Starting phenix.real_space_refine on Sat Feb 17 01:41:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptu_13638/02_2024/7ptu_13638.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptu_13638/02_2024/7ptu_13638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptu_13638/02_2024/7ptu_13638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptu_13638/02_2024/7ptu_13638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptu_13638/02_2024/7ptu_13638.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptu_13638/02_2024/7ptu_13638.pdb" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 10210 2.51 5 N 2675 2.21 5 O 4135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 180": "OE1" <-> "OE2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A ASP 507": "OD1" <-> "OD2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B ASP 360": "OD1" <-> "OD2" Residue "B ASP 507": "OD1" <-> "OD2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C ASP 360": "OD1" <-> "OD2" Residue "C ASP 507": "OD1" <-> "OD2" Residue "D GLU 180": "OE1" <-> "OE2" Residue "D ASP 360": "OD1" <-> "OD2" Residue "D ASP 507": "OD1" <-> "OD2" Residue "E GLU 180": "OE1" <-> "OE2" Residue "E ASP 360": "OD1" <-> "OD2" Residue "E ASP 507": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17035 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3396 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 9, 'TRANS': 464} Chain: "B" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3396 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 9, 'TRANS': 464} Chain: "C" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3396 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 9, 'TRANS': 464} Chain: "D" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3396 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 9, 'TRANS': 464} Chain: "E" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3396 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 9, 'TRANS': 464} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'BGC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'BGC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'BGC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'BGC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'BGC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.75, per 1000 atoms: 0.51 Number of scatterers: 17035 At special positions: 0 Unit cell: (147.4, 145.2, 103.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 4135 8.00 N 2675 7.00 C 10210 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.39 Conformation dependent library (CDL) restraints added in 3.3 seconds 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4180 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 40 sheets defined 11.2% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 removed outlier: 3.508A pdb=" N ALA A 41 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP A 42 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.627A pdb=" N SER A 82 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.539A pdb=" N VAL A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 287 through 292 removed outlier: 3.661A pdb=" N LYS A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.703A pdb=" N VAL A 369 " --> pdb=" O THR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 removed outlier: 3.794A pdb=" N GLU A 433 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 462 removed outlier: 3.821A pdb=" N SER A 458 " --> pdb=" O GLY A 454 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A 460 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 496 removed outlier: 3.705A pdb=" N GLY A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 43 removed outlier: 3.507A pdb=" N ALA B 41 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP B 42 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.627A pdb=" N SER B 82 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.540A pdb=" N VAL B 181 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 287 through 292 removed outlier: 3.660A pdb=" N LYS B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.703A pdb=" N VAL B 369 " --> pdb=" O THR B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 433 removed outlier: 3.794A pdb=" N GLU B 433 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 462 removed outlier: 3.821A pdb=" N SER B 458 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 496 removed outlier: 3.705A pdb=" N GLY B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 43 removed outlier: 3.508A pdb=" N ALA C 41 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP C 42 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.627A pdb=" N SER C 82 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 removed outlier: 3.540A pdb=" N VAL C 181 " --> pdb=" O ILE C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 287 through 292 removed outlier: 3.660A pdb=" N LYS C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 369 removed outlier: 3.704A pdb=" N VAL C 369 " --> pdb=" O THR C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 433 removed outlier: 3.794A pdb=" N GLU C 433 " --> pdb=" O GLY C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 462 removed outlier: 3.821A pdb=" N SER C 458 " --> pdb=" O GLY C 454 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU C 460 " --> pdb=" O GLY C 456 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU C 462 " --> pdb=" O SER C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 496 removed outlier: 3.706A pdb=" N GLY C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 removed outlier: 3.509A pdb=" N ALA D 41 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP D 42 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.627A pdb=" N SER D 82 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 182 removed outlier: 3.540A pdb=" N VAL D 181 " --> pdb=" O ILE D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 287 through 292 removed outlier: 3.660A pdb=" N LYS D 292 " --> pdb=" O THR D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 369 removed outlier: 3.704A pdb=" N VAL D 369 " --> pdb=" O THR D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 433 removed outlier: 3.794A pdb=" N GLU D 433 " --> pdb=" O GLY D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 462 removed outlier: 3.820A pdb=" N SER D 458 " --> pdb=" O GLY D 454 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU D 460 " --> pdb=" O GLY D 456 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU D 462 " --> pdb=" O SER D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 496 removed outlier: 3.705A pdb=" N GLY D 496 " --> pdb=" O GLU D 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 43 removed outlier: 3.508A pdb=" N ALA E 41 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP E 42 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.627A pdb=" N SER E 82 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 removed outlier: 3.540A pdb=" N VAL E 181 " --> pdb=" O ILE E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 287 through 292 removed outlier: 3.660A pdb=" N LYS E 292 " --> pdb=" O THR E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 369 removed outlier: 3.704A pdb=" N VAL E 369 " --> pdb=" O THR E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.793A pdb=" N GLU E 433 " --> pdb=" O GLY E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 462 removed outlier: 3.821A pdb=" N SER E 458 " --> pdb=" O GLY E 454 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE E 459 " --> pdb=" O ASP E 455 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU E 460 " --> pdb=" O GLY E 456 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU E 462 " --> pdb=" O SER E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 496 removed outlier: 3.705A pdb=" N GLY E 496 " --> pdb=" O GLU E 492 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 57 removed outlier: 6.064A pdb=" N VAL A 56 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 144 removed outlier: 3.709A pdb=" N SER A 240 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 249 Processing sheet with id=AA5, first strand: chain 'A' and resid 253 through 255 removed outlier: 6.394A pdb=" N VAL A 254 " --> pdb=" O GLU A 382 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A 375 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ASP A 355 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP A 278 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 357 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL A 274 " --> pdb=" O TYR A 359 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 275 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 303 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 388 Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 396 removed outlier: 6.547A pdb=" N GLY A 393 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR A 506 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR A 395 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 464 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE A 415 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 400 through 401 Processing sheet with id=AA9, first strand: chain 'B' and resid 55 through 57 removed outlier: 6.064A pdb=" N VAL B 56 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 125 through 131 Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 144 removed outlier: 3.709A pdb=" N SER B 240 " --> pdb=" O ILE B 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 246 through 249 Processing sheet with id=AB4, first strand: chain 'B' and resid 253 through 255 removed outlier: 6.394A pdb=" N VAL B 254 " --> pdb=" O GLU B 382 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN B 375 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ASP B 355 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASP B 278 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 357 " --> pdb=" O ALA B 276 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 274 " --> pdb=" O TYR B 359 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 275 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 303 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 386 through 388 Processing sheet with id=AB6, first strand: chain 'B' and resid 393 through 396 removed outlier: 6.549A pdb=" N GLY B 393 " --> pdb=" O ARG B 504 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR B 506 " --> pdb=" O GLY B 393 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR B 395 " --> pdb=" O THR B 506 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY B 464 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE B 415 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 400 through 401 Processing sheet with id=AB8, first strand: chain 'C' and resid 55 through 57 removed outlier: 6.064A pdb=" N VAL C 56 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 125 through 131 Processing sheet with id=AC1, first strand: chain 'C' and resid 142 through 144 removed outlier: 3.710A pdb=" N SER C 240 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 246 through 249 Processing sheet with id=AC3, first strand: chain 'C' and resid 253 through 255 removed outlier: 6.394A pdb=" N VAL C 254 " --> pdb=" O GLU C 382 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN C 375 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ASP C 355 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASP C 278 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU C 357 " --> pdb=" O ALA C 276 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL C 274 " --> pdb=" O TYR C 359 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 275 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 303 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 386 through 388 Processing sheet with id=AC5, first strand: chain 'C' and resid 393 through 396 removed outlier: 6.547A pdb=" N GLY C 393 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR C 506 " --> pdb=" O GLY C 393 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR C 395 " --> pdb=" O THR C 506 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY C 464 " --> pdb=" O VAL C 505 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE C 415 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 400 through 401 Processing sheet with id=AC7, first strand: chain 'D' and resid 55 through 57 removed outlier: 6.064A pdb=" N VAL D 56 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 125 through 131 Processing sheet with id=AC9, first strand: chain 'D' and resid 142 through 144 removed outlier: 3.710A pdb=" N SER D 240 " --> pdb=" O ILE D 143 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 246 through 249 Processing sheet with id=AD2, first strand: chain 'D' and resid 253 through 255 removed outlier: 6.395A pdb=" N VAL D 254 " --> pdb=" O GLU D 382 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN D 375 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ASP D 355 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP D 278 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 357 " --> pdb=" O ALA D 276 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL D 274 " --> pdb=" O TYR D 359 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 275 " --> pdb=" O ALA D 331 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU D 303 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 386 through 388 Processing sheet with id=AD4, first strand: chain 'D' and resid 393 through 396 removed outlier: 6.548A pdb=" N GLY D 393 " --> pdb=" O ARG D 504 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR D 506 " --> pdb=" O GLY D 393 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR D 395 " --> pdb=" O THR D 506 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY D 464 " --> pdb=" O VAL D 505 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE D 415 " --> pdb=" O LEU D 426 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 400 through 401 Processing sheet with id=AD6, first strand: chain 'E' and resid 55 through 57 removed outlier: 6.064A pdb=" N VAL E 56 " --> pdb=" O LEU E 121 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 125 through 131 Processing sheet with id=AD8, first strand: chain 'E' and resid 142 through 144 removed outlier: 3.710A pdb=" N SER E 240 " --> pdb=" O ILE E 143 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 246 through 249 Processing sheet with id=AE1, first strand: chain 'E' and resid 253 through 255 removed outlier: 6.394A pdb=" N VAL E 254 " --> pdb=" O GLU E 382 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN E 375 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ASP E 355 " --> pdb=" O ASP E 278 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP E 278 " --> pdb=" O ASP E 355 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU E 357 " --> pdb=" O ALA E 276 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL E 274 " --> pdb=" O TYR E 359 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL E 275 " --> pdb=" O ALA E 331 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU E 303 " --> pdb=" O VAL E 332 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 386 through 388 Processing sheet with id=AE3, first strand: chain 'E' and resid 393 through 396 removed outlier: 6.547A pdb=" N GLY E 393 " --> pdb=" O ARG E 504 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR E 506 " --> pdb=" O GLY E 393 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR E 395 " --> pdb=" O THR E 506 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY E 464 " --> pdb=" O VAL E 505 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE E 415 " --> pdb=" O LEU E 426 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 400 through 401 460 hydrogen bonds defined for protein. 1200 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: 6.03 Time building geometry restraints manager: 6.78 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: 6101 1.34 - 1.45: 2062 1.45 - 1.57: 8992 1.57 - 1.69: 0 1.69 - 1.80: 30 Bond restraints: 17185 Sorted by residual: bond pdb=" CA ASP E 420 " pdb=" CB ASP E 420 " ideal model delta sigma weight residual 1.529 1.556 -0.027 1.62e-02 3.81e+03 2.86e+00 bond pdb=" CA ASP D 420 " pdb=" CB ASP D 420 " ideal model delta sigma weight residual 1.529 1.556 -0.027 1.62e-02 3.81e+03 2.84e+00 bond pdb=" CA ASP A 420 " pdb=" CB ASP A 420 " ideal model delta sigma weight residual 1.529 1.556 -0.027 1.62e-02 3.81e+03 2.81e+00 bond pdb=" CA ASP B 420 " pdb=" CB ASP B 420 " ideal model delta sigma weight residual 1.529 1.556 -0.027 1.62e-02 3.81e+03 2.77e+00 bond pdb=" CA ASP C 420 " pdb=" CB ASP C 420 " ideal model delta sigma weight residual 1.529 1.556 -0.027 1.62e-02 3.81e+03 2.68e+00 ... (remaining 17180 not shown) Histogram of bond angle deviations from ideal: 98.51 - 105.60: 214 105.60 - 112.69: 9445 112.69 - 119.78: 5639 119.78 - 126.87: 8102 126.87 - 133.96: 65 Bond angle restraints: 23465 Sorted by residual: angle pdb=" N GLN D 242 " pdb=" CA GLN D 242 " pdb=" C GLN D 242 " ideal model delta sigma weight residual 110.80 101.32 9.48 2.13e+00 2.20e-01 1.98e+01 angle pdb=" N GLN A 242 " pdb=" CA GLN A 242 " pdb=" C GLN A 242 " ideal model delta sigma weight residual 110.80 101.34 9.46 2.13e+00 2.20e-01 1.97e+01 angle pdb=" N GLN E 242 " pdb=" CA GLN E 242 " pdb=" C GLN E 242 " ideal model delta sigma weight residual 110.80 101.35 9.45 2.13e+00 2.20e-01 1.97e+01 angle pdb=" N GLN B 242 " pdb=" CA GLN B 242 " pdb=" C GLN B 242 " ideal model delta sigma weight residual 110.80 101.36 9.44 2.13e+00 2.20e-01 1.97e+01 angle pdb=" N GLN C 242 " pdb=" CA GLN C 242 " pdb=" C GLN C 242 " ideal model delta sigma weight residual 110.80 101.36 9.44 2.13e+00 2.20e-01 1.96e+01 ... (remaining 23460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9386 17.92 - 35.84: 684 35.84 - 53.76: 120 53.76 - 71.69: 20 71.69 - 89.61: 20 Dihedral angle restraints: 10230 sinusoidal: 3625 harmonic: 6605 Sorted by residual: dihedral pdb=" N ASP C 420 " pdb=" C ASP C 420 " pdb=" CA ASP C 420 " pdb=" CB ASP C 420 " ideal model delta harmonic sigma weight residual 122.80 131.86 -9.06 0 2.50e+00 1.60e-01 1.31e+01 dihedral pdb=" N ASP A 420 " pdb=" C ASP A 420 " pdb=" CA ASP A 420 " pdb=" CB ASP A 420 " ideal model delta harmonic sigma weight residual 122.80 131.83 -9.03 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" N ASP B 420 " pdb=" C ASP B 420 " pdb=" CA ASP B 420 " pdb=" CB ASP B 420 " ideal model delta harmonic sigma weight residual 122.80 131.81 -9.01 0 2.50e+00 1.60e-01 1.30e+01 ... (remaining 10227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2237 0.053 - 0.106: 511 0.106 - 0.159: 107 0.159 - 0.212: 15 0.212 - 0.265: 5 Chirality restraints: 2875 Sorted by residual: chirality pdb=" CA ASP C 420 " pdb=" N ASP C 420 " pdb=" C ASP C 420 " pdb=" CB ASP C 420 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ASP B 420 " pdb=" N ASP B 420 " pdb=" C ASP B 420 " pdb=" CB ASP B 420 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ASP A 420 " pdb=" N ASP A 420 " pdb=" C ASP A 420 " pdb=" CB ASP A 420 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 2872 not shown) Planarity restraints: 3185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 419 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C ASP D 419 " -0.055 2.00e-02 2.50e+03 pdb=" O ASP D 419 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP D 420 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 419 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ASP A 419 " 0.055 2.00e-02 2.50e+03 pdb=" O ASP A 419 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A 420 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 419 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ASP C 419 " -0.055 2.00e-02 2.50e+03 pdb=" O ASP C 419 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP C 420 " 0.019 2.00e-02 2.50e+03 ... (remaining 3182 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1063 2.72 - 3.26: 17930 3.26 - 3.81: 26123 3.81 - 4.35: 31816 4.35 - 4.90: 55036 Nonbonded interactions: 131968 Sorted by model distance: nonbonded pdb=" OG1 THR C 406 " pdb=" O ASP C 440 " model vdw 2.173 2.440 nonbonded pdb=" OG1 THR D 406 " pdb=" O ASP D 440 " model vdw 2.173 2.440 nonbonded pdb=" OG1 THR E 406 " pdb=" O ASP E 440 " model vdw 2.173 2.440 nonbonded pdb=" OG1 THR B 406 " pdb=" O ASP B 440 " model vdw 2.173 2.440 nonbonded pdb=" OG1 THR A 406 " pdb=" O ASP A 440 " model vdw 2.174 2.440 ... (remaining 131963 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 7.670 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 45.910 Find NCS groups from input model: 1.160 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: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 : 0.003 0.027 17185 Z= 0.210 Angle : 0.793 9.477 23465 Z= 0.451 Chirality : 0.049 0.265 2875 Planarity : 0.005 0.046 3185 Dihedral : 13.562 89.606 6050 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.26 % Allowed : 1.30 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.16), residues: 2360 helix: -1.54 (0.60), residues: 60 sheet: -0.35 (0.18), residues: 810 loop : -1.37 (0.14), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 423 HIS 0.002 0.001 HIS E 273 PHE 0.020 0.002 PHE E 228 TYR 0.016 0.002 TYR E 159 ARG 0.003 0.000 ARG E 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 1.976 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 30 average time/residue: 0.2742 time to fit residues: 15.2712 Evaluate side-chains 25 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 10.0000 chunk 178 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 60 optimal weight: 0.0030 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 184 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 213 optimal weight: 0.0370 overall best weight: 2.7672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17185 Z= 0.250 Angle : 0.554 7.468 23465 Z= 0.305 Chirality : 0.044 0.154 2875 Planarity : 0.004 0.040 3185 Dihedral : 4.427 18.265 2555 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.26 % Allowed : 7.43 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.16), residues: 2360 helix: -1.31 (0.43), residues: 125 sheet: -0.02 (0.20), residues: 690 loop : -1.41 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP C 423 HIS 0.001 0.000 HIS C 273 PHE 0.015 0.002 PHE C 295 TYR 0.011 0.001 TYR D 466 ARG 0.003 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 1.880 Fit side-chains revert: symmetry clash REVERT: D 235 MET cc_start: 0.8148 (mtp) cc_final: 0.7875 (mtp) outliers start: 5 outliers final: 5 residues processed: 33 average time/residue: 0.2307 time to fit residues: 15.0783 Evaluate side-chains 26 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain E residue 165 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 118 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 177 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 213 optimal weight: 0.0070 chunk 230 optimal weight: 0.0970 chunk 190 optimal weight: 0.7980 chunk 212 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17185 Z= 0.126 Angle : 0.478 7.713 23465 Z= 0.260 Chirality : 0.043 0.154 2875 Planarity : 0.003 0.031 3185 Dihedral : 3.879 15.967 2555 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.17), residues: 2360 helix: -0.89 (0.44), residues: 125 sheet: 0.34 (0.20), residues: 740 loop : -1.23 (0.15), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 423 HIS 0.001 0.000 HIS E 273 PHE 0.006 0.001 PHE E 57 TYR 0.008 0.001 TYR E 159 ARG 0.002 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 1.957 Fit side-chains REVERT: A 282 LEU cc_start: 0.9269 (tp) cc_final: 0.9022 (pp) REVERT: B 208 MET cc_start: 0.8954 (tpt) cc_final: 0.8686 (tpt) REVERT: D 235 MET cc_start: 0.8166 (mtp) cc_final: 0.7898 (mtp) REVERT: E 282 LEU cc_start: 0.9391 (tp) cc_final: 0.9185 (pp) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.2292 time to fit residues: 11.7358 Evaluate side-chains 23 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 211 optimal weight: 4.9990 chunk 160 optimal weight: 8.9990 chunk 110 optimal weight: 0.0010 chunk 23 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 227 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 203 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 overall best weight: 3.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS B 273 HIS C 273 HIS D 273 HIS E 273 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17185 Z= 0.285 Angle : 0.554 7.521 23465 Z= 0.299 Chirality : 0.044 0.160 2875 Planarity : 0.003 0.029 3185 Dihedral : 4.457 18.028 2555 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.13 % Allowed : 10.91 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.17), residues: 2360 helix: -1.07 (0.43), residues: 130 sheet: 0.42 (0.21), residues: 675 loop : -1.23 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP B 423 HIS 0.001 0.001 HIS C 273 PHE 0.017 0.002 PHE C 295 TYR 0.010 0.001 TYR C 348 ARG 0.002 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 27 time to evaluate : 1.691 Fit side-chains REVERT: D 235 MET cc_start: 0.8280 (mtp) cc_final: 0.8064 (mtp) outliers start: 41 outliers final: 28 residues processed: 65 average time/residue: 0.2030 time to fit residues: 24.2335 Evaluate side-chains 48 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 20 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 189 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 193 optimal weight: 0.3980 chunk 157 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 HIS D 273 HIS E 273 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17185 Z= 0.201 Angle : 0.501 7.962 23465 Z= 0.268 Chirality : 0.043 0.157 2875 Planarity : 0.003 0.026 3185 Dihedral : 4.175 15.535 2555 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.23 % Allowed : 12.16 % Favored : 85.61 % 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: -0.94 (0.18), residues: 2360 helix: -0.82 (0.46), residues: 130 sheet: 0.51 (0.21), residues: 740 loop : -1.26 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.002 TRP E 423 HIS 0.001 0.000 HIS E 273 PHE 0.010 0.001 PHE D 295 TYR 0.007 0.001 TYR B 466 ARG 0.001 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 20 time to evaluate : 1.850 Fit side-chains REVERT: C 131 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6526 (pp) outliers start: 43 outliers final: 32 residues processed: 62 average time/residue: 0.1877 time to fit residues: 22.3483 Evaluate side-chains 53 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 20 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 235 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 76 optimal weight: 0.8980 chunk 204 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 HIS D 273 HIS E 273 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17185 Z= 0.332 Angle : 0.580 10.107 23465 Z= 0.309 Chirality : 0.044 0.160 2875 Planarity : 0.003 0.024 3185 Dihedral : 4.739 16.167 2555 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.75 % Allowed : 13.56 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.18), residues: 2360 helix: -1.67 (0.40), residues: 160 sheet: 0.27 (0.20), residues: 755 loop : -1.28 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP E 423 HIS 0.001 0.001 HIS B 273 PHE 0.015 0.002 PHE C 295 TYR 0.009 0.002 TYR A 466 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 21 time to evaluate : 2.118 Fit side-chains REVERT: A 277 MET cc_start: 0.9091 (tpp) cc_final: 0.8851 (tpp) REVERT: C 131 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6636 (pp) outliers start: 53 outliers final: 40 residues processed: 74 average time/residue: 0.1975 time to fit residues: 27.7778 Evaluate side-chains 61 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 20 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 219 optimal weight: 8.9990 chunk 25 optimal weight: 0.0070 chunk 129 optimal weight: 9.9990 chunk 166 optimal weight: 0.0870 chunk 128 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 226 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 overall best weight: 1.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 GLN E 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17185 Z= 0.169 Angle : 0.497 8.053 23465 Z= 0.262 Chirality : 0.043 0.155 2875 Planarity : 0.002 0.029 3185 Dihedral : 4.160 14.271 2555 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.70 % Allowed : 13.92 % Favored : 83.38 % 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: -0.99 (0.18), residues: 2360 helix: -1.48 (0.41), residues: 160 sheet: 0.49 (0.21), residues: 690 loop : -1.17 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 423 HIS 0.001 0.001 HIS C 273 PHE 0.010 0.001 PHE C 295 TYR 0.007 0.001 TYR B 466 ARG 0.001 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 20 time to evaluate : 1.962 Fit side-chains REVERT: A 277 MET cc_start: 0.9056 (tpp) cc_final: 0.8724 (tpp) REVERT: C 131 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6410 (pp) outliers start: 52 outliers final: 41 residues processed: 71 average time/residue: 0.2002 time to fit residues: 27.0280 Evaluate side-chains 62 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 20 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 235 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 140 optimal weight: 5.9990 chunk 90 optimal weight: 0.0370 chunk 135 optimal weight: 30.0000 chunk 68 optimal weight: 0.0060 chunk 44 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 178 optimal weight: 20.0000 overall best weight: 2.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN E 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17185 Z= 0.221 Angle : 0.516 8.909 23465 Z= 0.271 Chirality : 0.043 0.149 2875 Planarity : 0.002 0.024 3185 Dihedral : 4.239 14.753 2555 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.60 % Allowed : 14.65 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.18), residues: 2360 helix: -1.43 (0.42), residues: 160 sheet: 0.41 (0.20), residues: 720 loop : -1.32 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP D 423 HIS 0.001 0.001 HIS C 273 PHE 0.012 0.001 PHE C 295 TYR 0.008 0.001 TYR D 466 ARG 0.001 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 20 time to evaluate : 2.522 Fit side-chains REVERT: A 277 MET cc_start: 0.9021 (tpp) cc_final: 0.8738 (tpp) REVERT: C 131 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6537 (pp) outliers start: 50 outliers final: 46 residues processed: 69 average time/residue: 0.1929 time to fit residues: 25.7442 Evaluate side-chains 67 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 20 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 235 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 206 optimal weight: 8.9990 chunk 216 optimal weight: 20.0000 chunk 197 optimal weight: 7.9990 chunk 211 optimal weight: 20.0000 chunk 127 optimal weight: 0.2980 chunk 91 optimal weight: 0.0020 chunk 165 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 190 optimal weight: 0.0670 chunk 199 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 overall best weight: 2.4730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17185 Z= 0.209 Angle : 0.510 9.125 23465 Z= 0.266 Chirality : 0.043 0.150 2875 Planarity : 0.002 0.025 3185 Dihedral : 4.178 14.351 2555 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.96 % Allowed : 14.55 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.18), residues: 2360 helix: -0.60 (0.48), residues: 130 sheet: 0.39 (0.20), residues: 720 loop : -1.45 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.002 TRP C 423 HIS 0.001 0.001 HIS E 273 PHE 0.012 0.001 PHE C 295 TYR 0.008 0.001 TYR D 466 ARG 0.001 0.000 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 20 time to evaluate : 2.047 Fit side-chains REVERT: A 277 MET cc_start: 0.9001 (tpp) cc_final: 0.8679 (tpp) REVERT: C 131 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6530 (pp) REVERT: C 208 MET cc_start: 0.9071 (tpt) cc_final: 0.8860 (tpt) REVERT: E 278 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8498 (p0) outliers start: 57 outliers final: 51 residues processed: 76 average time/residue: 0.1992 time to fit residues: 28.4356 Evaluate side-chains 73 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 20 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 235 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 138 optimal weight: 8.9990 chunk 223 optimal weight: 8.9990 chunk 136 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 186 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17185 Z= 0.393 Angle : 0.612 9.338 23465 Z= 0.324 Chirality : 0.045 0.156 2875 Planarity : 0.003 0.027 3185 Dihedral : 4.858 16.958 2555 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.01 % Allowed : 14.91 % Favored : 82.08 % 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: -1.44 (0.18), residues: 2360 helix: -0.70 (0.49), residues: 130 sheet: 0.10 (0.20), residues: 745 loop : -1.62 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.004 TRP E 423 HIS 0.002 0.001 HIS B 273 PHE 0.016 0.002 PHE C 295 TYR 0.011 0.002 TYR D 466 ARG 0.002 0.000 ARG C 296 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 20 time to evaluate : 1.920 Fit side-chains REVERT: A 277 MET cc_start: 0.8999 (tpp) cc_final: 0.8746 (tpp) REVERT: C 131 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6654 (pp) outliers start: 58 outliers final: 51 residues processed: 77 average time/residue: 0.1913 time to fit residues: 27.8767 Evaluate side-chains 72 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 20 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 235 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 148 optimal weight: 6.9990 chunk 198 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 191 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.037797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.027065 restraints weight = 165446.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.027894 restraints weight = 93714.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.028430 restraints weight = 63922.343| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17185 Z= 0.290 Angle : 0.560 9.522 23465 Z= 0.294 Chirality : 0.044 0.152 2875 Planarity : 0.003 0.028 3185 Dihedral : 4.632 16.539 2555 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.91 % Allowed : 15.27 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 2360 helix: -0.73 (0.47), residues: 130 sheet: 0.06 (0.20), residues: 745 loop : -1.60 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP E 423 HIS 0.001 0.001 HIS B 273 PHE 0.014 0.002 PHE C 295 TYR 0.012 0.002 TYR B 466 ARG 0.001 0.000 ARG B 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2399.93 seconds wall clock time: 45 minutes 40.11 seconds (2740.11 seconds total)