Starting phenix.real_space_refine (version: dev) on Thu Feb 23 00:14:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0z_14435/02_2023/7z0z_14435.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0z_14435/02_2023/7z0z_14435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0z_14435/02_2023/7z0z_14435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0z_14435/02_2023/7z0z_14435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0z_14435/02_2023/7z0z_14435.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0z_14435/02_2023/7z0z_14435.pdb" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 29130 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 7": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A ARG 521": "NH1" <-> "NH2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "B GLU 438": "OE1" <-> "OE2" Residue "B TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "B ARG 521": "NH1" <-> "NH2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "C GLU 7": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C GLU 459": "OE1" <-> "OE2" Residue "C ARG 521": "NH1" <-> "NH2" Residue "C PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 578": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "D GLU 7": "OE1" <-> "OE2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D ARG 271": "NH1" <-> "NH2" Residue "D GLU 317": "OE1" <-> "OE2" Residue "D GLU 328": "OE1" <-> "OE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "D GLU 438": "OE1" <-> "OE2" Residue "D TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "D GLU 459": "OE1" <-> "OE2" Residue "D ARG 521": "NH1" <-> "NH2" Residue "D PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 578": "OE1" <-> "OE2" Residue "D GLU 583": "OE1" <-> "OE2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E ARG 20": "NH1" <-> "NH2" Residue "E ARG 221": "NH1" <-> "NH2" Residue "E GLU 225": "OE1" <-> "OE2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E GLU 261": "OE1" <-> "OE2" Residue "E ARG 271": "NH1" <-> "NH2" Residue "E GLU 317": "OE1" <-> "OE2" Residue "E GLU 328": "OE1" <-> "OE2" Residue "E GLU 396": "OE1" <-> "OE2" Residue "E GLU 438": "OE1" <-> "OE2" Residue "E TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "E GLU 459": "OE1" <-> "OE2" Residue "E ARG 521": "NH1" <-> "NH2" Residue "E PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 578": "OE1" <-> "OE2" Residue "E GLU 583": "OE1" <-> "OE2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F ARG 20": "NH1" <-> "NH2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "F GLU 225": "OE1" <-> "OE2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F GLU 261": "OE1" <-> "OE2" Residue "F ARG 271": "NH1" <-> "NH2" Residue "F GLU 317": "OE1" <-> "OE2" Residue "F GLU 328": "OE1" <-> "OE2" Residue "F GLU 396": "OE1" <-> "OE2" Residue "F GLU 438": "OE1" <-> "OE2" Residue "F TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 450": "OE1" <-> "OE2" Residue "F GLU 459": "OE1" <-> "OE2" Residue "F ARG 521": "NH1" <-> "NH2" Residue "F PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 578": "OE1" <-> "OE2" Residue "F GLU 583": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 29466 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4911 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4911 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4911 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4911 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4911 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4911 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 11.61, per 1000 atoms: 0.39 Number of scatterers: 29466 At special positions: 0 Unit cell: (163.18, 147.6, 115.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 5508 8.00 N 4722 7.00 C 19122 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: 8.63 Conformation dependent library (CDL) restraints added in 3.8 seconds 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6792 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 12 sheets defined 64.0% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 0 through 13 Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.827A pdb=" N SER A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 116 through 127 removed outlier: 3.857A pdb=" N PHE A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 217 through 238 removed outlier: 3.528A pdb=" N ARG A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 273 Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR A 282 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 310 through 331 Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 372 through 384 removed outlier: 3.688A pdb=" N ASP A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 402 Processing helix chain 'A' and resid 404 through 419 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 435 through 449 Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 504 removed outlier: 3.537A pdb=" N LYS A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 517 through 530 Processing helix chain 'A' and resid 534 through 545 Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 570 through 582 Processing helix chain 'B' and resid 1 through 13 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 57 through 67 removed outlier: 3.828A pdb=" N SER B 66 " --> pdb=" O ASP B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 116 through 127 removed outlier: 3.856A pdb=" N PHE B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 153 Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 217 through 238 removed outlier: 3.529A pdb=" N ARG B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 273 Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR B 282 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 310 through 331 Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 372 through 384 removed outlier: 3.687A pdb=" N ASP B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 402 Processing helix chain 'B' and resid 404 through 419 Processing helix chain 'B' and resid 419 through 434 Processing helix chain 'B' and resid 435 through 449 Processing helix chain 'B' and resid 456 through 461 Processing helix chain 'B' and resid 462 through 464 No H-bonds generated for 'chain 'B' and resid 462 through 464' Processing helix chain 'B' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 504 removed outlier: 3.536A pdb=" N LYS B 494 " --> pdb=" O LYS B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 517 through 530 Processing helix chain 'B' and resid 534 through 545 Processing helix chain 'B' and resid 559 through 564 Processing helix chain 'B' and resid 570 through 582 Processing helix chain 'C' and resid 1 through 13 Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.828A pdb=" N SER C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 116 through 127 removed outlier: 3.856A pdb=" N PHE C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 153 Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP C 178 " --> pdb=" O HIS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 217 through 238 removed outlier: 3.528A pdb=" N ARG C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 273 Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR C 282 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 310 through 331 Processing helix chain 'C' and resid 339 through 351 Processing helix chain 'C' and resid 354 through 364 Processing helix chain 'C' and resid 372 through 384 removed outlier: 3.687A pdb=" N ASP C 384 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 402 Processing helix chain 'C' and resid 404 through 419 Processing helix chain 'C' and resid 419 through 434 Processing helix chain 'C' and resid 435 through 449 Processing helix chain 'C' and resid 456 through 461 Processing helix chain 'C' and resid 462 through 464 No H-bonds generated for 'chain 'C' and resid 462 through 464' Processing helix chain 'C' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 504 removed outlier: 3.537A pdb=" N LYS C 494 " --> pdb=" O LYS C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 517 through 530 Processing helix chain 'C' and resid 534 through 545 Processing helix chain 'C' and resid 559 through 564 Processing helix chain 'C' and resid 570 through 582 Processing helix chain 'D' and resid 1 through 13 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 57 through 67 removed outlier: 3.827A pdb=" N SER D 66 " --> pdb=" O ASP D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 73 Processing helix chain 'D' and resid 102 through 116 Processing helix chain 'D' and resid 116 through 127 removed outlier: 3.857A pdb=" N PHE D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 153 Processing helix chain 'D' and resid 166 through 171 Processing helix chain 'D' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP D 178 " --> pdb=" O HIS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 217 through 238 removed outlier: 3.529A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 273 Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR D 282 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 300 Processing helix chain 'D' and resid 310 through 331 Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'D' and resid 354 through 364 Processing helix chain 'D' and resid 372 through 384 removed outlier: 3.688A pdb=" N ASP D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 402 Processing helix chain 'D' and resid 404 through 419 Processing helix chain 'D' and resid 419 through 434 Processing helix chain 'D' and resid 435 through 449 Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'D' and resid 462 through 464 No H-bonds generated for 'chain 'D' and resid 462 through 464' Processing helix chain 'D' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN D 483 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 504 removed outlier: 3.536A pdb=" N LYS D 494 " --> pdb=" O LYS D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 515 Processing helix chain 'D' and resid 517 through 530 Processing helix chain 'D' and resid 534 through 545 Processing helix chain 'D' and resid 559 through 564 Processing helix chain 'D' and resid 570 through 582 Processing helix chain 'E' and resid 1 through 13 Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 57 through 67 removed outlier: 3.827A pdb=" N SER E 66 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 102 through 116 Processing helix chain 'E' and resid 116 through 127 removed outlier: 3.857A pdb=" N PHE E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU E 122 " --> pdb=" O LYS E 118 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 153 Processing helix chain 'E' and resid 166 through 171 Processing helix chain 'E' and resid 174 through 182 removed outlier: 4.198A pdb=" N TRP E 178 " --> pdb=" O HIS E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 217 through 238 removed outlier: 3.528A pdb=" N ARG E 221 " --> pdb=" O ASN E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 273 Processing helix chain 'E' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR E 282 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 300 Processing helix chain 'E' and resid 310 through 331 Processing helix chain 'E' and resid 339 through 351 Processing helix chain 'E' and resid 354 through 364 Processing helix chain 'E' and resid 372 through 384 removed outlier: 3.688A pdb=" N ASP E 384 " --> pdb=" O LEU E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 402 Processing helix chain 'E' and resid 404 through 419 Processing helix chain 'E' and resid 419 through 434 Processing helix chain 'E' and resid 435 through 449 Processing helix chain 'E' and resid 456 through 461 Processing helix chain 'E' and resid 462 through 464 No H-bonds generated for 'chain 'E' and resid 462 through 464' Processing helix chain 'E' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN E 483 " --> pdb=" O LEU E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 504 removed outlier: 3.538A pdb=" N LYS E 494 " --> pdb=" O LYS E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 515 Processing helix chain 'E' and resid 517 through 530 Processing helix chain 'E' and resid 534 through 545 Processing helix chain 'E' and resid 559 through 564 Processing helix chain 'E' and resid 570 through 582 Processing helix chain 'F' and resid 1 through 13 Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 57 through 67 removed outlier: 3.826A pdb=" N SER F 66 " --> pdb=" O ASP F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 73 Processing helix chain 'F' and resid 102 through 116 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.857A pdb=" N PHE F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL F 123 " --> pdb=" O GLU F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 153 Processing helix chain 'F' and resid 166 through 171 Processing helix chain 'F' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP F 178 " --> pdb=" O HIS F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 187 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 217 through 238 removed outlier: 3.528A pdb=" N ARG F 221 " --> pdb=" O ASN F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 273 Processing helix chain 'F' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR F 282 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 300 Processing helix chain 'F' and resid 310 through 331 Processing helix chain 'F' and resid 339 through 351 Processing helix chain 'F' and resid 354 through 364 Processing helix chain 'F' and resid 372 through 384 removed outlier: 3.688A pdb=" N ASP F 384 " --> pdb=" O LEU F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 402 Processing helix chain 'F' and resid 404 through 419 Processing helix chain 'F' and resid 419 through 434 Processing helix chain 'F' and resid 435 through 449 Processing helix chain 'F' and resid 456 through 461 Processing helix chain 'F' and resid 462 through 464 No H-bonds generated for 'chain 'F' and resid 462 through 464' Processing helix chain 'F' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN F 483 " --> pdb=" O LEU F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 504 removed outlier: 3.536A pdb=" N LYS F 494 " --> pdb=" O LYS F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 517 through 530 Processing helix chain 'F' and resid 534 through 545 Processing helix chain 'F' and resid 559 through 564 Processing helix chain 'F' and resid 570 through 582 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89 Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 245 Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 89 Processing sheet with id=AA4, first strand: chain 'B' and resid 243 through 245 Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 89 Processing sheet with id=AA6, first strand: chain 'C' and resid 243 through 245 Processing sheet with id=AA7, first strand: chain 'D' and resid 84 through 89 Processing sheet with id=AA8, first strand: chain 'D' and resid 243 through 245 Processing sheet with id=AA9, first strand: chain 'E' and resid 84 through 89 Processing sheet with id=AB1, first strand: chain 'E' and resid 243 through 245 Processing sheet with id=AB2, first strand: chain 'F' and resid 84 through 89 Processing sheet with id=AB3, first strand: chain 'F' and resid 243 through 245 1567 hydrogen bonds defined for protein. 4485 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.52 Time building geometry restraints manager: 9.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4865 1.31 - 1.43: 8737 1.43 - 1.56: 16404 1.56 - 1.68: 0 1.68 - 1.81: 174 Bond restraints: 30180 Sorted by residual: bond pdb=" C TYR D 245 " pdb=" O TYR D 245 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.17e-02 7.31e+03 1.83e+01 bond pdb=" C TYR F 245 " pdb=" O TYR F 245 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.17e-02 7.31e+03 1.81e+01 bond pdb=" C TYR A 245 " pdb=" O TYR A 245 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.17e-02 7.31e+03 1.80e+01 bond pdb=" C TYR C 245 " pdb=" O TYR C 245 " ideal model delta sigma weight residual 1.236 1.186 0.049 1.17e-02 7.31e+03 1.78e+01 bond pdb=" C TYR E 245 " pdb=" O TYR E 245 " ideal model delta sigma weight residual 1.236 1.187 0.049 1.17e-02 7.31e+03 1.76e+01 ... (remaining 30175 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.33: 442 106.33 - 113.27: 15669 113.27 - 120.21: 11821 120.21 - 127.15: 12538 127.15 - 134.08: 198 Bond angle restraints: 40668 Sorted by residual: angle pdb=" N GLU B 489 " pdb=" CA GLU B 489 " pdb=" C GLU B 489 " ideal model delta sigma weight residual 114.56 102.69 11.87 1.27e+00 6.20e-01 8.73e+01 angle pdb=" N GLU A 489 " pdb=" CA GLU A 489 " pdb=" C GLU A 489 " ideal model delta sigma weight residual 114.56 102.70 11.86 1.27e+00 6.20e-01 8.72e+01 angle pdb=" N GLU E 489 " pdb=" CA GLU E 489 " pdb=" C GLU E 489 " ideal model delta sigma weight residual 114.56 102.71 11.85 1.27e+00 6.20e-01 8.71e+01 angle pdb=" N GLU C 489 " pdb=" CA GLU C 489 " pdb=" C GLU C 489 " ideal model delta sigma weight residual 114.56 102.71 11.85 1.27e+00 6.20e-01 8.70e+01 angle pdb=" N GLU D 489 " pdb=" CA GLU D 489 " pdb=" C GLU D 489 " ideal model delta sigma weight residual 114.56 102.72 11.84 1.27e+00 6.20e-01 8.69e+01 ... (remaining 40663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 16137 18.02 - 36.04: 1404 36.04 - 54.06: 246 54.06 - 72.08: 63 72.08 - 90.10: 54 Dihedral angle restraints: 17904 sinusoidal: 7398 harmonic: 10506 Sorted by residual: dihedral pdb=" C VAL A 246 " pdb=" N VAL A 246 " pdb=" CA VAL A 246 " pdb=" CB VAL A 246 " ideal model delta harmonic sigma weight residual -122.00 -135.85 13.85 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" C VAL F 246 " pdb=" N VAL F 246 " pdb=" CA VAL F 246 " pdb=" CB VAL F 246 " ideal model delta harmonic sigma weight residual -122.00 -135.85 13.85 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" C VAL E 246 " pdb=" N VAL E 246 " pdb=" CA VAL E 246 " pdb=" CB VAL E 246 " ideal model delta harmonic sigma weight residual -122.00 -135.84 13.84 0 2.50e+00 1.60e-01 3.07e+01 ... (remaining 17901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3829 0.078 - 0.155: 429 0.155 - 0.233: 32 0.233 - 0.311: 6 0.311 - 0.389: 6 Chirality restraints: 4302 Sorted by residual: chirality pdb=" CA VAL E 246 " pdb=" N VAL E 246 " pdb=" C VAL E 246 " pdb=" CB VAL E 246 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA VAL B 246 " pdb=" N VAL B 246 " pdb=" C VAL B 246 " pdb=" CB VAL B 246 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA VAL F 246 " pdb=" N VAL F 246 " pdb=" C VAL F 246 " pdb=" CB VAL F 246 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.76e+00 ... (remaining 4299 not shown) Planarity restraints: 5190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 185 " 0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ALA D 185 " -0.071 2.00e-02 2.50e+03 pdb=" O ALA D 185 " 0.027 2.00e-02 2.50e+03 pdb=" N SER D 186 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 185 " 0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ALA E 185 " -0.071 2.00e-02 2.50e+03 pdb=" O ALA E 185 " 0.027 2.00e-02 2.50e+03 pdb=" N SER E 186 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 185 " -0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C ALA A 185 " 0.071 2.00e-02 2.50e+03 pdb=" O ALA A 185 " -0.027 2.00e-02 2.50e+03 pdb=" N SER A 186 " -0.024 2.00e-02 2.50e+03 ... (remaining 5187 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 372 2.65 - 3.22: 28315 3.22 - 3.78: 47268 3.78 - 4.34: 70523 4.34 - 4.90: 112653 Nonbonded interactions: 259131 Sorted by model distance: nonbonded pdb=" OH TYR E 522 " pdb=" O VAL E 584 " model vdw 2.092 2.440 nonbonded pdb=" OH TYR F 522 " pdb=" O VAL F 584 " model vdw 2.092 2.440 nonbonded pdb=" OH TYR C 522 " pdb=" O VAL C 584 " model vdw 2.092 2.440 nonbonded pdb=" OH TYR A 522 " pdb=" O VAL A 584 " model vdw 2.092 2.440 nonbonded pdb=" OH TYR D 522 " pdb=" O VAL D 584 " model vdw 2.092 2.440 ... (remaining 259126 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 19122 2.51 5 N 4722 2.21 5 O 5508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.010 Extract box with map and model: 12.260 Check model and map are aligned: 0.310 Process input model: 56.820 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:8.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 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 : 0.006 0.072 30180 Z= 0.378 Angle : 0.718 11.868 40668 Z= 0.446 Chirality : 0.053 0.389 4302 Planarity : 0.004 0.041 5190 Dihedral : 14.672 90.096 11112 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.87 % Favored : 97.96 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3474 helix: 0.82 (0.11), residues: 2124 sheet: 0.80 (0.41), residues: 156 loop : -0.59 (0.19), residues: 1194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 558 time to evaluate : 2.667 Fit side-chains outliers start: 18 outliers final: 2 residues processed: 561 average time/residue: 1.2664 time to fit residues: 819.3170 Evaluate side-chains 393 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 391 time to evaluate : 2.671 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 3.6557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 9.9990 chunk 263 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 272 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 87 ASN A 273 ASN A 389 ASN A 399 ASN A 433 ASN A 505 ASN A 543 GLN B 30 ASN B 273 ASN B 399 ASN B 433 ASN B 436 ASN B 543 GLN C 30 ASN C 87 ASN C 273 ASN C 389 ASN C 399 ASN C 433 ASN C 436 ASN C 548 ASN D 30 ASN D 87 ASN D 273 ASN D 286 ASN D 389 ASN D 399 ASN D 433 ASN D 436 ASN D 548 ASN E 30 ASN E 87 ASN E 110 ASN E 273 ASN E 399 ASN E 433 ASN E 436 ASN E 543 GLN F 30 ASN F 67 HIS F 110 ASN F 273 ASN F 399 ASN F 433 ASN F 436 ASN F 543 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 30180 Z= 0.197 Angle : 0.475 5.734 40668 Z= 0.263 Chirality : 0.041 0.139 4302 Planarity : 0.003 0.036 5190 Dihedral : 4.335 23.947 3798 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.41 % Favored : 98.42 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.15), residues: 3474 helix: 1.17 (0.11), residues: 2190 sheet: 0.65 (0.44), residues: 156 loop : -0.42 (0.20), residues: 1128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 450 time to evaluate : 2.704 Fit side-chains outliers start: 47 outliers final: 13 residues processed: 467 average time/residue: 1.1683 time to fit residues: 637.1119 Evaluate side-chains 397 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 384 time to evaluate : 2.674 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.6107 time to fit residues: 7.6019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 263 optimal weight: 0.8980 chunk 215 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 316 optimal weight: 0.7980 chunk 342 optimal weight: 0.9980 chunk 281 optimal weight: 7.9990 chunk 313 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 253 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 87 ASN A 110 ASN A 436 ASN A 543 GLN B 30 ASN B 87 ASN C 30 ASN C 110 ASN C 280 ASN C 548 ASN D 30 ASN D 110 ASN D 389 ASN D 548 ASN E 30 ASN E 110 ASN F 30 ASN F 67 HIS F 87 ASN F 110 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 30180 Z= 0.185 Angle : 0.436 5.344 40668 Z= 0.243 Chirality : 0.040 0.142 4302 Planarity : 0.003 0.036 5190 Dihedral : 4.077 22.168 3798 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.47 % Favored : 98.36 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.16 (0.15), residues: 3474 helix: 1.41 (0.11), residues: 2190 sheet: 0.43 (0.44), residues: 156 loop : -0.34 (0.19), residues: 1128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 423 time to evaluate : 2.674 Fit side-chains outliers start: 66 outliers final: 15 residues processed: 458 average time/residue: 1.1796 time to fit residues: 630.0884 Evaluate side-chains 408 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 393 time to evaluate : 2.661 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 8 residues processed: 7 average time/residue: 0.8899 time to fit residues: 11.1689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 212 optimal weight: 3.9990 chunk 317 optimal weight: 4.9990 chunk 336 optimal weight: 1.9990 chunk 165 optimal weight: 0.2980 chunk 301 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 110 ASN B 30 ASN B 260 GLN B 543 GLN C 30 ASN C 110 ASN C 311 ASN C 548 ASN D 30 ASN D 543 GLN D 548 ASN E 30 ASN E 110 ASN E 543 GLN F 30 ASN F 67 HIS F 110 ASN F 543 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 30180 Z= 0.187 Angle : 0.435 5.410 40668 Z= 0.241 Chirality : 0.040 0.141 4302 Planarity : 0.003 0.036 5190 Dihedral : 4.002 21.854 3798 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.67 % Favored : 98.16 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.25 (0.15), residues: 3474 helix: 1.50 (0.11), residues: 2190 sheet: 0.28 (0.44), residues: 156 loop : -0.33 (0.19), residues: 1128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 416 time to evaluate : 2.668 Fit side-chains outliers start: 59 outliers final: 22 residues processed: 445 average time/residue: 1.2033 time to fit residues: 626.2295 Evaluate side-chains 405 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 383 time to evaluate : 2.669 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 12 residues processed: 10 average time/residue: 0.7832 time to fit residues: 13.4747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 0.9990 chunk 190 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 250 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 287 optimal weight: 8.9990 chunk 232 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 171 optimal weight: 7.9990 chunk 301 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 543 GLN B 30 ASN B 87 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 ASN C 30 ASN C 110 ASN C 548 ASN D 30 ASN D 110 ASN D 548 ASN E 110 ASN E 548 ASN F 30 ASN F 67 HIS F 87 ASN F 110 ASN F 260 GLN F 311 ASN F 548 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 30180 Z= 0.167 Angle : 0.425 7.402 40668 Z= 0.236 Chirality : 0.039 0.140 4302 Planarity : 0.003 0.035 5190 Dihedral : 3.910 22.187 3798 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.73 % Favored : 98.10 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.32 (0.15), residues: 3474 helix: 1.56 (0.11), residues: 2190 sheet: 0.20 (0.43), residues: 156 loop : -0.31 (0.19), residues: 1128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 399 time to evaluate : 2.652 Fit side-chains outliers start: 63 outliers final: 28 residues processed: 428 average time/residue: 1.1562 time to fit residues: 579.5903 Evaluate side-chains 411 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 383 time to evaluate : 2.677 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 16 residues processed: 12 average time/residue: 0.7342 time to fit residues: 14.6815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 8.9990 chunk 302 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 336 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 111 optimal weight: 0.1980 chunk 176 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 311 ASN A 360 ASN A 543 GLN B 30 ASN B 110 ASN B 311 ASN C 30 ASN C 548 ASN D 30 ASN D 543 GLN D 548 ASN E 30 ASN E 110 ASN E 543 GLN E 548 ASN F 30 ASN F 67 HIS F 548 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 30180 Z= 0.288 Angle : 0.476 9.975 40668 Z= 0.262 Chirality : 0.042 0.145 4302 Planarity : 0.003 0.035 5190 Dihedral : 4.076 23.922 3798 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.04 % Favored : 97.78 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.18 (0.15), residues: 3474 helix: 1.44 (0.11), residues: 2190 sheet: 0.16 (0.43), residues: 156 loop : -0.33 (0.19), residues: 1128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 393 time to evaluate : 2.746 Fit side-chains outliers start: 62 outliers final: 31 residues processed: 427 average time/residue: 1.2291 time to fit residues: 612.6632 Evaluate side-chains 412 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 381 time to evaluate : 2.682 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 19 residues processed: 12 average time/residue: 0.6411 time to fit residues: 13.6945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 245 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 283 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 335 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 217 ASN A 311 ASN A 360 ASN B 110 ASN B 543 GLN B 548 ASN C 30 ASN C 548 ASN D 30 ASN D 110 ASN D 548 ASN E 110 ASN F 30 ASN F 67 HIS F 110 ASN F 543 GLN F 548 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 30180 Z= 0.279 Angle : 0.470 6.538 40668 Z= 0.259 Chirality : 0.041 0.146 4302 Planarity : 0.003 0.035 5190 Dihedral : 4.106 24.737 3798 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.84 % Favored : 97.99 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.12 (0.15), residues: 3474 helix: 1.39 (0.11), residues: 2184 sheet: 0.09 (0.42), residues: 156 loop : -0.33 (0.19), residues: 1134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 392 time to evaluate : 2.730 Fit side-chains outliers start: 63 outliers final: 29 residues processed: 423 average time/residue: 1.2063 time to fit residues: 595.2079 Evaluate side-chains 410 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 381 time to evaluate : 2.678 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 19 residues processed: 10 average time/residue: 0.8141 time to fit residues: 13.6670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 228 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 263 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 110 ASN A 217 ASN A 257 ASN A 311 ASN A 360 ASN A 543 GLN B 110 ASN B 217 ASN C 30 ASN C 548 ASN D 30 ASN D 217 ASN D 548 ASN E 543 GLN E 548 ASN F 30 ASN F 67 HIS F 110 ASN F 217 ASN F 548 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 30180 Z= 0.181 Angle : 0.440 7.378 40668 Z= 0.243 Chirality : 0.039 0.142 4302 Planarity : 0.003 0.036 5190 Dihedral : 3.964 22.158 3798 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.84 % Favored : 97.99 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.24 (0.15), residues: 3474 helix: 1.51 (0.11), residues: 2190 sheet: 0.03 (0.42), residues: 156 loop : -0.32 (0.19), residues: 1128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 393 time to evaluate : 2.703 Fit side-chains outliers start: 52 outliers final: 26 residues processed: 421 average time/residue: 1.1944 time to fit residues: 590.3728 Evaluate side-chains 403 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 377 time to evaluate : 2.676 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 20 residues processed: 6 average time/residue: 1.1134 time to fit residues: 11.5663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 0.7980 chunk 321 optimal weight: 0.5980 chunk 293 optimal weight: 9.9990 chunk 312 optimal weight: 0.7980 chunk 188 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 295 optimal weight: 0.7980 chunk 311 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 217 ASN A 311 ASN A 360 ASN B 30 ASN B 87 ASN B 110 ASN B 548 ASN C 30 ASN C 110 ASN C 548 ASN D 30 ASN D 217 ASN D 548 ASN E 30 ASN E 110 ASN E 217 ASN E 280 ASN E 548 ASN F 67 HIS F 87 ASN F 110 ASN F 548 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 30180 Z= 0.179 Angle : 0.445 8.464 40668 Z= 0.244 Chirality : 0.039 0.141 4302 Planarity : 0.003 0.035 5190 Dihedral : 3.903 21.014 3798 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.84 % Favored : 97.99 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.29 (0.15), residues: 3474 helix: 1.53 (0.11), residues: 2196 sheet: 0.05 (0.42), residues: 156 loop : -0.27 (0.19), residues: 1122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 388 time to evaluate : 2.694 Fit side-chains outliers start: 34 outliers final: 20 residues processed: 412 average time/residue: 1.2011 time to fit residues: 581.6597 Evaluate side-chains 400 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 380 time to evaluate : 2.694 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 0.7009 time to fit residues: 5.4978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 0.7980 chunk 330 optimal weight: 2.9990 chunk 201 optimal weight: 0.2980 chunk 156 optimal weight: 0.9980 chunk 229 optimal weight: 6.9990 chunk 346 optimal weight: 0.9990 chunk 319 optimal weight: 10.0000 chunk 276 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 213 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 217 ASN A 311 ASN A 360 ASN A 543 GLN B 30 ASN B 110 ASN B 217 ASN C 30 ASN C 217 ASN C 548 ASN D 30 ASN D 217 ASN D 257 ASN D 548 ASN E 110 ASN E 543 GLN F 67 HIS F 548 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 30180 Z= 0.176 Angle : 0.443 9.898 40668 Z= 0.243 Chirality : 0.039 0.188 4302 Planarity : 0.003 0.035 5190 Dihedral : 3.868 20.496 3798 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.87 % Favored : 97.96 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.32 (0.15), residues: 3474 helix: 1.55 (0.11), residues: 2196 sheet: 0.07 (0.42), residues: 156 loop : -0.26 (0.19), residues: 1122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 393 time to evaluate : 2.683 Fit side-chains outliers start: 38 outliers final: 19 residues processed: 423 average time/residue: 1.1832 time to fit residues: 585.7198 Evaluate side-chains 398 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 379 time to evaluate : 2.687 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.7844 time to fit residues: 5.5888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 0.6980 chunk 294 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 254 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 276 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 283 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 217 ASN A 311 ASN A 360 ASN A 543 GLN B 30 ASN B 87 ASN B 110 ASN B 543 GLN B 548 ASN C 30 ASN D 30 ASN D 217 ASN D 311 ASN D 360 ASN E 30 ASN E 548 ASN F 67 HIS F 543 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.122790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.100026 restraints weight = 36804.191| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.82 r_work: 0.3035 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 30180 Z= 0.184 Angle : 0.449 11.498 40668 Z= 0.246 Chirality : 0.039 0.142 4302 Planarity : 0.003 0.035 5190 Dihedral : 3.872 20.997 3798 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.99 % Favored : 97.84 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.32 (0.15), residues: 3474 helix: 1.54 (0.11), residues: 2196 sheet: 0.06 (0.42), residues: 156 loop : -0.25 (0.19), residues: 1122 =============================================================================== Job complete usr+sys time: 9028.36 seconds wall clock time: 158 minutes 16.42 seconds (9496.42 seconds total)