 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 411 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 337 time to evaluate : 1.664 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: A 94 ARG cc_start: 0.5876 (OUTLIER) cc_final: 0.5053 (mmp80) REVERT: A 267 ILE cc_start: 0.8404 (mm) cc_final: 0.8031 (mm) REVERT: A 270 TRP cc_start: 0.6582 (t-100) cc_final: 0.5994 (t-100) REVERT: A 332 ARG cc_start: 0.7964 (mtp85) cc_final: 0.6066 (ttp80) REVERT: A 336 PHE cc_start: 0.6660 (m-80) cc_final: 0.5680 (m-80) REVERT: B 239 LYS cc_start: 0.8424 (mtmt) cc_final: 0.7862 (mttt) REVERT: B 314 ARG cc_start: 0.8348 (mmm160) cc_final: 0.7751 (tpt90) REVERT: B 336 PHE cc_start: 0.6725 (m-80) cc_final: 0.6337 (m-80) REVERT: C 58 LYS cc_start: 0.7091 (mttt) cc_final: 0.6534 (mttt) REVERT: C 131 PHE cc_start: 0.7494 (m-80) cc_final: 0.7278 (m-10) REVERT: D 179 LEU cc_start: 0.7815 (mp) cc_final: 0.7158 (tp) REVERT: D 234 ASP cc_start: 0.6852 (m-30) cc_final: 0.6626 (t0) REVERT: E 37 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.7121 (mt0) REVERT: E 80 ASP cc_start: 0.8882 (m-30) cc_final: 0.8659 (m-30) REVERT: E 125 TYR cc_start: 0.8368 (t80) cc_final: 0.8080 (t80) REVERT: E 129 GLN cc_start: 0.7996 (tp-100) cc_final: 0.7760 (tp40) REVERT: E 131 PHE cc_start: 0.6808 (m-80) cc_final: 0.6292 (m-80) REVERT: E 176 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.5430 (m-80) REVERT: F 46 GLU cc_start: 0.7288 (tt0) cc_final: 0.7044 (tt0) outliers start: 74 outliers final: 58 residues processed: 380 average time/residue: 0.2962 time to fit residues: 160.7790 Evaluate side-chains 388 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 327 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 53 TRP Chi-restraints excluded: chain M residue 73 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 9.9990 chunk 118 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 187 optimal weight: 0.0070 chunk 162 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN B 129 GLN ** 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 329 ASN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN D 329 ASN E 256 HIS ** E 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.6683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15710 Z= 0.214 Angle : 0.820 18.687 21627 Z= 0.414 Chirality : 0.044 0.395 2615 Planarity : 0.006 0.088 2759 Dihedral : 16.661 171.929 2768 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.44 % Allowed : 14.16 % Favored : 85.40 % Rotamer: Outliers : 3.76 % Allowed : 23.43 % Favored : 72.81 % 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: -4.21 (0.17), residues: 2055 helix: -1.28 (0.25), residues: 460 sheet: -3.22 (0.23), residues: 374 loop : -3.43 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 270 HIS 0.006 0.001 HIS F 256 PHE 0.022 0.002 PHE F 131 TYR 0.017 0.001 TYR M 20 ARG 0.005 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 371 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 320 time to evaluate : 1.689 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: A 94 ARG cc_start: 0.5663 (OUTLIER) cc_final: 0.4926 (mmp80) REVERT: A 267 ILE cc_start: 0.8161 (mm) cc_final: 0.7803 (mm) REVERT: A 270 TRP cc_start: 0.6154 (t-100) cc_final: 0.5626 (t-100) REVERT: A 300 GLN cc_start: 0.6317 (mt0) cc_final: 0.5159 (tt0) REVERT: B 37 GLN cc_start: 0.5554 (mt0) cc_final: 0.5325 (mt0) REVERT: B 239 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7542 (mttt) REVERT: B 314 ARG cc_start: 0.7937 (mmm160) cc_final: 0.7628 (tpt90) REVERT: C 58 LYS cc_start: 0.7027 (mttt) cc_final: 0.6665 (mttt) REVERT: C 265 ARG cc_start: 0.7368 (ttp-110) cc_final: 0.6350 (mtt90) REVERT: C 300 GLN cc_start: 0.7681 (mt0) cc_final: 0.7453 (mt0) REVERT: C 314 ARG cc_start: 0.6832 (tmt170) cc_final: 0.6114 (tpt90) REVERT: D 58 LYS cc_start: 0.8414 (mttt) cc_final: 0.7847 (pttt) REVERT: D 179 LEU cc_start: 0.7657 (mp) cc_final: 0.6991 (tp) REVERT: D 210 LEU cc_start: 0.7489 (mp) cc_final: 0.6995 (mp) REVERT: D 234 ASP cc_start: 0.6979 (m-30) cc_final: 0.6631 (t0) REVERT: E 80 ASP cc_start: 0.8745 (m-30) cc_final: 0.8516 (m-30) REVERT: E 125 TYR cc_start: 0.8058 (t80) cc_final: 0.7663 (t80) REVERT: E 129 GLN cc_start: 0.7887 (tp-100) cc_final: 0.7644 (tp40) REVERT: E 131 PHE cc_start: 0.6387 (m-80) cc_final: 0.5937 (m-80) REVERT: E 176 PHE cc_start: 0.6298 (OUTLIER) cc_final: 0.5422 (m-10) REVERT: F 46 GLU cc_start: 0.6820 (tt0) cc_final: 0.6554 (tt0) outliers start: 51 outliers final: 40 residues processed: 348 average time/residue: 0.3023 time to fit residues: 150.2911 Evaluate side-chains 354 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 312 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 53 TRP Chi-restraints excluded: chain M residue 73 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.0770 chunk 143 optimal weight: 0.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- 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 329 ASN B 163 ASN ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN C 129 GLN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN ** E 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 ASN F 151 ASN N 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.220978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.199100 restraints weight = 19231.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.198733 restraints weight = 20171.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.200102 restraints weight = 16724.272| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.6824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15710 Z= 0.213 Angle : 0.784 18.475 21627 Z= 0.397 Chirality : 0.043 0.405 2615 Planarity : 0.006 0.088 2759 Dihedral : 16.419 170.045 2768 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.39 % Allowed : 15.82 % Favored : 83.80 % Rotamer: Outliers : 3.39 % Allowed : 23.95 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.17), residues: 2055 helix: -1.12 (0.24), residues: 490 sheet: -3.27 (0.22), residues: 387 loop : -3.31 (0.16), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 270 HIS 0.004 0.001 HIS D 208 PHE 0.024 0.002 PHE F 131 TYR 0.015 0.001 TYR M 20 ARG 0.005 0.001 ARG D 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3461.87 seconds wall clock time: 62 minutes 51.15 seconds (3771.15 seconds total)