Starting phenix.real_space_refine on Wed Jun 11 14:02:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tf4_25861/06_2025/7tf4_25861.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tf4_25861/06_2025/7tf4_25861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tf4_25861/06_2025/7tf4_25861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tf4_25861/06_2025/7tf4_25861.map" model { file = "/net/cci-nas-00/data/ceres_data/7tf4_25861/06_2025/7tf4_25861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tf4_25861/06_2025/7tf4_25861.cif" } resolution = 3.01 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= 0.027 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 54 5.16 5 C 8166 2.51 5 N 2136 2.21 5 O 2436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12792 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2104 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 252} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2104 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 252} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2104 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 252} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2104 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 252} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2104 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 252} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2104 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 252} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.39, per 1000 atoms: 0.66 Number of scatterers: 12792 At special positions: 0 Unit cell: (111.8, 109.2, 139.1, 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 54 16.00 O 2436 8.00 N 2136 7.00 C 8166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.04 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.06 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 343 " " NAG D1301 " - " ASN D 331 " " NAG D1302 " - " ASN D 343 " " NAG E1301 " - " ASN E 331 " " NAG E1302 " - " ASN E 343 " " NAG F1301 " - " ASN F 331 " " NAG F1302 " - " ASN F 343 " Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.5 seconds 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2988 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 31 sheets defined 14.5% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.707A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.676A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.565A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.803A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.967A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.641A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.742A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.085A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.710A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'D' and resid 337 through 343 removed outlier: 3.603A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.834A pdb=" N TRP D 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 371 removed outlier: 3.511A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 390 removed outlier: 4.278A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 390 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 365 through 371 removed outlier: 3.856A pdb=" N SER E 371 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 removed outlier: 3.921A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 407 No H-bonds generated for 'chain 'E' and resid 405 through 407' Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 364 through 370 removed outlier: 4.396A pdb=" N LEU F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 removed outlier: 4.074A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 411 " --> pdb=" O ARG F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'F' and resid 438 through 443 removed outlier: 3.505A pdb=" N SER F 443 " --> pdb=" O ASN F 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.220A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.694A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.963A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.304A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 removed outlier: 7.146A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AB3, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.006A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.063A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.098A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB8, first strand: chain 'D' and resid 326 through 328 removed outlier: 5.430A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY D 566 " --> pdb=" O ASP D 574 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AC1, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.548A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AC3, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AC4, first strand: chain 'E' and resid 324 through 328 removed outlier: 3.783A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL E 539 " --> pdb=" O GLY E 550 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.768A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ASN E 437 " --> pdb=" O PHE E 374 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE E 374 " --> pdb=" O ASN E 437 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'F' and resid 325 through 328 Processing sheet with id=AD1, first strand: chain 'F' and resid 354 through 358 removed outlier: 3.996A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'F' and resid 553 through 554 353 hydrogen bonds defined for protein. 906 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: 3.53 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4101 1.35 - 1.48: 3552 1.48 - 1.61: 5409 1.61 - 1.73: 0 1.73 - 1.86: 54 Bond restraints: 13116 Sorted by residual: bond pdb=" C1 NAG F1301 " pdb=" O5 NAG F1301 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CA LEU A 517 " pdb=" CB LEU A 517 " ideal model delta sigma weight residual 1.527 1.581 -0.054 1.75e-02 3.27e+03 9.45e+00 bond pdb=" C TYR D 505 " pdb=" N GLN D 506 " ideal model delta sigma weight residual 1.329 1.382 -0.053 1.86e-02 2.89e+03 8.10e+00 bond pdb=" C TYR B 505 " pdb=" N GLN B 506 " ideal model delta sigma weight residual 1.331 1.278 0.053 2.07e-02 2.33e+03 6.50e+00 bond pdb=" C TYR C 505 " pdb=" N GLN C 506 " ideal model delta sigma weight residual 1.331 1.281 0.050 2.07e-02 2.33e+03 5.89e+00 ... (remaining 13111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 17746 3.83 - 7.67: 88 7.67 - 11.50: 7 11.50 - 15.33: 2 15.33 - 19.17: 1 Bond angle restraints: 17844 Sorted by residual: angle pdb=" N ILE F 410 " pdb=" CA ILE F 410 " pdb=" C ILE F 410 " ideal model delta sigma weight residual 111.91 104.62 7.29 8.90e-01 1.26e+00 6.72e+01 angle pdb=" CA CYS F 391 " pdb=" CB CYS F 391 " pdb=" SG CYS F 391 " ideal model delta sigma weight residual 114.40 127.46 -13.06 2.30e+00 1.89e-01 3.22e+01 angle pdb=" C PHE F 515 " pdb=" N GLU F 516 " pdb=" CA GLU F 516 " ideal model delta sigma weight residual 122.65 114.85 7.80 1.49e+00 4.50e-01 2.74e+01 angle pdb=" CA GLN C 506 " pdb=" CB GLN C 506 " pdb=" CG GLN C 506 " ideal model delta sigma weight residual 114.10 121.77 -7.67 2.00e+00 2.50e-01 1.47e+01 angle pdb=" CB GLU C 471 " pdb=" CG GLU C 471 " pdb=" CD GLU C 471 " ideal model delta sigma weight residual 112.60 118.63 -6.03 1.70e+00 3.46e-01 1.26e+01 ... (remaining 17839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 7136 16.25 - 32.50: 687 32.50 - 48.75: 111 48.75 - 65.00: 15 65.00 - 81.25: 13 Dihedral angle restraints: 7962 sinusoidal: 3282 harmonic: 4680 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -144.12 58.12 1 1.00e+01 1.00e-02 4.53e+01 dihedral pdb=" CA CYS F 391 " pdb=" C CYS F 391 " pdb=" N PHE F 392 " pdb=" CA PHE F 392 " ideal model delta harmonic sigma weight residual 180.00 -150.67 -29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 46.97 46.03 1 1.00e+01 1.00e-02 2.93e+01 ... (remaining 7959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1555 0.062 - 0.125: 368 0.125 - 0.187: 44 0.187 - 0.249: 5 0.249 - 0.312: 2 Chirality restraints: 1974 Sorted by residual: chirality pdb=" CB ILE A 326 " pdb=" CA ILE A 326 " pdb=" CG1 ILE A 326 " pdb=" CG2 ILE A 326 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C1 NAG F1301 " pdb=" ND2 ASN F 331 " pdb=" C2 NAG F1301 " pdb=" O5 NAG F1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C1 NAG E1301 " pdb=" ND2 ASN E 331 " pdb=" C2 NAG E1301 " pdb=" O5 NAG E1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1971 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 560 " 0.054 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO B 561 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 560 " 0.052 5.00e-02 4.00e+02 7.89e-02 9.97e+00 pdb=" N PRO E 561 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO E 561 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 561 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 392 " -0.014 2.00e-02 2.50e+03 2.28e-02 9.10e+00 pdb=" CG PHE F 392 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE F 392 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE F 392 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE F 392 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 392 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 392 " 0.002 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3442 2.80 - 3.33: 10332 3.33 - 3.85: 21118 3.85 - 4.38: 24812 4.38 - 4.90: 42275 Nonbonded interactions: 101979 Sorted by model distance: nonbonded pdb=" OD2 ASP D 578 " pdb=" OG1 THR D 581 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR E 393 " pdb=" O GLU E 516 " model vdw 2.291 3.040 nonbonded pdb=" O TYR A 495 " pdb=" OH TYR A 505 " model vdw 2.292 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.305 3.040 nonbonded pdb=" O TYR E 495 " pdb=" OH TYR E 505 " model vdw 2.314 3.040 ... (remaining 101974 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.630 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 : 0.005 0.073 13152 Z= 0.232 Angle : 0.867 19.166 17928 Z= 0.480 Chirality : 0.054 0.312 1974 Planarity : 0.008 0.082 2328 Dihedral : 12.758 81.255 4902 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -1.60 (0.18), residues: 1596 helix: -4.07 (0.20), residues: 144 sheet: 0.08 (0.29), residues: 320 loop : -1.03 (0.16), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 353 PHE 0.051 0.002 PHE F 392 TYR 0.033 0.002 TYR E 495 ARG 0.009 0.001 ARG F 577 Details of bonding type rmsd link_NAG-ASN : bond 0.01031 ( 12) link_NAG-ASN : angle 3.82597 ( 36) hydrogen bonds : bond 0.17143 ( 353) hydrogen bonds : angle 9.38720 ( 906) SS BOND : bond 0.00584 ( 24) SS BOND : angle 1.41985 ( 48) covalent geometry : bond 0.00488 (13116) covalent geometry : angle 0.84873 (17844) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 406 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7988 (mt-10) REVERT: F 580 GLN cc_start: 0.6631 (mm-40) cc_final: 0.5798 (tp-100) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2901 time to fit residues: 51.0532 Evaluate side-chains 85 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.0980 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 GLN E 394 ASN E 493 GLN F 409 GLN F 414 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.099613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.080734 restraints weight = 30356.406| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.25 r_work: 0.3218 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13152 Z= 0.119 Angle : 0.548 13.031 17928 Z= 0.277 Chirality : 0.046 0.311 1974 Planarity : 0.005 0.062 2328 Dihedral : 4.945 36.433 2016 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.29 % Allowed : 4.55 % Favored : 95.17 % 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: -1.23 (0.19), residues: 1596 helix: -3.34 (0.27), residues: 166 sheet: 0.11 (0.28), residues: 352 loop : -0.71 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 436 PHE 0.015 0.001 PHE F 392 TYR 0.012 0.001 TYR F 369 ARG 0.005 0.000 ARG F 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 12) link_NAG-ASN : angle 2.33421 ( 36) hydrogen bonds : bond 0.03861 ( 353) hydrogen bonds : angle 6.97800 ( 906) SS BOND : bond 0.00307 ( 24) SS BOND : angle 0.72435 ( 48) covalent geometry : bond 0.00265 (13116) covalent geometry : angle 0.53753 (17844) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 428 ASP cc_start: 0.7737 (p0) cc_final: 0.7527 (p0) REVERT: B 471 GLU cc_start: 0.8614 (tp30) cc_final: 0.8367 (tp30) REVERT: C 406 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8435 (mt-10) REVERT: F 392 PHE cc_start: 0.7284 (m-80) cc_final: 0.7077 (m-10) REVERT: F 414 GLN cc_start: 0.8067 (tp-100) cc_final: 0.7763 (mm-40) REVERT: F 580 GLN cc_start: 0.6854 (mm-40) cc_final: 0.6441 (mm110) outliers start: 4 outliers final: 3 residues processed: 101 average time/residue: 0.2933 time to fit residues: 41.7820 Evaluate side-chains 83 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain D residue 468 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 61 optimal weight: 0.0270 chunk 84 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 139 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 36 optimal weight: 0.0970 chunk 56 optimal weight: 7.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.099250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.080197 restraints weight = 30594.356| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.28 r_work: 0.3207 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13152 Z= 0.113 Angle : 0.509 8.818 17928 Z= 0.257 Chirality : 0.045 0.304 1974 Planarity : 0.004 0.055 2328 Dihedral : 4.434 33.085 2016 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.51 % Allowed : 6.42 % Favored : 93.07 % 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: -0.98 (0.19), residues: 1596 helix: -3.42 (0.32), residues: 138 sheet: 0.19 (0.27), residues: 350 loop : -0.54 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 436 PHE 0.011 0.001 PHE A 559 TYR 0.010 0.001 TYR C 380 ARG 0.005 0.000 ARG F 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 12) link_NAG-ASN : angle 2.19722 ( 36) hydrogen bonds : bond 0.03488 ( 353) hydrogen bonds : angle 6.58987 ( 906) SS BOND : bond 0.00225 ( 24) SS BOND : angle 0.73796 ( 48) covalent geometry : bond 0.00256 (13116) covalent geometry : angle 0.49952 (17844) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 516 GLU cc_start: 0.8051 (pm20) cc_final: 0.7653 (pm20) REVERT: B 414 GLN cc_start: 0.8239 (tp40) cc_final: 0.7953 (tp40) REVERT: B 428 ASP cc_start: 0.7740 (p0) cc_final: 0.7527 (p0) REVERT: B 471 GLU cc_start: 0.8615 (tp30) cc_final: 0.8351 (tp30) REVERT: F 406 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: F 567 ARG cc_start: 0.2069 (mtm-85) cc_final: 0.1132 (mtm-85) outliers start: 7 outliers final: 4 residues processed: 93 average time/residue: 0.2691 time to fit residues: 36.5345 Evaluate side-chains 79 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 406 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 108 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 GLN F 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.097838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.078884 restraints weight = 30380.469| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.18 r_work: 0.3179 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13152 Z= 0.143 Angle : 0.506 9.134 17928 Z= 0.258 Chirality : 0.045 0.312 1974 Planarity : 0.004 0.053 2328 Dihedral : 4.345 29.666 2016 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.08 % Allowed : 7.29 % Favored : 91.63 % 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: -0.83 (0.20), residues: 1596 helix: -3.05 (0.37), residues: 126 sheet: 0.16 (0.27), residues: 354 loop : -0.46 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 436 PHE 0.016 0.001 PHE A 559 TYR 0.012 0.001 TYR C 505 ARG 0.004 0.000 ARG F 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 12) link_NAG-ASN : angle 2.18889 ( 36) hydrogen bonds : bond 0.03428 ( 353) hydrogen bonds : angle 6.51106 ( 906) SS BOND : bond 0.00211 ( 24) SS BOND : angle 0.72305 ( 48) covalent geometry : bond 0.00327 (13116) covalent geometry : angle 0.49662 (17844) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 1.381 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7290 (pm20) cc_final: 0.6972 (pm20) REVERT: B 471 GLU cc_start: 0.8642 (tp30) cc_final: 0.8366 (tp30) REVERT: F 567 ARG cc_start: 0.2543 (mtm-85) cc_final: 0.0887 (mtm-85) outliers start: 15 outliers final: 7 residues processed: 95 average time/residue: 0.2657 time to fit residues: 36.4282 Evaluate side-chains 81 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 515 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.5980 chunk 153 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 128 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 GLN E 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.097905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.079063 restraints weight = 30218.727| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.18 r_work: 0.3187 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13152 Z= 0.124 Angle : 0.501 9.749 17928 Z= 0.254 Chirality : 0.045 0.306 1974 Planarity : 0.004 0.053 2328 Dihedral : 4.271 28.966 2016 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.87 % Allowed : 8.44 % Favored : 90.69 % 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: -0.63 (0.20), residues: 1596 helix: -2.32 (0.51), residues: 94 sheet: -0.01 (0.27), residues: 362 loop : -0.36 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 436 PHE 0.012 0.001 PHE A 559 TYR 0.008 0.001 TYR C 380 ARG 0.003 0.000 ARG F 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 12) link_NAG-ASN : angle 2.12347 ( 36) hydrogen bonds : bond 0.03312 ( 353) hydrogen bonds : angle 6.41565 ( 906) SS BOND : bond 0.00225 ( 24) SS BOND : angle 0.78780 ( 48) covalent geometry : bond 0.00286 (13116) covalent geometry : angle 0.49120 (17844) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 1.544 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7239 (pm20) cc_final: 0.6920 (pm20) REVERT: B 471 GLU cc_start: 0.8642 (tp30) cc_final: 0.8374 (tp30) REVERT: F 567 ARG cc_start: 0.2562 (mtm-85) cc_final: 0.0817 (mtm-85) outliers start: 12 outliers final: 9 residues processed: 85 average time/residue: 0.2816 time to fit residues: 34.9970 Evaluate side-chains 78 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain F residue 387 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 84 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 50 optimal weight: 0.0060 chunk 143 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 79 optimal weight: 0.0050 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 overall best weight: 0.7212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 GLN E 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.098084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.079148 restraints weight = 30817.303| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.21 r_work: 0.3187 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13152 Z= 0.120 Angle : 0.489 10.220 17928 Z= 0.249 Chirality : 0.045 0.303 1974 Planarity : 0.004 0.052 2328 Dihedral : 4.166 27.421 2016 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.08 % Allowed : 9.02 % Favored : 89.90 % 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: -0.69 (0.20), residues: 1596 helix: -2.73 (0.41), residues: 126 sheet: 0.15 (0.27), residues: 354 loop : -0.35 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 PHE 0.011 0.001 PHE A 559 TYR 0.008 0.001 TYR C 380 ARG 0.007 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00563 ( 12) link_NAG-ASN : angle 2.07473 ( 36) hydrogen bonds : bond 0.03216 ( 353) hydrogen bonds : angle 6.30674 ( 906) SS BOND : bond 0.00204 ( 24) SS BOND : angle 0.72809 ( 48) covalent geometry : bond 0.00277 (13116) covalent geometry : angle 0.48017 (17844) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7245 (pm20) cc_final: 0.6929 (pm20) REVERT: B 471 GLU cc_start: 0.8660 (tp30) cc_final: 0.8394 (tp30) REVERT: F 567 ARG cc_start: 0.2814 (OUTLIER) cc_final: 0.0920 (mtm-85) REVERT: F 577 ARG cc_start: 0.6399 (ttp-110) cc_final: 0.5619 (ttm110) outliers start: 15 outliers final: 12 residues processed: 85 average time/residue: 0.2674 time to fit residues: 33.6869 Evaluate side-chains 81 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 498 GLN Chi-restraints excluded: chain F residue 567 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 117 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 15 optimal weight: 0.0370 chunk 121 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 GLN E 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.098014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.079161 restraints weight = 30375.993| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.18 r_work: 0.3190 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13152 Z= 0.117 Angle : 0.490 10.403 17928 Z= 0.249 Chirality : 0.045 0.303 1974 Planarity : 0.004 0.052 2328 Dihedral : 4.077 26.087 2016 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.08 % Allowed : 9.52 % Favored : 89.39 % 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: -0.64 (0.20), residues: 1596 helix: -2.61 (0.42), residues: 126 sheet: 0.17 (0.27), residues: 352 loop : -0.32 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 PHE 0.010 0.001 PHE A 559 TYR 0.008 0.001 TYR C 380 ARG 0.004 0.000 ARG F 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 12) link_NAG-ASN : angle 2.03732 ( 36) hydrogen bonds : bond 0.03185 ( 353) hydrogen bonds : angle 6.25082 ( 906) SS BOND : bond 0.00201 ( 24) SS BOND : angle 0.66861 ( 48) covalent geometry : bond 0.00271 (13116) covalent geometry : angle 0.48097 (17844) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 1.535 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7287 (pm20) cc_final: 0.6962 (pm20) REVERT: B 471 GLU cc_start: 0.8680 (tp30) cc_final: 0.8383 (tp30) REVERT: C 505 TYR cc_start: 0.8363 (m-80) cc_final: 0.8007 (t80) REVERT: F 567 ARG cc_start: 0.2474 (OUTLIER) cc_final: 0.0279 (ptp90) outliers start: 15 outliers final: 13 residues processed: 85 average time/residue: 0.2445 time to fit residues: 31.2082 Evaluate side-chains 80 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 498 GLN Chi-restraints excluded: chain F residue 567 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 chunk 146 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 GLN E 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.098187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.079249 restraints weight = 30690.942| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.21 r_work: 0.3187 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13152 Z= 0.119 Angle : 0.489 10.965 17928 Z= 0.249 Chirality : 0.045 0.302 1974 Planarity : 0.004 0.051 2328 Dihedral : 4.044 24.797 2016 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.23 % Allowed : 9.74 % Favored : 89.03 % 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: -0.60 (0.20), residues: 1596 helix: -2.55 (0.43), residues: 126 sheet: 0.20 (0.27), residues: 352 loop : -0.30 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 PHE 0.010 0.001 PHE A 559 TYR 0.007 0.001 TYR A 369 ARG 0.005 0.000 ARG F 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 12) link_NAG-ASN : angle 2.01031 ( 36) hydrogen bonds : bond 0.03197 ( 353) hydrogen bonds : angle 6.25125 ( 906) SS BOND : bond 0.00209 ( 24) SS BOND : angle 0.73434 ( 48) covalent geometry : bond 0.00277 (13116) covalent geometry : angle 0.48037 (17844) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 1.563 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7282 (pm20) cc_final: 0.6986 (pm20) REVERT: B 471 GLU cc_start: 0.8671 (tp30) cc_final: 0.8381 (tp30) REVERT: C 505 TYR cc_start: 0.8337 (m-80) cc_final: 0.8068 (t80) REVERT: F 567 ARG cc_start: 0.2556 (OUTLIER) cc_final: 0.0308 (mtt90) REVERT: F 577 ARG cc_start: 0.6710 (ttp-110) cc_final: 0.5968 (ttm110) outliers start: 17 outliers final: 15 residues processed: 87 average time/residue: 0.2494 time to fit residues: 32.5598 Evaluate side-chains 87 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 498 GLN Chi-restraints excluded: chain F residue 567 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 82 optimal weight: 0.0670 chunk 119 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 GLN B 493 GLN E 414 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.096473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.077555 restraints weight = 30584.073| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.19 r_work: 0.3162 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13152 Z= 0.166 Angle : 0.526 10.892 17928 Z= 0.268 Chirality : 0.045 0.298 1974 Planarity : 0.004 0.051 2328 Dihedral : 4.179 23.581 2016 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.37 % Allowed : 10.03 % Favored : 88.60 % 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: -0.65 (0.20), residues: 1596 helix: -2.56 (0.43), residues: 122 sheet: 0.14 (0.27), residues: 354 loop : -0.33 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 436 PHE 0.018 0.001 PHE F 392 TYR 0.008 0.001 TYR C 505 ARG 0.004 0.000 ARG F 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 12) link_NAG-ASN : angle 2.02086 ( 36) hydrogen bonds : bond 0.03358 ( 353) hydrogen bonds : angle 6.41257 ( 906) SS BOND : bond 0.00205 ( 24) SS BOND : angle 0.81416 ( 48) covalent geometry : bond 0.00389 (13116) covalent geometry : angle 0.51766 (17844) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 1.370 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7354 (pm20) cc_final: 0.7057 (pm20) REVERT: B 471 GLU cc_start: 0.8684 (tp30) cc_final: 0.8362 (tp30) REVERT: F 567 ARG cc_start: 0.2560 (OUTLIER) cc_final: 0.0130 (mtt90) REVERT: F 577 ARG cc_start: 0.6704 (ttp-110) cc_final: 0.6141 (ttm110) outliers start: 19 outliers final: 15 residues processed: 88 average time/residue: 0.2535 time to fit residues: 33.1729 Evaluate side-chains 85 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 498 GLN Chi-restraints excluded: chain F residue 567 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 134 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 0.0870 chunk 92 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 58 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 GLN E 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.097021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.078198 restraints weight = 30403.454| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.17 r_work: 0.3172 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13152 Z= 0.139 Angle : 0.512 11.175 17928 Z= 0.262 Chirality : 0.045 0.302 1974 Planarity : 0.004 0.051 2328 Dihedral : 4.129 22.664 2016 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.30 % Allowed : 10.10 % Favored : 88.60 % 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: -0.62 (0.20), residues: 1596 helix: -2.47 (0.43), residues: 122 sheet: 0.15 (0.27), residues: 354 loop : -0.32 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 PHE 0.019 0.001 PHE F 392 TYR 0.007 0.001 TYR A 473 ARG 0.005 0.000 ARG F 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 12) link_NAG-ASN : angle 1.99543 ( 36) hydrogen bonds : bond 0.03266 ( 353) hydrogen bonds : angle 6.34570 ( 906) SS BOND : bond 0.00204 ( 24) SS BOND : angle 0.76264 ( 48) covalent geometry : bond 0.00324 (13116) covalent geometry : angle 0.50347 (17844) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7387 (pm20) cc_final: 0.7091 (pm20) REVERT: B 471 GLU cc_start: 0.8701 (tp30) cc_final: 0.8375 (tp30) REVERT: F 567 ARG cc_start: 0.2798 (OUTLIER) cc_final: 0.1439 (mtm-85) REVERT: F 577 ARG cc_start: 0.6670 (ttp-110) cc_final: 0.6164 (ttm110) outliers start: 18 outliers final: 15 residues processed: 82 average time/residue: 0.2816 time to fit residues: 34.3742 Evaluate side-chains 86 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 498 GLN Chi-restraints excluded: chain F residue 567 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 2 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.097368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.078491 restraints weight = 30478.675| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.19 r_work: 0.3176 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13152 Z= 0.134 Angle : 0.514 11.259 17928 Z= 0.262 Chirality : 0.045 0.302 1974 Planarity : 0.004 0.051 2328 Dihedral : 4.088 22.057 2016 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.15 % Allowed : 10.10 % Favored : 88.74 % 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: -0.61 (0.20), residues: 1596 helix: -2.49 (0.43), residues: 122 sheet: 0.17 (0.27), residues: 354 loop : -0.31 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 PHE 0.019 0.001 PHE F 392 TYR 0.007 0.001 TYR A 473 ARG 0.004 0.000 ARG F 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 12) link_NAG-ASN : angle 1.96977 ( 36) hydrogen bonds : bond 0.03229 ( 353) hydrogen bonds : angle 6.31636 ( 906) SS BOND : bond 0.00203 ( 24) SS BOND : angle 0.73927 ( 48) covalent geometry : bond 0.00315 (13116) covalent geometry : angle 0.50600 (17844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6033.83 seconds wall clock time: 104 minutes 48.69 seconds (6288.69 seconds total)