Starting phenix.real_space_refine on Fri Jul 3 07:34:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tf4_25861/07_2026/7tf4_25861.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tf4_25861/07_2026/7tf4_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7tf4_25861/07_2026/7tf4_25861.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tf4_25861/07_2026/7tf4_25861.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tf4_25861/07_2026/7tf4_25861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tf4_25861/07_2026/7tf4_25861.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tf4_25861/07_2026/7tf4_25861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tf4_25861/07_2026/7tf4_25861.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 'HIS:plan': 1, 'ASP: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, 'HIS:plan': 1, 'ASP: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, 'HIS:plan': 1, 'ASP: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, 'HIS:plan': 1, 'ASP: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, 'HIS:plan': 1, 'ASP: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, 'HIS:plan': 1, 'ASP: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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 3.15, per 1000 atoms: 0.25 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: 1.07 Conformation dependent library (CDL) restraints added in 704.3 milliseconds 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: 0.40 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: 2.23 Time building geometry restraints manager: 1.45 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: 6912 16.25 - 32.50: 669 32.50 - 48.75: 103 48.75 - 65.00: 13 65.00 - 81.25: 13 Dihedral angle restraints: 7710 sinusoidal: 3030 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 7707 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: 0.01 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: 6.340 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.530 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 12.822 81.255 4650 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.009 0.001 ARG F 577 TYR 0.033 0.002 TYR E 495 PHE 0.051 0.002 PHE F 392 TRP 0.016 0.002 TRP F 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.23 (13116) covalent geometry : angle 0.84873 / 0.48 (17844) SS BOND : bond 0.00584 / 0.31 ( 24) SS BOND : angle 1.41985 / 1.07 ( 48) hydrogen bonds : bond 0.17143 / 11.41 ( 353) hydrogen bonds : angle 9.38720 / 6.64 ( 906) link_NAG-ASN : bond 0.01031 / 0.61 ( 12) link_NAG-ASN : angle 3.82597 / 2.53 ( 36) *********************** 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 : 0.525 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: 0.6630 (mm-40) cc_final: 0.5798 (tp-100) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1244 time to fit residues: 22.1514 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 : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN E 493 GLN F 409 GLN F 414 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.094769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.075364 restraints weight = 30806.511| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.25 r_work: 0.3110 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 13152 Z= 0.324 Angle : 0.680 13.408 17928 Z= 0.347 Chirality : 0.049 0.291 1974 Planarity : 0.006 0.063 2328 Dihedral : 5.109 28.899 1764 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.43 % Allowed : 5.92 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.19), residues: 1596 helix: -3.06 (0.33), residues: 134 sheet: -0.23 (0.27), residues: 344 loop : -0.75 (0.17), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 567 TYR 0.015 0.002 TYR E 495 PHE 0.033 0.002 PHE A 559 TRP 0.016 0.002 TRP B 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.32 (13116) covalent geometry : angle 0.66946 / 0.34 (17844) SS BOND : bond 0.00334 / 0.20 ( 24) SS BOND : angle 1.04415 / 0.68 ( 48) hydrogen bonds : bond 0.04432 / 2.92 ( 353) hydrogen bonds : angle 7.49435 / 5.21 ( 906) link_NAG-ASN : bond 0.00634 / 0.37 ( 12) link_NAG-ASN : angle 2.56983 / 1.71 ( 36) *********************** 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 97 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7705 (pm20) cc_final: 0.7180 (pm20) REVERT: B 340 GLU cc_start: 0.8094 (pp20) cc_final: 0.7873 (pp20) REVERT: B 428 ASP cc_start: 0.7897 (p0) cc_final: 0.7677 (p0) REVERT: B 471 GLU cc_start: 0.8642 (tp30) cc_final: 0.8408 (tp30) REVERT: C 406 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8320 (mt-10) REVERT: E 584 ILE cc_start: 0.8231 (mm) cc_final: 0.7951 (mm) REVERT: F 392 PHE cc_start: 0.7450 (m-80) cc_final: 0.7182 (m-10) REVERT: F 403 ARG cc_start: 0.8441 (ptt90) cc_final: 0.8084 (ptt-90) REVERT: F 580 GLN cc_start: 0.7030 (mm-40) cc_final: 0.6819 (mm110) outliers start: 6 outliers final: 3 residues processed: 94 average time/residue: 0.1447 time to fit residues: 18.8951 Evaluate side-chains 77 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 87 optimal weight: 0.0070 chunk 72 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 409 GLN F 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.098032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.079231 restraints weight = 30591.589| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.18 r_work: 0.3191 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13152 Z= 0.103 Angle : 0.520 8.834 17928 Z= 0.263 Chirality : 0.045 0.311 1974 Planarity : 0.004 0.056 2328 Dihedral : 4.305 23.487 1764 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.58 % Allowed : 7.00 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.19), residues: 1596 helix: -3.12 (0.32), residues: 154 sheet: -0.00 (0.27), residues: 354 loop : -0.61 (0.17), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 577 TYR 0.011 0.001 TYR C 380 PHE 0.012 0.001 PHE F 392 TRP 0.012 0.001 TRP D 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (13116) covalent geometry : angle 0.51004 / 0.26 (17844) SS BOND : bond 0.00246 / 0.14 ( 24) SS BOND : angle 0.68722 / 0.42 ( 48) hydrogen bonds : bond 0.03501 / 2.30 ( 353) hydrogen bonds : angle 6.75323 / 4.70 ( 906) link_NAG-ASN : bond 0.00590 / 0.35 ( 12) link_NAG-ASN : angle 2.29943 / 1.53 ( 36) *********************** 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: 8 poor density : 87 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7454 (pm20) cc_final: 0.6969 (pm20) REVERT: A 516 GLU cc_start: 0.8167 (pm20) cc_final: 0.7719 (pm20) REVERT: B 340 GLU cc_start: 0.8033 (pp20) cc_final: 0.7805 (pp20) REVERT: B 471 GLU cc_start: 0.8642 (tp30) cc_final: 0.8370 (tp30) REVERT: C 406 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8387 (mt-10) REVERT: F 567 ARG cc_start: 0.2811 (mtm-85) cc_final: 0.1846 (mtm-85) outliers start: 8 outliers final: 3 residues processed: 92 average time/residue: 0.1315 time to fit residues: 17.3745 Evaluate side-chains 76 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain F residue 387 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 139 optimal weight: 0.0270 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 54 optimal weight: 0.0870 chunk 72 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.098812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.079954 restraints weight = 30529.773| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.24 r_work: 0.3203 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13152 Z= 0.092 Angle : 0.484 9.350 17928 Z= 0.247 Chirality : 0.045 0.325 1974 Planarity : 0.004 0.053 2328 Dihedral : 3.987 21.914 1764 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.65 % Allowed : 8.37 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.20), residues: 1596 helix: -3.15 (0.35), residues: 138 sheet: 0.14 (0.27), residues: 352 loop : -0.43 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 577 TYR 0.013 0.001 TYR B 365 PHE 0.008 0.001 PHE F 392 TRP 0.011 0.001 TRP D 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (13116) covalent geometry : angle 0.47347 / 0.24 (17844) SS BOND : bond 0.00221 / 0.12 ( 24) SS BOND : angle 0.76491 / 0.48 ( 48) hydrogen bonds : bond 0.03194 / 2.10 ( 353) hydrogen bonds : angle 6.33918 / 4.41 ( 906) link_NAG-ASN : bond 0.00570 / 0.34 ( 12) link_NAG-ASN : angle 2.20781 / 1.43 ( 36) *********************** 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 94 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7468 (pm20) cc_final: 0.6940 (pm20) REVERT: B 340 GLU cc_start: 0.7978 (pp20) cc_final: 0.7738 (pp20) REVERT: B 471 GLU cc_start: 0.8633 (tp30) cc_final: 0.8382 (tp30) REVERT: B 539 VAL cc_start: 0.8933 (m) cc_final: 0.8633 (p) REVERT: C 406 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8397 (mt-10) REVERT: F 567 ARG cc_start: 0.2703 (mtm-85) cc_final: 0.1606 (mtm-85) outliers start: 9 outliers final: 7 residues processed: 91 average time/residue: 0.1148 time to fit residues: 15.1629 Evaluate side-chains 78 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL 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 C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain F residue 387 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 140 optimal weight: 0.0020 chunk 73 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 0.0040 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN C 484 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.096426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.077159 restraints weight = 30672.533| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.28 r_work: 0.3146 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13152 Z= 0.173 Angle : 0.527 9.636 17928 Z= 0.268 Chirality : 0.046 0.314 1974 Planarity : 0.004 0.053 2328 Dihedral : 4.228 23.634 1764 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.79 % Allowed : 9.45 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.20), residues: 1596 helix: -3.02 (0.37), residues: 138 sheet: 0.06 (0.27), residues: 352 loop : -0.41 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 577 TYR 0.013 0.001 TYR B 365 PHE 0.014 0.001 PHE F 392 TRP 0.011 0.001 TRP B 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (13116) covalent geometry : angle 0.51794 / 0.27 (17844) SS BOND : bond 0.00224 / 0.13 ( 24) SS BOND : angle 0.78724 / 0.50 ( 48) hydrogen bonds : bond 0.03460 / 2.27 ( 353) hydrogen bonds : angle 6.56712 / 4.56 ( 906) link_NAG-ASN : bond 0.00548 / 0.33 ( 12) link_NAG-ASN : angle 2.15531 / 1.38 ( 36) *********************** 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: 11 poor density : 77 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7488 (pm20) cc_final: 0.7050 (pm20) REVERT: A 389 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8062 (t0) REVERT: B 340 GLU cc_start: 0.8059 (pp20) cc_final: 0.7839 (pp20) REVERT: B 471 GLU cc_start: 0.8699 (tp30) cc_final: 0.8411 (tp30) REVERT: C 406 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8407 (mt-10) REVERT: F 567 ARG cc_start: 0.2685 (OUTLIER) cc_final: 0.1086 (mtm-85) outliers start: 11 outliers final: 7 residues processed: 85 average time/residue: 0.1018 time to fit residues: 12.8279 Evaluate side-chains 79 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP 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 C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 567 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 0.1980 chunk 20 optimal weight: 0.0020 chunk 63 optimal weight: 1.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.098447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.079696 restraints weight = 30390.066| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.19 r_work: 0.3199 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13152 Z= 0.096 Angle : 0.487 10.274 17928 Z= 0.248 Chirality : 0.045 0.316 1974 Planarity : 0.004 0.052 2328 Dihedral : 3.974 22.814 1764 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.72 % Allowed : 10.17 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.20), residues: 1596 helix: -2.62 (0.44), residues: 106 sheet: 0.04 (0.27), residues: 360 loop : -0.28 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 577 TYR 0.012 0.001 TYR B 365 PHE 0.007 0.001 PHE E 565 TRP 0.010 0.001 TRP D 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (13116) covalent geometry : angle 0.47763 / 0.25 (17844) SS BOND : bond 0.00205 / 0.12 ( 24) SS BOND : angle 0.69798 / 0.41 ( 48) hydrogen bonds : bond 0.03148 / 2.06 ( 353) hydrogen bonds : angle 6.25064 / 4.35 ( 906) link_NAG-ASN : bond 0.00542 / 0.33 ( 12) link_NAG-ASN : angle 2.07622 / 1.33 ( 36) *********************** 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 85 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7477 (pm20) cc_final: 0.6957 (pm20) REVERT: A 357 ARG cc_start: 0.5397 (ttt180) cc_final: 0.5113 (ttt180) REVERT: A 516 GLU cc_start: 0.8019 (pm20) cc_final: 0.7569 (pm20) REVERT: B 340 GLU cc_start: 0.8021 (pp20) cc_final: 0.7785 (pp20) REVERT: B 471 GLU cc_start: 0.8684 (tp30) cc_final: 0.8403 (tp30) REVERT: B 539 VAL cc_start: 0.8888 (m) cc_final: 0.8606 (p) REVERT: C 406 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8357 (mt-10) REVERT: F 567 ARG cc_start: 0.2470 (OUTLIER) cc_final: 0.0695 (mtt90) outliers start: 10 outliers final: 8 residues processed: 81 average time/residue: 0.1228 time to fit residues: 14.6474 Evaluate side-chains 80 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain F residue 387 LEU 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 149 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 117 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.098010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.079035 restraints weight = 30650.668| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.23 r_work: 0.3184 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2306 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= 0.115 Angle : 0.494 10.403 17928 Z= 0.251 Chirality : 0.045 0.313 1974 Planarity : 0.004 0.052 2328 Dihedral : 3.934 22.286 1764 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.94 % Allowed : 10.39 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.20), residues: 1596 helix: -2.86 (0.38), residues: 138 sheet: 0.20 (0.27), residues: 352 loop : -0.28 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 408 TYR 0.010 0.001 TYR B 365 PHE 0.014 0.001 PHE F 392 TRP 0.009 0.001 TRP B 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (13116) covalent geometry : angle 0.48573 / 0.25 (17844) SS BOND : bond 0.00215 / 0.12 ( 24) SS BOND : angle 0.71188 / 0.42 ( 48) hydrogen bonds : bond 0.03157 / 2.07 ( 353) hydrogen bonds : angle 6.23917 / 4.33 ( 906) link_NAG-ASN : bond 0.00539 / 0.33 ( 12) link_NAG-ASN : angle 2.02877 / 1.28 ( 36) *********************** 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: 13 poor density : 76 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7482 (pm20) cc_final: 0.7046 (pm20) REVERT: A 357 ARG cc_start: 0.5621 (ttt180) cc_final: 0.5393 (ttt180) REVERT: A 495 TYR cc_start: 0.9234 (OUTLIER) cc_final: 0.8869 (m-80) REVERT: B 340 GLU cc_start: 0.8020 (pp20) cc_final: 0.7782 (pp20) REVERT: B 471 GLU cc_start: 0.8664 (tp30) cc_final: 0.8413 (tp30) REVERT: B 539 VAL cc_start: 0.8956 (m) cc_final: 0.8688 (p) REVERT: C 406 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8338 (mt-10) REVERT: F 567 ARG cc_start: 0.2638 (OUTLIER) cc_final: 0.0337 (mtt90) REVERT: F 577 ARG cc_start: 0.6712 (ttp-110) cc_final: 0.6459 (ttm110) outliers start: 13 outliers final: 9 residues processed: 87 average time/residue: 0.1194 time to fit residues: 15.3444 Evaluate side-chains 80 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 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 C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 468 ILE 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 96 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 128 optimal weight: 0.0670 chunk 98 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 93 optimal weight: 0.2980 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.096633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.077749 restraints weight = 30366.665| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.18 r_work: 0.3160 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2395 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= 0.157 Angle : 0.508 10.941 17928 Z= 0.259 Chirality : 0.045 0.309 1974 Planarity : 0.004 0.051 2328 Dihedral : 4.070 23.026 1764 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.30 % Allowed : 10.53 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.20), residues: 1596 helix: -2.92 (0.37), residues: 138 sheet: 0.10 (0.27), residues: 356 loop : -0.27 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 408 TYR 0.010 0.001 TYR B 365 PHE 0.011 0.001 PHE A 559 TRP 0.009 0.001 TRP D 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (13116) covalent geometry : angle 0.49927 / 0.26 (17844) SS BOND : bond 0.00213 / 0.13 ( 24) SS BOND : angle 0.75460 / 0.47 ( 48) hydrogen bonds : bond 0.03314 / 2.18 ( 353) hydrogen bonds : angle 6.36708 / 4.41 ( 906) link_NAG-ASN : bond 0.00532 / 0.32 ( 12) link_NAG-ASN : angle 2.02196 / 1.26 ( 36) *********************** 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 90 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7453 (pm20) cc_final: 0.7011 (pm20) REVERT: B 340 GLU cc_start: 0.8037 (pp20) cc_final: 0.7807 (pp20) REVERT: B 471 GLU cc_start: 0.8673 (tp30) cc_final: 0.8393 (tp30) REVERT: C 406 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8332 (mt-10) REVERT: F 324 GLU cc_start: 0.8251 (pt0) cc_final: 0.8026 (pm20) REVERT: F 567 ARG cc_start: 0.2874 (OUTLIER) cc_final: 0.0438 (mtt90) outliers start: 18 outliers final: 13 residues processed: 87 average time/residue: 0.1169 time to fit residues: 15.1974 Evaluate side-chains 85 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 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 F residue 387 LEU Chi-restraints excluded: chain F residue 534 VAL 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 116 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 439 ASN B 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.096592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.077656 restraints weight = 30697.243| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.21 r_work: 0.3158 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13152 Z= 0.154 Angle : 0.518 10.892 17928 Z= 0.263 Chirality : 0.045 0.307 1974 Planarity : 0.004 0.052 2328 Dihedral : 4.104 23.405 1764 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.15 % Allowed : 10.61 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.20), residues: 1596 helix: -2.83 (0.39), residues: 134 sheet: 0.13 (0.27), residues: 352 loop : -0.30 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 408 TYR 0.009 0.001 TYR B 365 PHE 0.010 0.001 PHE A 559 TRP 0.009 0.001 TRP D 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (13116) covalent geometry : angle 0.50962 / 0.26 (17844) SS BOND : bond 0.00211 / 0.13 ( 24) SS BOND : angle 0.73598 / 0.46 ( 48) hydrogen bonds : bond 0.03297 / 2.17 ( 353) hydrogen bonds : angle 6.39100 / 4.43 ( 906) link_NAG-ASN : bond 0.00526 / 0.32 ( 12) link_NAG-ASN : angle 1.99760 / 1.24 ( 36) *********************** 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 90 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7366 (pm20) cc_final: 0.6923 (pm20) REVERT: B 340 GLU cc_start: 0.8082 (pp20) cc_final: 0.7818 (pp20) REVERT: B 471 GLU cc_start: 0.8690 (tp30) cc_final: 0.8393 (tp30) REVERT: C 406 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8346 (mt-10) REVERT: F 324 GLU cc_start: 0.8348 (pt0) cc_final: 0.8066 (pm20) REVERT: F 567 ARG cc_start: 0.3028 (OUTLIER) cc_final: 0.0209 (mtt90) REVERT: F 577 ARG cc_start: 0.6678 (ttp-110) cc_final: 0.6391 (ttm110) outliers start: 16 outliers final: 13 residues processed: 87 average time/residue: 0.1194 time to fit residues: 15.5041 Evaluate side-chains 84 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 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 F residue 387 LEU Chi-restraints excluded: chain F residue 534 VAL 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 140 optimal weight: 0.0470 chunk 78 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 493 GLN F 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.096477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.077296 restraints weight = 30726.592| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.30 r_work: 0.3155 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13152 Z= 0.141 Angle : 0.514 11.233 17928 Z= 0.263 Chirality : 0.045 0.308 1974 Planarity : 0.004 0.051 2328 Dihedral : 4.097 24.376 1764 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.15 % Allowed : 10.75 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.20), residues: 1596 helix: -2.78 (0.39), residues: 134 sheet: 0.15 (0.27), residues: 352 loop : -0.28 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 408 TYR 0.009 0.001 TYR B 365 PHE 0.009 0.001 PHE A 559 TRP 0.009 0.001 TRP D 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (13116) covalent geometry : angle 0.50622 / 0.26 (17844) SS BOND : bond 0.00209 / 0.12 ( 24) SS BOND : angle 0.79480 / 0.47 ( 48) hydrogen bonds : bond 0.03290 / 2.17 ( 353) hydrogen bonds : angle 6.37388 / 4.42 ( 906) link_NAG-ASN : bond 0.00525 / 0.32 ( 12) link_NAG-ASN : angle 1.97390 / 1.22 ( 36) ********************** 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: 16 poor density : 72 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7424 (pm20) cc_final: 0.6964 (pm20) REVERT: B 340 GLU cc_start: 0.8071 (pp20) cc_final: 0.7797 (pp20) REVERT: B 471 GLU cc_start: 0.8695 (tp30) cc_final: 0.8389 (tp30) REVERT: C 406 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8354 (mt-10) REVERT: F 567 ARG cc_start: 0.3096 (OUTLIER) cc_final: 0.0287 (mtt90) REVERT: F 577 ARG cc_start: 0.6657 (ttp-110) cc_final: 0.6434 (ttm110) outliers start: 16 outliers final: 14 residues processed: 84 average time/residue: 0.1179 time to fit residues: 14.7815 Evaluate side-chains 84 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL 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 F residue 387 LEU Chi-restraints excluded: chain F residue 534 VAL 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 139 optimal weight: 0.0070 chunk 152 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 43 optimal weight: 0.0020 chunk 96 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 106 optimal weight: 0.4980 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.098185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.079515 restraints weight = 30525.970| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.19 r_work: 0.3201 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 13152 Z= 0.098 Angle : 0.502 11.408 17928 Z= 0.256 Chirality : 0.045 0.312 1974 Planarity : 0.004 0.052 2328 Dihedral : 3.902 24.170 1764 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.15 % Allowed : 11.11 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.20), residues: 1596 helix: -2.81 (0.38), residues: 138 sheet: 0.25 (0.27), residues: 350 loop : -0.23 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 408 TYR 0.009 0.001 TYR B 365 PHE 0.006 0.001 PHE C 497 TRP 0.010 0.001 TRP D 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (13116) covalent geometry : angle 0.49401 / 0.25 (17844) SS BOND : bond 0.00209 / 0.12 ( 24) SS BOND : angle 0.69979 / 0.40 ( 48) hydrogen bonds : bond 0.03087 / 2.04 ( 353) hydrogen bonds : angle 6.14265 / 4.26 ( 906) link_NAG-ASN : bond 0.00522 / 0.32 ( 12) link_NAG-ASN : angle 1.93415 / 1.20 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2768.57 seconds wall clock time: 48 minutes 35.07 seconds (2915.07 seconds total)