Starting phenix.real_space_refine on Sat Mar 16 23:17:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz3_30022/03_2024/6lz3_30022_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz3_30022/03_2024/6lz3_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_30022/03_2024/6lz3_30022.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz3_30022/03_2024/6lz3_30022.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz3_30022/03_2024/6lz3_30022_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz3_30022/03_2024/6lz3_30022_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 8.79, per 1000 atoms: 0.55 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: 6.08 Conformation dependent library (CDL) restraints added in 2.7 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: 2.90 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: 3.88 Time building geometry restraints manager: 6.58 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: 8776 22.03 - 44.05: 752 44.05 - 66.08: 192 66.08 - 88.10: 16 88.10 - 110.13: 12 Dihedral angle restraints: 9748 sinusoidal: 4084 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 9745 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 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.590 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 41.940 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 : 17.574 110.126 6092 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 % Allowed : 8.45 % Favored : 87.68 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP B 483 HIS 0.005 0.001 HIS C 95 PHE 0.028 0.003 PHE D 313 TYR 0.029 0.003 TYR C 43 ARG 0.004 0.001 ARG A 406 *********************** 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 : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5564 (mmt) cc_final: 0.5347 (mmt) REVERT: B 413 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6586 (tp30) REVERT: C 113 LEU cc_start: 0.8772 (tp) cc_final: 0.8563 (tp) REVERT: D 1 MET cc_start: 0.5536 (mmt) cc_final: 0.5266 (mmt) outliers start: 64 outliers final: 12 residues processed: 310 average time/residue: 0.3503 time to fit residues: 150.8112 Evaluate side-chains 175 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 475 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.8980 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: 0.9790 ------------------------------------------------------------------------------- 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 210 ASN A 244 HIS A 246 HIS A 263 GLN B 58 ASN B 59 HIS B 154 ASN B 210 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 210 ASN D 244 HIS D 246 HIS D 263 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16480 Z= 0.208 Angle : 0.695 9.495 22508 Z= 0.344 Chirality : 0.042 0.144 2336 Planarity : 0.006 0.087 2884 Dihedral : 11.853 89.830 2372 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 3.08 % Allowed : 11.41 % Favored : 85.51 % 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: -4.89 (0.15), residues: 1936 helix: -3.10 (0.12), residues: 980 sheet: -3.41 (0.35), residues: 132 loop : -3.26 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 483 HIS 0.004 0.001 HIS C 59 PHE 0.009 0.001 PHE D 417 TYR 0.022 0.002 TYR C 43 ARG 0.007 0.001 ARG B 474 *********************** 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 223 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 172 time to evaluate : 1.646 Fit side-chains REVERT: A 1 MET cc_start: 0.5791 (mmt) cc_final: 0.5498 (mmt) REVERT: A 113 LEU cc_start: 0.8853 (tp) cc_final: 0.8530 (mm) REVERT: B 113 LEU cc_start: 0.8687 (tp) cc_final: 0.8462 (mm) REVERT: B 365 GLN cc_start: 0.6553 (OUTLIER) cc_final: 0.6326 (mm-40) REVERT: B 474 ARG cc_start: 0.7320 (tpt90) cc_final: 0.6909 (tpt90) REVERT: C 113 LEU cc_start: 0.8870 (tp) cc_final: 0.8578 (mm) REVERT: C 474 ARG cc_start: 0.7075 (tpt90) cc_final: 0.6736 (tpt90) REVERT: D 1 MET cc_start: 0.5694 (mmt) cc_final: 0.5311 (mmt) REVERT: D 139 VAL cc_start: 0.8319 (t) cc_final: 0.8102 (m) outliers start: 51 outliers final: 33 residues processed: 212 average time/residue: 0.2923 time to fit residues: 90.5324 Evaluate side-chains 177 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 143 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 412 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 485 LEU 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: 6.9990 chunk 145 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 188 optimal weight: 0.0670 chunk 155 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 16480 Z= 0.337 Angle : 0.701 7.165 22508 Z= 0.344 Chirality : 0.045 0.159 2336 Planarity : 0.005 0.063 2884 Dihedral : 11.357 63.229 2358 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 4.53 % Allowed : 14.19 % Favored : 81.28 % 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: -3.91 (0.16), residues: 1936 helix: -2.19 (0.14), residues: 988 sheet: -3.12 (0.36), residues: 132 loop : -2.91 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 6 HIS 0.007 0.001 HIS C 349 PHE 0.012 0.002 PHE D 417 TYR 0.025 0.002 TYR A 43 ARG 0.007 0.001 ARG B 47 *********************** 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 229 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 154 time to evaluate : 1.894 Fit side-chains REVERT: A 1 MET cc_start: 0.5755 (mmt) cc_final: 0.5296 (mmt) REVERT: A 113 LEU cc_start: 0.9000 (tp) cc_final: 0.8675 (mm) REVERT: B 113 LEU cc_start: 0.8881 (tp) cc_final: 0.8640 (mm) REVERT: B 394 ILE cc_start: 0.7973 (tp) cc_final: 0.7740 (tp) REVERT: C 113 LEU cc_start: 0.8977 (tp) cc_final: 0.8745 (mm) REVERT: D 1 MET cc_start: 0.5707 (mmt) cc_final: 0.5223 (mmt) REVERT: D 139 VAL cc_start: 0.8407 (t) cc_final: 0.8201 (m) outliers start: 75 outliers final: 55 residues processed: 207 average time/residue: 0.2603 time to fit residues: 81.8416 Evaluate side-chains 191 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 136 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 412 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 83 optimal weight: 0.2980 chunk 117 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 chunk 185 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16480 Z= 0.181 Angle : 0.574 6.291 22508 Z= 0.284 Chirality : 0.041 0.139 2336 Planarity : 0.004 0.058 2884 Dihedral : 10.414 59.640 2357 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 3.62 % Allowed : 16.12 % Favored : 80.25 % 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: -3.15 (0.18), residues: 1936 helix: -1.47 (0.15), residues: 984 sheet: -3.04 (0.36), residues: 132 loop : -2.60 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 443 HIS 0.003 0.001 HIS A 349 PHE 0.008 0.001 PHE B 312 TYR 0.019 0.001 TYR D 43 ARG 0.004 0.000 ARG C 353 *********************** 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 213 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 153 time to evaluate : 1.668 Fit side-chains REVERT: A 1 MET cc_start: 0.5673 (mmt) cc_final: 0.5148 (mmt) REVERT: A 113 LEU cc_start: 0.8929 (tp) cc_final: 0.8631 (mm) REVERT: A 394 ILE cc_start: 0.7836 (tp) cc_final: 0.7468 (tp) REVERT: A 409 ASN cc_start: 0.6232 (t0) cc_final: 0.5947 (t0) REVERT: B 113 LEU cc_start: 0.8837 (tp) cc_final: 0.8606 (mm) REVERT: B 394 ILE cc_start: 0.8177 (tp) cc_final: 0.7924 (tp) REVERT: B 485 LEU cc_start: -0.3114 (OUTLIER) cc_final: -0.3333 (tp) REVERT: C 74 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7638 (m) REVERT: C 113 LEU cc_start: 0.8894 (tp) cc_final: 0.8642 (mm) REVERT: D 1 MET cc_start: 0.5750 (mmt) cc_final: 0.5178 (mmt) REVERT: D 86 GLN cc_start: 0.8361 (tp40) cc_final: 0.8082 (tp40) REVERT: D 139 VAL cc_start: 0.8327 (t) cc_final: 0.8105 (m) REVERT: D 394 ILE cc_start: 0.8092 (tp) cc_final: 0.7603 (tp) outliers start: 60 outliers final: 45 residues processed: 195 average time/residue: 0.2593 time to fit residues: 77.3074 Evaluate side-chains 183 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 136 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 412 PHE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 485 LEU 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: 0.6980 chunk 2 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 210 ASN ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3338 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= 0.202 Angle : 0.565 6.463 22508 Z= 0.279 Chirality : 0.041 0.147 2336 Planarity : 0.004 0.050 2884 Dihedral : 10.156 59.906 2356 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 4.17 % Allowed : 16.67 % Favored : 79.17 % 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: -2.79 (0.18), residues: 1936 helix: -1.16 (0.16), residues: 996 sheet: -2.90 (0.37), residues: 132 loop : -2.46 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 6 HIS 0.009 0.001 HIS A 298 PHE 0.012 0.001 PHE D 417 TYR 0.019 0.001 TYR A 43 ARG 0.004 0.000 ARG B 353 *********************** 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 214 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 145 time to evaluate : 1.701 Fit side-chains REVERT: A 1 MET cc_start: 0.5720 (mmt) cc_final: 0.5166 (mmt) REVERT: A 113 LEU cc_start: 0.8952 (tp) cc_final: 0.8658 (mm) REVERT: A 409 ASN cc_start: 0.6185 (t0) cc_final: 0.5900 (t0) REVERT: B 113 LEU cc_start: 0.8777 (tp) cc_final: 0.8567 (mm) REVERT: B 485 LEU cc_start: -0.3173 (OUTLIER) cc_final: -0.3386 (tp) REVERT: C 74 THR cc_start: 0.7887 (OUTLIER) cc_final: 0.7649 (m) REVERT: C 113 LEU cc_start: 0.8878 (tp) cc_final: 0.8610 (mm) REVERT: C 394 ILE cc_start: 0.8239 (tp) cc_final: 0.7906 (tp) REVERT: D 1 MET cc_start: 0.5728 (mmt) cc_final: 0.5078 (mmt) REVERT: D 86 GLN cc_start: 0.8329 (tp40) cc_final: 0.8072 (tp40) REVERT: D 139 VAL cc_start: 0.8339 (t) cc_final: 0.8113 (m) REVERT: D 394 ILE cc_start: 0.8266 (tp) cc_final: 0.7919 (tp) REVERT: D 413 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6443 (pt0) outliers start: 69 outliers final: 46 residues processed: 194 average time/residue: 0.2517 time to fit residues: 75.5858 Evaluate side-chains 183 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 135 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 412 PHE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 0.0050 chunk 45 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 297 ASN ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3539 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= 0.153 Angle : 0.523 6.074 22508 Z= 0.259 Chirality : 0.040 0.134 2336 Planarity : 0.004 0.046 2884 Dihedral : 9.863 60.239 2356 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 3.74 % Allowed : 17.63 % Favored : 78.62 % 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: -2.39 (0.19), residues: 1936 helix: -0.82 (0.16), residues: 996 sheet: -2.79 (0.38), residues: 132 loop : -2.28 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 443 HIS 0.003 0.001 HIS C 95 PHE 0.009 0.001 PHE D 417 TYR 0.015 0.001 TYR C 43 ARG 0.003 0.000 ARG B 76 *********************** 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 220 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 158 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: A 113 LEU cc_start: 0.8918 (tp) cc_final: 0.8621 (mm) REVERT: B 113 LEU cc_start: 0.8777 (tp) cc_final: 0.8560 (mm) REVERT: B 485 LEU cc_start: -0.3253 (OUTLIER) cc_final: -0.3453 (tp) REVERT: C 74 THR cc_start: 0.7875 (OUTLIER) cc_final: 0.7675 (m) REVERT: C 86 GLN cc_start: 0.8238 (tp40) cc_final: 0.7928 (tp40) REVERT: C 113 LEU cc_start: 0.8826 (tp) cc_final: 0.8578 (mm) REVERT: D 1 MET cc_start: 0.5758 (mmt) cc_final: 0.5042 (mmt) REVERT: D 86 GLN cc_start: 0.8302 (tp40) cc_final: 0.8044 (tp40) REVERT: D 89 ARG cc_start: 0.7658 (tpp-160) cc_final: 0.7349 (mmp80) REVERT: D 139 VAL cc_start: 0.8313 (t) cc_final: 0.8095 (m) REVERT: D 394 ILE cc_start: 0.8198 (tp) cc_final: 0.7822 (tp) outliers start: 62 outliers final: 41 residues processed: 203 average time/residue: 0.2654 time to fit residues: 82.2570 Evaluate side-chains 187 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 144 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 185 optimal weight: 0.1980 chunk 115 optimal weight: 6.9990 chunk 112 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 GLN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16480 Z= 0.218 Angle : 0.564 6.647 22508 Z= 0.279 Chirality : 0.042 0.146 2336 Planarity : 0.004 0.052 2884 Dihedral : 9.999 59.262 2356 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.50 % Allowed : 18.42 % Favored : 78.08 % 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: -2.28 (0.19), residues: 1936 helix: -0.71 (0.16), residues: 996 sheet: -2.63 (0.39), residues: 132 loop : -2.28 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 443 HIS 0.004 0.001 HIS A 349 PHE 0.008 0.001 PHE A 281 TYR 0.016 0.002 TYR A 43 ARG 0.005 0.000 ARG B 353 *********************** 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 205 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 147 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.8904 (tp) cc_final: 0.8627 (mm) REVERT: A 479 LEU cc_start: 0.4793 (OUTLIER) cc_final: 0.4549 (tp) REVERT: B 113 LEU cc_start: 0.8784 (tp) cc_final: 0.8553 (mm) REVERT: B 394 ILE cc_start: 0.8324 (tp) cc_final: 0.7945 (tp) REVERT: C 74 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7740 (m) REVERT: C 86 GLN cc_start: 0.8285 (tp40) cc_final: 0.8042 (tp40) REVERT: C 113 LEU cc_start: 0.8814 (tp) cc_final: 0.8537 (mm) REVERT: C 394 ILE cc_start: 0.8327 (tp) cc_final: 0.8075 (tp) REVERT: D 74 THR cc_start: 0.7868 (OUTLIER) cc_final: 0.7616 (m) REVERT: D 86 GLN cc_start: 0.8341 (tp40) cc_final: 0.8100 (tp40) REVERT: D 89 ARG cc_start: 0.7663 (tpp-160) cc_final: 0.7332 (mmp80) REVERT: D 139 VAL cc_start: 0.8341 (t) cc_final: 0.8118 (m) REVERT: D 394 ILE cc_start: 0.8455 (tp) cc_final: 0.8211 (tp) outliers start: 58 outliers final: 44 residues processed: 190 average time/residue: 0.2556 time to fit residues: 74.8821 Evaluate side-chains 190 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 143 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 126 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 297 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** 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: 0.8071 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16480 Z= 0.261 Angle : 0.589 8.503 22508 Z= 0.289 Chirality : 0.042 0.140 2336 Planarity : 0.004 0.050 2884 Dihedral : 10.507 58.939 2356 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 3.93 % Allowed : 18.54 % Favored : 77.54 % 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: -2.26 (0.19), residues: 1936 helix: -0.70 (0.16), residues: 996 sheet: -2.53 (0.39), residues: 132 loop : -2.29 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 6 HIS 0.004 0.001 HIS A 349 PHE 0.009 0.001 PHE A 281 TYR 0.018 0.002 TYR C 43 ARG 0.006 0.000 ARG B 353 *********************** 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 203 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 138 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.8839 (tp) cc_final: 0.8569 (mm) REVERT: A 297 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7957 (t0) REVERT: A 394 ILE cc_start: 0.8496 (tp) cc_final: 0.8288 (tp) REVERT: A 479 LEU cc_start: 0.4822 (OUTLIER) cc_final: 0.4582 (tp) REVERT: B 113 LEU cc_start: 0.8805 (tp) cc_final: 0.8553 (mm) REVERT: B 394 ILE cc_start: 0.8372 (tp) cc_final: 0.7971 (tp) REVERT: C 86 GLN cc_start: 0.8314 (tp40) cc_final: 0.8088 (tp40) REVERT: C 113 LEU cc_start: 0.8830 (tp) cc_final: 0.8542 (mm) REVERT: D 86 GLN cc_start: 0.8388 (tp40) cc_final: 0.8155 (tp40) REVERT: D 89 ARG cc_start: 0.7675 (tpp-160) cc_final: 0.7327 (mmp80) REVERT: D 139 VAL cc_start: 0.8387 (t) cc_final: 0.8156 (m) REVERT: D 394 ILE cc_start: 0.8539 (tp) cc_final: 0.8337 (tp) outliers start: 65 outliers final: 54 residues processed: 185 average time/residue: 0.2591 time to fit residues: 74.1200 Evaluate side-chains 190 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 134 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 485 LEU 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: 9.9990 chunk 172 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16480 Z= 0.315 Angle : 0.623 8.474 22508 Z= 0.305 Chirality : 0.044 0.148 2336 Planarity : 0.004 0.047 2884 Dihedral : 10.953 59.770 2356 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 3.56 % Allowed : 19.08 % Favored : 77.36 % 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: -2.32 (0.18), residues: 1936 helix: -0.76 (0.16), residues: 1004 sheet: -2.48 (0.40), residues: 132 loop : -2.31 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 6 HIS 0.007 0.001 HIS A 298 PHE 0.014 0.001 PHE A 296 TYR 0.014 0.002 TYR A 293 ARG 0.007 0.000 ARG C 353 *********************** 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 196 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 137 time to evaluate : 1.647 Fit side-chains revert: symmetry clash REVERT: A 113 LEU cc_start: 0.8784 (tp) cc_final: 0.8541 (mm) REVERT: A 321 TYR cc_start: 0.8428 (m-10) cc_final: 0.8181 (m-80) REVERT: A 479 LEU cc_start: 0.4875 (OUTLIER) cc_final: 0.4629 (tp) REVERT: B 395 THR cc_start: 0.7905 (OUTLIER) cc_final: 0.7700 (m) REVERT: C 86 GLN cc_start: 0.8369 (tp40) cc_final: 0.8154 (tp40) REVERT: C 113 LEU cc_start: 0.8864 (tp) cc_final: 0.8568 (mm) REVERT: C 479 LEU cc_start: 0.4064 (OUTLIER) cc_final: 0.3823 (tp) REVERT: D 86 GLN cc_start: 0.8422 (tp40) cc_final: 0.8213 (tp40) REVERT: D 144 GLN cc_start: 0.7482 (mm110) cc_final: 0.7273 (mm110) outliers start: 59 outliers final: 52 residues processed: 179 average time/residue: 0.2583 time to fit residues: 70.8406 Evaluate side-chains 188 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 133 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16480 Z= 0.290 Angle : 0.611 8.260 22508 Z= 0.299 Chirality : 0.043 0.143 2336 Planarity : 0.004 0.046 2884 Dihedral : 11.101 59.969 2356 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 3.32 % Allowed : 19.44 % Favored : 77.23 % 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: -2.32 (0.18), residues: 1936 helix: -0.73 (0.16), residues: 1000 sheet: -2.47 (0.40), residues: 132 loop : -2.35 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 6 HIS 0.005 0.001 HIS A 349 PHE 0.008 0.001 PHE A 281 TYR 0.018 0.002 TYR C 43 ARG 0.006 0.000 ARG C 353 ********************** 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 190 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 135 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.8788 (tp) cc_final: 0.8523 (mm) REVERT: A 144 GLN cc_start: 0.7891 (mm110) cc_final: 0.7589 (tp40) REVERT: A 321 TYR cc_start: 0.8419 (m-10) cc_final: 0.8176 (m-80) REVERT: A 479 LEU cc_start: 0.4883 (OUTLIER) cc_final: 0.4656 (tp) REVERT: C 86 GLN cc_start: 0.8376 (tp40) cc_final: 0.8162 (tp40) REVERT: C 113 LEU cc_start: 0.8859 (tp) cc_final: 0.8570 (mm) REVERT: C 479 LEU cc_start: 0.4098 (OUTLIER) cc_final: 0.3861 (tp) REVERT: D 139 VAL cc_start: 0.8391 (t) cc_final: 0.8134 (m) REVERT: D 144 GLN cc_start: 0.7567 (mm110) cc_final: 0.7272 (mm110) outliers start: 55 outliers final: 52 residues processed: 175 average time/residue: 0.2602 time to fit residues: 69.9496 Evaluate side-chains 188 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 134 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 430 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 156 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** C 58 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.157021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.116472 restraints weight = 21905.853| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.49 r_work: 0.3324 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16480 Z= 0.162 Angle : 0.542 7.529 22508 Z= 0.267 Chirality : 0.040 0.141 2336 Planarity : 0.004 0.044 2884 Dihedral : 10.531 59.737 2356 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.78 % Allowed : 20.17 % Favored : 77.05 % 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: -2.06 (0.19), residues: 1936 helix: -0.50 (0.17), residues: 992 sheet: -2.50 (0.39), residues: 132 loop : -2.22 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 427 HIS 0.003 0.001 HIS C 95 PHE 0.009 0.001 PHE D 417 TYR 0.014 0.001 TYR A 43 ARG 0.003 0.000 ARG C 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3034.89 seconds wall clock time: 55 minutes 46.61 seconds (3346.61 seconds total)