Starting phenix.real_space_refine (version: dev) on Tue Feb 21 23:31:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz3_30022/02_2023/6lz3_30022_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz3_30022/02_2023/6lz3_30022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz3_30022/02_2023/6lz3_30022.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz3_30022/02_2023/6lz3_30022.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz3_30022/02_2023/6lz3_30022_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz3_30022/02_2023/6lz3_30022_updated.pdb" } resolution = 3.2 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= 0.001 sd= 0.008 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 Process input model Symmetric amino acids flipped Residue "A ASP 10": "OD1" <-> "OD2" Residue "A TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 90": "OD1" <-> "OD2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 162": "OD1" <-> "OD2" Residue "A ASP 190": "OD1" <-> "OD2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ASP 383": "OD1" <-> "OD2" Residue "A ASP 387": "OD1" <-> "OD2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A ASP 469": "OD1" <-> "OD2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A GLU 481": "OE1" <-> "OE2" Residue "B ASP 10": "OD1" <-> "OD2" Residue "B TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 90": "OD1" <-> "OD2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "B ASP 130": "OD1" <-> "OD2" Residue "B ASP 141": "OD1" <-> "OD2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 150": "OD1" <-> "OD2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 162": "OD1" <-> "OD2" Residue "B ASP 190": "OD1" <-> "OD2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ASP 383": "OD1" <-> "OD2" Residue "B ASP 387": "OD1" <-> "OD2" Residue "B ASP 400": "OD1" <-> "OD2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 413": "OE1" <-> "OE2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B ASP 469": "OD1" <-> "OD2" Residue "B ARG 474": "NH1" <-> "NH2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "C ASP 10": "OD1" <-> "OD2" Residue "C TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C ASP 130": "OD1" <-> "OD2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 150": "OD1" <-> "OD2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 162": "OD1" <-> "OD2" Residue "C ASP 190": "OD1" <-> "OD2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 275": "OE1" <-> "OE2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ASP 383": "OD1" <-> "OD2" Residue "C ASP 387": "OD1" <-> "OD2" Residue "C ASP 400": "OD1" <-> "OD2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 413": "OE1" <-> "OE2" Residue "C GLU 422": "OE1" <-> "OE2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C ASP 469": "OD1" <-> "OD2" Residue "C ARG 474": "NH1" <-> "NH2" Residue "C GLU 481": "OE1" <-> "OE2" Residue "D ASP 10": "OD1" <-> "OD2" Residue "D TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 90": "OD1" <-> "OD2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 112": "NH1" <-> "NH2" Residue "D ASP 130": "OD1" <-> "OD2" Residue "D ASP 141": "OD1" <-> "OD2" Residue "D PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 150": "OD1" <-> "OD2" Residue "D TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 162": "OD1" <-> "OD2" Residue "D ASP 190": "OD1" <-> "OD2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 275": "OE1" <-> "OE2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 341": "OE1" <-> "OE2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ASP 383": "OD1" <-> "OD2" Residue "D ASP 387": "OD1" <-> "OD2" Residue "D ASP 400": "OD1" <-> "OD2" Residue "D ASP 405": "OD1" <-> "OD2" Residue "D PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 413": "OE1" <-> "OE2" Residue "D GLU 422": "OE1" <-> "OE2" Residue "D GLU 456": "OE1" <-> "OE2" Residue "D ASP 469": "OD1" <-> "OD2" Residue "D ARG 474": "NH1" <-> "NH2" Residue "D GLU 481": "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: 15968 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3939 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 33, 'TRANS': 452} Chain: "B" Number of atoms: 3939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3939 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 33, 'TRANS': 452} Chain: "C" Number of atoms: 3939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3939 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 33, 'TRANS': 452} Chain: "D" Number of atoms: 3939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3939 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 33, 'TRANS': 452} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.54, per 1000 atoms: 0.53 Number of scatterers: 15968 At special positions: 0 Unit cell: (82.758, 124.137, 124.137, 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 48 16.00 P 8 15.00 O 2880 8.00 N 2804 7.00 C 10228 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.65 Conformation dependent library (CDL) restraints added in 2.2 seconds 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 8 sheets defined 42.0% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 20 through 23 No H-bonds generated for 'chain 'A' and resid 20 through 23' Processing helix chain 'A' and resid 49 through 64 removed outlier: 3.774A pdb=" N ILE A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 54 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 55 " --> pdb=" O TRP A 51 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 91 Processing helix chain 'A' and resid 104 through 120 removed outlier: 3.945A pdb=" N VAL A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 156 removed outlier: 3.683A pdb=" N ASN A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 209 through 219 removed outlier: 3.608A pdb=" N LYS A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 252 through 267 removed outlier: 3.602A pdb=" N LEU A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 removed outlier: 3.905A pdb=" N CYS A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.509A pdb=" N ARG A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 327 Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.897A pdb=" N TRP A 343 " --> pdb=" O MET A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 362 removed outlier: 3.634A pdb=" N VAL A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 377 removed outlier: 3.616A pdb=" N ASP A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 424 through 427 No H-bonds generated for 'chain 'A' and resid 424 through 427' Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 468 through 481 removed outlier: 3.857A pdb=" N GLY A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 480 " --> pdb=" O GLN A 476 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 23 No H-bonds generated for 'chain 'B' and resid 20 through 23' Processing helix chain 'B' and resid 49 through 64 removed outlier: 3.774A pdb=" N ILE B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER B 54 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 55 " --> pdb=" O TRP B 51 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 62 " --> pdb=" O ASN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'B' and resid 104 through 120 removed outlier: 3.945A pdb=" N VAL B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B 109 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 156 removed outlier: 3.684A pdb=" N ASN B 154 " --> pdb=" O ASP B 150 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.580A pdb=" N ALA B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG B 202 " --> pdb=" O LEU B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 202' Processing helix chain 'B' and resid 209 through 219 removed outlier: 3.607A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 252 through 267 removed outlier: 3.602A pdb=" N LEU B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 265 " --> pdb=" O MET B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.906A pdb=" N CYS B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 296 removed outlier: 3.510A pdb=" N ARG B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 327 Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.897A pdb=" N TRP B 343 " --> pdb=" O MET B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 362 removed outlier: 3.634A pdb=" N VAL B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 377 removed outlier: 3.616A pdb=" N ASP B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 424 through 427 No H-bonds generated for 'chain 'B' and resid 424 through 427' Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 442 through 444 No H-bonds generated for 'chain 'B' and resid 442 through 444' Processing helix chain 'B' and resid 447 through 451 Processing helix chain 'B' and resid 468 through 481 removed outlier: 3.858A pdb=" N GLY B 473 " --> pdb=" O ASP B 469 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN B 476 " --> pdb=" O LYS B 472 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 480 " --> pdb=" O GLN B 476 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 23 No H-bonds generated for 'chain 'C' and resid 20 through 23' Processing helix chain 'C' and resid 49 through 64 removed outlier: 3.773A pdb=" N ILE C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN C 55 " --> pdb=" O TRP C 51 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA C 62 " --> pdb=" O ASN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 104 through 120 removed outlier: 3.945A pdb=" N VAL C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 109 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C 119 " --> pdb=" O GLU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 156 removed outlier: 3.683A pdb=" N ASN C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG C 155 " --> pdb=" O PRO C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.580A pdb=" N ALA C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG C 202 " --> pdb=" O LEU C 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 202' Processing helix chain 'C' and resid 209 through 219 removed outlier: 3.608A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 252 through 267 removed outlier: 3.603A pdb=" N LEU C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL C 265 " --> pdb=" O MET C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 removed outlier: 3.905A pdb=" N CYS C 278 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 296 removed outlier: 3.510A pdb=" N ARG C 288 " --> pdb=" O SER C 284 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 296 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 Processing helix chain 'C' and resid 333 through 345 removed outlier: 3.896A pdb=" N TRP C 343 " --> pdb=" O MET C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 362 removed outlier: 3.634A pdb=" N VAL C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 377 removed outlier: 3.616A pdb=" N ASP C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 395 Processing helix chain 'C' and resid 424 through 427 No H-bonds generated for 'chain 'C' and resid 424 through 427' Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 442 through 444 No H-bonds generated for 'chain 'C' and resid 442 through 444' Processing helix chain 'C' and resid 447 through 451 Processing helix chain 'C' and resid 468 through 481 removed outlier: 3.857A pdb=" N GLY C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN C 476 " --> pdb=" O LYS C 472 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 480 " --> pdb=" O GLN C 476 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 23 No H-bonds generated for 'chain 'D' and resid 20 through 23' Processing helix chain 'D' and resid 49 through 64 removed outlier: 3.774A pdb=" N ILE D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER D 54 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 55 " --> pdb=" O TRP D 51 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA D 62 " --> pdb=" O ASN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 91 Processing helix chain 'D' and resid 104 through 120 removed outlier: 3.945A pdb=" N VAL D 108 " --> pdb=" O PRO D 104 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA D 119 " --> pdb=" O GLU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 156 removed outlier: 3.683A pdb=" N ASN D 154 " --> pdb=" O ASP D 150 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG D 155 " --> pdb=" O PRO D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 209 through 219 removed outlier: 3.608A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 242 through 246 Processing helix chain 'D' and resid 252 through 267 removed outlier: 3.602A pdb=" N LEU D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL D 265 " --> pdb=" O MET D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 279 removed outlier: 3.906A pdb=" N CYS D 278 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.509A pdb=" N ARG D 288 " --> pdb=" O SER D 284 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE D 296 " --> pdb=" O ARG D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 Processing helix chain 'D' and resid 333 through 345 removed outlier: 3.897A pdb=" N TRP D 343 " --> pdb=" O MET D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 362 removed outlier: 3.634A pdb=" N VAL D 355 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 361 " --> pdb=" O ALA D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 377 removed outlier: 3.616A pdb=" N ASP D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 395 Processing helix chain 'D' and resid 424 through 427 No H-bonds generated for 'chain 'D' and resid 424 through 427' Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 442 through 444 No H-bonds generated for 'chain 'D' and resid 442 through 444' Processing helix chain 'D' and resid 447 through 451 Processing helix chain 'D' and resid 468 through 481 removed outlier: 3.857A pdb=" N GLY D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLN D 476 " --> pdb=" O LYS D 472 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER D 480 " --> pdb=" O GLN D 476 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU D 481 " --> pdb=" O ALA D 477 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 6 removed outlier: 6.701A pdb=" N VAL A 73 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N TRP A 35 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG A 75 " --> pdb=" O TRP A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 95 through 97 removed outlier: 6.902A pdb=" N VAL A 123 " --> pdb=" O VAL A 96 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 3 through 6 removed outlier: 6.702A pdb=" N VAL B 73 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N TRP B 35 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG B 75 " --> pdb=" O TRP B 35 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 95 through 97 removed outlier: 6.901A pdb=" N VAL B 123 " --> pdb=" O VAL B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 3 through 6 removed outlier: 6.701A pdb=" N VAL C 73 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TRP C 35 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG C 75 " --> pdb=" O TRP C 35 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 95 through 97 removed outlier: 6.901A pdb=" N VAL C 123 " --> pdb=" O VAL C 96 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 3 through 6 removed outlier: 6.702A pdb=" N VAL D 73 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TRP D 35 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG D 75 " --> pdb=" O TRP D 35 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 95 through 97 removed outlier: 6.902A pdb=" N VAL D 123 " --> pdb=" O VAL D 96 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 384 hydrogen bonds defined for protein. 1140 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: 3.74 Time building geometry restraints manager: 6.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5109 1.34 - 1.46: 3092 1.46 - 1.57: 8182 1.57 - 1.69: 13 1.69 - 1.81: 84 Bond restraints: 16480 Sorted by residual: bond pdb=" N LEU C 310 " pdb=" CA LEU C 310 " ideal model delta sigma weight residual 1.457 1.537 -0.080 1.29e-02 6.01e+03 3.82e+01 bond pdb=" N LEU D 310 " pdb=" CA LEU D 310 " ideal model delta sigma weight residual 1.457 1.537 -0.080 1.29e-02 6.01e+03 3.81e+01 bond pdb=" N LEU A 310 " pdb=" CA LEU A 310 " ideal model delta sigma weight residual 1.457 1.537 -0.079 1.29e-02 6.01e+03 3.78e+01 bond pdb=" N LEU B 310 " pdb=" CA LEU B 310 " ideal model delta sigma weight residual 1.457 1.537 -0.079 1.29e-02 6.01e+03 3.77e+01 bond pdb=" CA HIS B 309 " pdb=" C HIS B 309 " ideal model delta sigma weight residual 1.522 1.592 -0.070 1.20e-02 6.94e+03 3.40e+01 ... (remaining 16475 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.40: 696 106.40 - 113.59: 8602 113.59 - 120.78: 7752 120.78 - 127.97: 5150 127.97 - 135.16: 308 Bond angle restraints: 22508 Sorted by residual: angle pdb=" C LEU A 310 " pdb=" N ARG A 311 " pdb=" CA ARG A 311 " ideal model delta sigma weight residual 121.54 135.16 -13.62 1.91e+00 2.74e-01 5.09e+01 angle pdb=" C LEU B 310 " pdb=" N ARG B 311 " pdb=" CA ARG B 311 " ideal model delta sigma weight residual 121.54 135.10 -13.56 1.91e+00 2.74e-01 5.04e+01 angle pdb=" C LEU C 310 " pdb=" N ARG C 311 " pdb=" CA ARG C 311 " ideal model delta sigma weight residual 121.54 135.09 -13.55 1.91e+00 2.74e-01 5.03e+01 angle pdb=" C LEU D 310 " pdb=" N ARG D 311 " pdb=" CA ARG D 311 " ideal model delta sigma weight residual 121.54 135.06 -13.52 1.91e+00 2.74e-01 5.01e+01 angle pdb=" N VAL A 317 " pdb=" CA VAL A 317 " pdb=" C VAL A 317 " ideal model delta sigma weight residual 111.91 106.15 5.76 8.90e-01 1.26e+00 4.19e+01 ... (remaining 22503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.03: 8752 22.03 - 44.05: 660 44.05 - 66.08: 136 66.08 - 88.10: 16 88.10 - 110.13: 12 Dihedral angle restraints: 9576 sinusoidal: 3912 harmonic: 5664 Sorted by residual: dihedral pdb=" CA THR C 395 " pdb=" C THR C 395 " pdb=" N GLY C 396 " pdb=" CA GLY C 396 " ideal model delta harmonic sigma weight residual 180.00 135.58 44.42 0 5.00e+00 4.00e-02 7.89e+01 dihedral pdb=" CA THR A 395 " pdb=" C THR A 395 " pdb=" N GLY A 396 " pdb=" CA GLY A 396 " ideal model delta harmonic sigma weight residual 180.00 135.58 44.42 0 5.00e+00 4.00e-02 7.89e+01 dihedral pdb=" CA THR D 395 " pdb=" C THR D 395 " pdb=" N GLY D 396 " pdb=" CA GLY D 396 " ideal model delta harmonic sigma weight residual 180.00 135.62 44.38 0 5.00e+00 4.00e-02 7.88e+01 ... (remaining 9573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2059 0.085 - 0.170: 246 0.170 - 0.256: 27 0.256 - 0.341: 0 0.341 - 0.426: 4 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CG LEU C 398 " pdb=" CB LEU C 398 " pdb=" CD1 LEU C 398 " pdb=" CD2 LEU C 398 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" CG LEU B 398 " pdb=" CB LEU B 398 " pdb=" CD1 LEU B 398 " pdb=" CD2 LEU B 398 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CG LEU D 398 " pdb=" CB LEU D 398 " pdb=" CD1 LEU D 398 " pdb=" CD2 LEU D 398 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.47e+00 ... (remaining 2333 not shown) Planarity restraints: 2884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 304 " 0.074 5.00e-02 4.00e+02 1.14e-01 2.06e+01 pdb=" N PRO A 305 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 305 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 305 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 304 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO C 305 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO C 305 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO C 305 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 304 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO B 305 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO B 305 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 305 " -0.060 5.00e-02 4.00e+02 ... (remaining 2881 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1720 2.74 - 3.28: 14641 3.28 - 3.82: 26095 3.82 - 4.36: 32057 4.36 - 4.90: 53110 Nonbonded interactions: 127623 Sorted by model distance: nonbonded pdb=" O TRP C 391 " pdb=" OG1 THR C 395 " model vdw 2.201 2.440 nonbonded pdb=" O TRP B 391 " pdb=" OG1 THR B 395 " model vdw 2.201 2.440 nonbonded pdb=" O TRP D 391 " pdb=" OG1 THR D 395 " model vdw 2.201 2.440 nonbonded pdb=" O TRP A 391 " pdb=" OG1 THR A 395 " model vdw 2.202 2.440 nonbonded pdb=" O THR C 378 " pdb=" OG1 THR C 378 " model vdw 2.253 2.440 ... (remaining 127618 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 48 5.16 5 C 10228 2.51 5 N 2804 2.21 5 O 2880 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=0.00 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.350 Check model and map are aligned: 0.250 Process input model: 38.050 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.140 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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 : 0.007 0.091 16480 Z= 0.468 Angle : 1.201 17.232 22508 Z= 0.653 Chirality : 0.058 0.426 2336 Planarity : 0.009 0.114 2884 Dihedral : 16.422 110.126 5920 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.68 % Favored : 90.91 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -6.45 (0.11), residues: 1936 helix: -4.57 (0.06), residues: 984 sheet: -3.76 (0.32), residues: 132 loop : -3.81 (0.16), residues: 820 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 262 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 12 residues processed: 310 average time/residue: 0.3494 time to fit residues: 149.9783 Evaluate side-chains 174 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 162 time to evaluate : 1.832 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1366 time to fit residues: 5.6235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 77 optimal weight: 0.0010 chunk 150 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 174 optimal weight: 10.0000 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 59 HIS A 154 ASN A 244 HIS A 246 HIS A 263 GLN B 58 ASN B 59 HIS B 154 ASN B 244 HIS B 246 HIS B 257 HIS B 263 GLN B 365 GLN C 58 ASN C 59 HIS C 154 ASN C 244 HIS C 246 HIS C 257 HIS C 263 GLN D 58 ASN D 59 HIS D 154 ASN D 244 HIS D 246 HIS D 263 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 16480 Z= 0.212 Angle : 0.701 10.208 22508 Z= 0.348 Chirality : 0.042 0.155 2336 Planarity : 0.006 0.087 2884 Dihedral : 7.633 96.065 2180 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -4.93 (0.15), residues: 1936 helix: -3.15 (0.12), residues: 980 sheet: -3.39 (0.35), residues: 132 loop : -3.27 (0.18), residues: 824 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 1.880 Fit side-chains outliers start: 42 outliers final: 30 residues processed: 205 average time/residue: 0.3131 time to fit residues: 93.5884 Evaluate side-chains 172 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 1.840 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1469 time to fit residues: 10.7755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 HIS ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.102 16480 Z= 0.451 Angle : 0.779 7.979 22508 Z= 0.383 Chirality : 0.048 0.145 2336 Planarity : 0.006 0.062 2884 Dihedral : 7.074 73.114 2180 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.16), residues: 1936 helix: -2.31 (0.13), residues: 972 sheet: -3.12 (0.38), residues: 132 loop : -2.84 (0.20), residues: 832 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 141 time to evaluate : 1.758 Fit side-chains outliers start: 55 outliers final: 33 residues processed: 181 average time/residue: 0.2786 time to fit residues: 76.2223 Evaluate side-chains 154 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 121 time to evaluate : 1.978 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1488 time to fit residues: 11.8035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 90 optimal weight: 0.0770 chunk 19 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 91 optimal weight: 0.0870 chunk 166 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 365 GLN C 297 ASN D 210 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 16480 Z= 0.156 Angle : 0.571 6.353 22508 Z= 0.285 Chirality : 0.041 0.125 2336 Planarity : 0.004 0.059 2884 Dihedral : 6.563 77.818 2180 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer Outliers : 1.57 % 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: -3.28 (0.17), residues: 1936 helix: -1.57 (0.15), residues: 1000 sheet: -3.19 (0.35), residues: 132 loop : -2.69 (0.20), residues: 804 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 1.918 Fit side-chains outliers start: 26 outliers final: 14 residues processed: 168 average time/residue: 0.3034 time to fit residues: 75.3498 Evaluate side-chains 140 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 1.904 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1427 time to fit residues: 6.4081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 138 optimal weight: 0.2980 chunk 76 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 94 optimal weight: 0.0970 chunk 166 optimal weight: 2.9990 chunk 46 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 409 ASN B 365 GLN C 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 16480 Z= 0.142 Angle : 0.546 6.255 22508 Z= 0.270 Chirality : 0.040 0.144 2336 Planarity : 0.004 0.051 2884 Dihedral : 6.302 74.804 2180 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.76 (0.18), residues: 1936 helix: -1.12 (0.16), residues: 992 sheet: -2.97 (0.37), residues: 132 loop : -2.47 (0.21), residues: 812 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 2.021 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 165 average time/residue: 0.2857 time to fit residues: 71.8657 Evaluate side-chains 142 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.900 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1569 time to fit residues: 5.1504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 7.9990 chunk 167 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 409 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 16480 Z= 0.236 Angle : 0.582 6.385 22508 Z= 0.286 Chirality : 0.042 0.157 2336 Planarity : 0.004 0.046 2884 Dihedral : 6.281 73.719 2180 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer Outliers : 1.81 % 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: -2.54 (0.18), residues: 1936 helix: -0.89 (0.16), residues: 996 sheet: -2.81 (0.38), residues: 132 loop : -2.43 (0.21), residues: 808 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 6 residues processed: 164 average time/residue: 0.2785 time to fit residues: 70.1032 Evaluate side-chains 143 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 1.906 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1596 time to fit residues: 4.4230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 0.9990 chunk 20 optimal weight: 0.0770 chunk 105 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 185 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 409 ASN B 365 GLN C 58 ASN C 297 ASN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 16480 Z= 0.163 Angle : 0.544 7.395 22508 Z= 0.268 Chirality : 0.041 0.139 2336 Planarity : 0.004 0.044 2884 Dihedral : 6.108 74.326 2180 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer Outliers : 1.27 % 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: -2.27 (0.19), residues: 1936 helix: -0.65 (0.17), residues: 992 sheet: -2.78 (0.38), residues: 132 loop : -2.31 (0.21), residues: 812 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 163 average time/residue: 0.2846 time to fit residues: 70.2575 Evaluate side-chains 149 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 141 time to evaluate : 1.989 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1370 time to fit residues: 4.8156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 16480 Z= 0.226 Angle : 0.574 8.022 22508 Z= 0.280 Chirality : 0.042 0.143 2336 Planarity : 0.004 0.044 2884 Dihedral : 6.120 73.262 2180 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer Outliers : 0.97 % 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: -2.23 (0.19), residues: 1936 helix: -0.61 (0.16), residues: 992 sheet: -2.55 (0.39), residues: 132 loop : -2.35 (0.21), residues: 812 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 156 average time/residue: 0.2737 time to fit residues: 65.7299 Evaluate side-chains 144 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 138 time to evaluate : 1.848 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1548 time to fit residues: 4.1791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 3.9990 chunk 161 optimal weight: 0.0980 chunk 172 optimal weight: 0.5980 chunk 103 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 155 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN C 297 ASN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 16480 Z= 0.219 Angle : 0.570 7.131 22508 Z= 0.278 Chirality : 0.042 0.149 2336 Planarity : 0.004 0.050 2884 Dihedral : 6.110 74.027 2180 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer Outliers : 0.85 % 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: -2.19 (0.19), residues: 1936 helix: -0.64 (0.16), residues: 1016 sheet: -2.37 (0.40), residues: 132 loop : -2.31 (0.22), residues: 788 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 156 average time/residue: 0.2895 time to fit residues: 68.3885 Evaluate side-chains 150 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1404 time to fit residues: 4.7574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 117 optimal weight: 0.4980 chunk 93 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN C 58 ASN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 16480 Z= 0.240 Angle : 0.586 7.350 22508 Z= 0.285 Chirality : 0.042 0.146 2336 Planarity : 0.004 0.050 2884 Dihedral : 6.124 73.825 2180 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer Outliers : 0.30 % 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: -2.18 (0.19), residues: 1936 helix: -0.66 (0.16), residues: 1016 sheet: -2.38 (0.40), residues: 132 loop : -2.27 (0.22), residues: 788 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 145 average time/residue: 0.3010 time to fit residues: 65.5943 Evaluate side-chains 137 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.998 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 chunk 140 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 0.0570 chunk 152 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 156 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN B 58 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN C 58 ASN D 58 ASN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.157625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.117030 restraints weight = 21909.028| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.49 r_work: 0.3334 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 16480 Z= 0.148 Angle : 0.537 6.556 22508 Z= 0.262 Chirality : 0.040 0.144 2336 Planarity : 0.004 0.053 2884 Dihedral : 5.924 72.608 2180 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer Outliers : 0.30 % 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: -1.94 (0.19), residues: 1936 helix: -0.44 (0.16), residues: 1016 sheet: -2.41 (0.39), residues: 132 loop : -2.15 (0.22), residues: 788 =============================================================================== Job complete usr+sys time: 2870.58 seconds wall clock time: 52 minutes 48.34 seconds (3168.34 seconds total)