Starting phenix.real_space_refine on Wed Mar 4 10:24:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tf4_25861/03_2026/7tf4_25861.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tf4_25861/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tf4_25861/03_2026/7tf4_25861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tf4_25861/03_2026/7tf4_25861.map" model { file = "/net/cci-nas-00/data/ceres_data/7tf4_25861/03_2026/7tf4_25861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tf4_25861/03_2026/7tf4_25861.cif" } 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-5986/lib/python3.9/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 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: 3.09, per 1000 atoms: 0.24 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: 0.94 Conformation dependent library (CDL) restraints added in 498.9 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: 1.67 Time building geometry restraints manager: 1.32 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: 0.01 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.700 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.630 ------------------------------------------------------------------------------- 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 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 covalent geometry : bond 0.00488 (13116) covalent geometry : angle 0.84873 (17844) SS BOND : bond 0.00584 ( 24) SS BOND : angle 1.41985 ( 48) hydrogen bonds : bond 0.17143 ( 353) hydrogen bonds : angle 9.38720 ( 906) link_NAG-ASN : bond 0.01031 ( 12) link_NAG-ASN : angle 3.82597 ( 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 : 0.362 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: 0.1217 time to fit residues: 21.4155 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 : 0.365 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3589 r_free = 0.3589 target = 0.094647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.075348 restraints weight = 30838.053| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.21 r_work: 0.3110 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 13152 Z= 0.324 Angle : 0.680 12.647 17928 Z= 0.347 Chirality : 0.049 0.300 1974 Planarity : 0.006 0.062 2328 Dihedral : 5.538 34.613 2016 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.43 % Allowed : 5.99 % Favored : 93.58 % 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: -1.27 (0.19), residues: 1596 helix: -3.05 (0.34), residues: 134 sheet: -0.24 (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 F 369 PHE 0.035 0.002 PHE A 559 TRP 0.016 0.002 TRP D 436 Details of bonding type rmsd covalent geometry : bond 0.00749 (13116) covalent geometry : angle 0.67032 (17844) SS BOND : bond 0.00405 ( 24) SS BOND : angle 1.06608 ( 48) hydrogen bonds : bond 0.04380 ( 353) hydrogen bonds : angle 7.49718 ( 906) link_NAG-ASN : bond 0.00578 ( 12) link_NAG-ASN : angle 2.52474 ( 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 : 0.514 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7752 (pm20) cc_final: 0.7173 (pm20) REVERT: B 340 GLU cc_start: 0.8078 (pp20) cc_final: 0.7864 (pp20) REVERT: B 428 ASP cc_start: 0.7933 (p0) cc_final: 0.7718 (p0) REVERT: B 471 GLU cc_start: 0.8646 (tp30) cc_final: 0.8397 (tp30) REVERT: C 406 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8347 (mt-10) REVERT: E 584 ILE cc_start: 0.8239 (mm) cc_final: 0.7940 (mm) REVERT: F 392 PHE cc_start: 0.7477 (m-80) cc_final: 0.7210 (m-10) REVERT: F 580 GLN cc_start: 0.7044 (mm-40) cc_final: 0.6821 (mm110) outliers start: 6 outliers final: 3 residues processed: 94 average time/residue: 0.1349 time to fit residues: 17.5715 Evaluate side-chains 78 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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: 0.0030 chunk 72 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 147 optimal weight: 0.7980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3639 r_free = 0.3639 target = 0.097515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.078687 restraints weight = 30605.487| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.18 r_work: 0.3182 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13152 Z= 0.112 Angle : 0.522 8.707 17928 Z= 0.264 Chirality : 0.046 0.296 1974 Planarity : 0.004 0.056 2328 Dihedral : 4.699 33.688 2016 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.65 % Allowed : 7.22 % Favored : 92.14 % 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: -1.14 (0.19), residues: 1596 helix: -3.13 (0.32), residues: 154 sheet: -0.03 (0.27), residues: 354 loop : -0.63 (0.17), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 covalent geometry : bond 0.00253 (13116) covalent geometry : angle 0.51186 (17844) SS BOND : bond 0.00243 ( 24) SS BOND : angle 0.70736 ( 48) hydrogen bonds : bond 0.03522 ( 353) hydrogen bonds : angle 6.79218 ( 906) link_NAG-ASN : bond 0.00598 ( 12) link_NAG-ASN : angle 2.29771 ( 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: 9 poor density : 86 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7472 (pm20) cc_final: 0.6961 (pm20) REVERT: A 516 GLU cc_start: 0.8191 (pm20) cc_final: 0.7718 (pm20) REVERT: B 340 GLU cc_start: 0.8030 (pp20) cc_final: 0.7811 (pp20) REVERT: B 471 GLU cc_start: 0.8602 (tp30) cc_final: 0.8322 (tp30) REVERT: C 406 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8387 (mt-10) REVERT: F 406 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8164 (pm20) REVERT: F 567 ARG cc_start: 0.2573 (mtm-85) cc_final: 0.1608 (mtm-85) outliers start: 9 outliers final: 4 residues processed: 92 average time/residue: 0.1247 time to fit residues: 16.5315 Evaluate side-chains 81 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 390 LEU 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 89 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 139 optimal weight: 0.0470 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.097854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.078952 restraints weight = 30551.413| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.21 r_work: 0.3185 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2038 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= 0.110 Angle : 0.493 9.310 17928 Z= 0.251 Chirality : 0.045 0.315 1974 Planarity : 0.004 0.053 2328 Dihedral : 4.369 31.979 2016 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.72 % Allowed : 8.30 % 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: -0.93 (0.20), residues: 1596 helix: -3.21 (0.35), residues: 138 sheet: 0.07 (0.27), residues: 352 loop : -0.47 (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 0.010 0.001 PHE A 559 TRP 0.011 0.001 TRP D 436 Details of bonding type rmsd covalent geometry : bond 0.00251 (13116) covalent geometry : angle 0.48205 (17844) SS BOND : bond 0.00220 ( 24) SS BOND : angle 0.74204 ( 48) hydrogen bonds : bond 0.03297 ( 353) hydrogen bonds : angle 6.48179 ( 906) link_NAG-ASN : bond 0.00573 ( 12) link_NAG-ASN : angle 2.23451 ( 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 97 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7508 (pm20) cc_final: 0.6948 (pm20) REVERT: B 340 GLU cc_start: 0.7995 (pp20) cc_final: 0.7780 (pp20) REVERT: B 471 GLU cc_start: 0.8666 (tp30) cc_final: 0.8382 (tp30) REVERT: C 406 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8417 (mt-10) REVERT: D 378 LYS cc_start: 0.9377 (mmtm) cc_final: 0.9145 (mmmt) REVERT: F 465 GLU cc_start: 0.8059 (pt0) cc_final: 0.7805 (pt0) REVERT: F 567 ARG cc_start: 0.2720 (mtm-85) cc_final: 0.1651 (mtm-85) outliers start: 10 outliers final: 8 residues processed: 95 average time/residue: 0.1249 time to fit residues: 17.0996 Evaluate side-chains 81 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 D residue 468 ILE 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: 3.9990 chunk 80 optimal weight: 3.9990 chunk 140 optimal weight: 0.0270 chunk 73 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3639 r_free = 0.3639 target = 0.097522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.078646 restraints weight = 30711.282| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.19 r_work: 0.3175 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13152 Z= 0.126 Angle : 0.495 9.817 17928 Z= 0.252 Chirality : 0.045 0.307 1974 Planarity : 0.004 0.052 2328 Dihedral : 4.303 29.941 2016 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: -3.12 (0.36), residues: 138 sheet: 0.08 (0.27), residues: 352 loop : -0.40 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 577 TYR 0.013 0.001 TYR B 365 PHE 0.015 0.001 PHE F 392 TRP 0.010 0.001 TRP B 436 Details of bonding type rmsd covalent geometry : bond 0.00290 (13116) covalent geometry : angle 0.48540 (17844) SS BOND : bond 0.00214 ( 24) SS BOND : angle 0.70443 ( 48) hydrogen bonds : bond 0.03280 ( 353) hydrogen bonds : angle 6.42573 ( 906) link_NAG-ASN : bond 0.00570 ( 12) link_NAG-ASN : angle 2.16155 ( 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 91 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7508 (pm20) cc_final: 0.6969 (pm20) REVERT: B 340 GLU cc_start: 0.8010 (pp20) cc_final: 0.7782 (pp20) REVERT: B 471 GLU cc_start: 0.8685 (tp30) cc_final: 0.8410 (tp30) REVERT: C 406 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8395 (mt-10) REVERT: F 406 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8189 (pm20) REVERT: F 465 GLU cc_start: 0.8127 (pt0) cc_final: 0.7842 (pt0) REVERT: F 567 ARG cc_start: 0.2537 (OUTLIER) cc_final: 0.1389 (mtm-85) outliers start: 11 outliers final: 8 residues processed: 88 average time/residue: 0.1235 time to fit residues: 15.6529 Evaluate side-chains 82 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 D residue 468 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 406 GLU 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: 0.8980 chunk 80 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3635 r_free = 0.3635 target = 0.097249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.078315 restraints weight = 30510.412| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.21 r_work: 0.3174 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13152 Z= 0.125 Angle : 0.497 10.298 17928 Z= 0.253 Chirality : 0.045 0.304 1974 Planarity : 0.004 0.052 2328 Dihedral : 4.246 28.410 2016 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.15 % Allowed : 10.32 % Favored : 88.53 % 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: -0.67 (0.20), residues: 1596 helix: -2.67 (0.44), residues: 106 sheet: -0.02 (0.27), residues: 360 loop : -0.32 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 577 TYR 0.011 0.001 TYR B 365 PHE 0.009 0.001 PHE A 559 TRP 0.010 0.001 TRP B 436 Details of bonding type rmsd covalent geometry : bond 0.00291 (13116) covalent geometry : angle 0.48744 (17844) SS BOND : bond 0.00213 ( 24) SS BOND : angle 0.77821 ( 48) hydrogen bonds : bond 0.03250 ( 353) hydrogen bonds : angle 6.37150 ( 906) link_NAG-ASN : bond 0.00568 ( 12) link_NAG-ASN : angle 2.11609 ( 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 90 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7491 (pm20) cc_final: 0.7023 (pm20) REVERT: A 516 GLU cc_start: 0.8135 (pm20) cc_final: 0.7699 (pm20) REVERT: B 340 GLU cc_start: 0.8008 (pp20) cc_final: 0.7771 (pp20) REVERT: B 471 GLU cc_start: 0.8649 (tp30) cc_final: 0.8409 (tp30) REVERT: C 406 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8335 (mt-10) REVERT: F 406 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8158 (pm20) REVERT: F 465 GLU cc_start: 0.8086 (pt0) cc_final: 0.7854 (pt0) REVERT: F 567 ARG cc_start: 0.2657 (OUTLIER) cc_final: 0.0930 (mtt90) outliers start: 16 outliers final: 10 residues processed: 84 average time/residue: 0.1152 time to fit residues: 14.6624 Evaluate side-chains 83 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 D residue 468 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 406 GLU 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 149 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 117 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3632 r_free = 0.3632 target = 0.097025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.078061 restraints weight = 30665.858| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.20 r_work: 0.3166 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2331 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= 0.137 Angle : 0.498 10.385 17928 Z= 0.254 Chirality : 0.045 0.302 1974 Planarity : 0.004 0.051 2328 Dihedral : 4.211 26.875 2016 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.15 % Allowed : 10.46 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.77 (0.20), residues: 1596 helix: -2.91 (0.38), residues: 138 sheet: 0.11 (0.27), residues: 352 loop : -0.36 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 577 TYR 0.010 0.001 TYR B 365 PHE 0.009 0.001 PHE A 559 TRP 0.010 0.001 TRP B 436 Details of bonding type rmsd covalent geometry : bond 0.00317 (13116) covalent geometry : angle 0.48898 (17844) SS BOND : bond 0.00221 ( 24) SS BOND : angle 0.75998 ( 48) hydrogen bonds : bond 0.03253 ( 353) hydrogen bonds : angle 6.37656 ( 906) link_NAG-ASN : bond 0.00563 ( 12) link_NAG-ASN : angle 2.08776 ( 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 90 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7501 (pm20) cc_final: 0.7069 (pm20) REVERT: B 340 GLU cc_start: 0.8025 (pp20) cc_final: 0.7791 (pp20) REVERT: B 471 GLU cc_start: 0.8682 (tp30) cc_final: 0.8415 (tp30) REVERT: C 406 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8327 (mt-10) REVERT: F 406 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8148 (pm20) REVERT: F 465 GLU cc_start: 0.8167 (pt0) cc_final: 0.7895 (pt0) REVERT: F 567 ARG cc_start: 0.2731 (OUTLIER) cc_final: 0.0753 (ptp90) REVERT: F 577 ARG cc_start: 0.6387 (ttp-110) cc_final: 0.5733 (ttm110) outliers start: 16 outliers final: 12 residues processed: 85 average time/residue: 0.1075 time to fit residues: 13.7101 Evaluate side-chains 82 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 484 GLN 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 387 LEU Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 498 GLN Chi-restraints excluded: chain F residue 534 VAL 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: 4.9990 chunk 124 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 493 GLN F 414 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.096269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.077355 restraints weight = 30447.472| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.18 r_work: 0.3156 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13152 Z= 0.160 Angle : 0.519 10.830 17928 Z= 0.263 Chirality : 0.045 0.300 1974 Planarity : 0.004 0.051 2328 Dihedral : 4.274 25.903 2016 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.44 % Allowed : 10.46 % 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: -0.76 (0.20), residues: 1596 helix: -2.80 (0.39), residues: 134 sheet: 0.01 (0.27), residues: 356 loop : -0.33 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 577 TYR 0.009 0.001 TYR B 365 PHE 0.009 0.001 PHE A 559 TRP 0.011 0.001 TRP B 436 Details of bonding type rmsd covalent geometry : bond 0.00373 (13116) covalent geometry : angle 0.50971 (17844) SS BOND : bond 0.00220 ( 24) SS BOND : angle 0.76168 ( 48) hydrogen bonds : bond 0.03338 ( 353) hydrogen bonds : angle 6.44405 ( 906) link_NAG-ASN : bond 0.00560 ( 12) link_NAG-ASN : angle 2.08442 ( 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 92 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7416 (pm20) cc_final: 0.6976 (pm20) REVERT: B 340 GLU cc_start: 0.8076 (pp20) cc_final: 0.7802 (pp20) REVERT: B 471 GLU cc_start: 0.8675 (tp30) cc_final: 0.8397 (tp30) REVERT: C 406 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8285 (mt-10) REVERT: F 406 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8247 (pm20) REVERT: F 465 GLU cc_start: 0.8211 (pt0) cc_final: 0.7906 (pt0) REVERT: F 567 ARG cc_start: 0.2807 (OUTLIER) cc_final: 0.0777 (ptp90) REVERT: F 577 ARG cc_start: 0.6755 (ttp-110) cc_final: 0.6195 (ttm110) outliers start: 20 outliers final: 16 residues processed: 87 average time/residue: 0.1104 time to fit residues: 14.4442 Evaluate side-chains 89 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 484 GLN 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 406 GLU 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 116 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 9 optimal weight: 0.0010 chunk 94 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 136 optimal weight: 7.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.097575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.078716 restraints weight = 30641.880| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.20 r_work: 0.3180 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13152 Z= 0.112 Angle : 0.491 11.010 17928 Z= 0.251 Chirality : 0.045 0.306 1974 Planarity : 0.004 0.052 2328 Dihedral : 4.109 24.421 2016 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.37 % Allowed : 10.53 % 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: -0.68 (0.20), residues: 1596 helix: -2.76 (0.40), residues: 134 sheet: 0.14 (0.27), residues: 352 loop : -0.31 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 577 TYR 0.009 0.001 TYR B 365 PHE 0.007 0.001 PHE A 559 TRP 0.010 0.001 TRP D 436 Details of bonding type rmsd covalent geometry : bond 0.00260 (13116) covalent geometry : angle 0.48241 (17844) SS BOND : bond 0.00210 ( 24) SS BOND : angle 0.66458 ( 48) hydrogen bonds : bond 0.03144 ( 353) hydrogen bonds : angle 6.26637 ( 906) link_NAG-ASN : bond 0.00551 ( 12) link_NAG-ASN : angle 2.03464 ( 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 102 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7414 (pm20) cc_final: 0.6950 (pm20) REVERT: B 340 GLU cc_start: 0.8056 (pp20) cc_final: 0.7774 (pp20) REVERT: B 471 GLU cc_start: 0.8689 (tp30) cc_final: 0.8397 (tp30) REVERT: B 539 VAL cc_start: 0.8906 (m) cc_final: 0.8686 (p) REVERT: C 357 ARG cc_start: 0.8574 (tpp80) cc_final: 0.8241 (mmm-85) REVERT: C 406 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8369 (mt-10) REVERT: F 406 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8243 (pm20) REVERT: F 465 GLU cc_start: 0.8198 (pt0) cc_final: 0.7916 (pt0) REVERT: F 567 ARG cc_start: 0.2784 (OUTLIER) cc_final: -0.0054 (mtt90) REVERT: F 577 ARG cc_start: 0.6672 (ttp-110) cc_final: 0.6240 (ttm110) outliers start: 19 outliers final: 14 residues processed: 97 average time/residue: 0.1147 time to fit residues: 16.2995 Evaluate side-chains 93 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 406 GLU Chi-restraints excluded: chain F residue 498 GLN 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: 0.6980 chunk 78 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 145 optimal weight: 0.0050 chunk 99 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3640 r_free = 0.3640 target = 0.097519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.078617 restraints weight = 30808.827| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.22 r_work: 0.3177 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2461 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= 0.120 Angle : 0.509 11.287 17928 Z= 0.260 Chirality : 0.045 0.305 1974 Planarity : 0.004 0.052 2328 Dihedral : 4.087 24.801 2016 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.37 % Allowed : 10.82 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.64 (0.20), residues: 1596 helix: -2.70 (0.39), residues: 134 sheet: 0.17 (0.27), residues: 352 loop : -0.29 (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 0.007 0.001 PHE A 559 TRP 0.010 0.001 TRP B 436 Details of bonding type rmsd covalent geometry : bond 0.00282 (13116) covalent geometry : angle 0.50084 (17844) SS BOND : bond 0.00207 ( 24) SS BOND : angle 0.82532 ( 48) hydrogen bonds : bond 0.03169 ( 353) hydrogen bonds : angle 6.26441 ( 906) link_NAG-ASN : bond 0.00546 ( 12) link_NAG-ASN : angle 2.00692 ( 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 98 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7407 (pm20) cc_final: 0.6967 (pm20) REVERT: B 340 GLU cc_start: 0.8045 (pp20) cc_final: 0.7765 (pp20) REVERT: B 471 GLU cc_start: 0.8645 (tp30) cc_final: 0.8380 (tp30) REVERT: B 498 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8823 (mm110) REVERT: B 539 VAL cc_start: 0.8927 (m) cc_final: 0.8688 (p) REVERT: C 406 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8309 (mt-10) REVERT: C 440 ASN cc_start: 0.8234 (p0) cc_final: 0.7897 (p0) REVERT: F 406 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8164 (pm20) REVERT: F 465 GLU cc_start: 0.8130 (pt0) cc_final: 0.7875 (pt0) REVERT: F 567 ARG cc_start: 0.2923 (OUTLIER) cc_final: 0.0069 (mtt90) REVERT: F 577 ARG cc_start: 0.6676 (ttp-110) cc_final: 0.6314 (ttm110) outliers start: 19 outliers final: 14 residues processed: 93 average time/residue: 0.1178 time to fit residues: 15.9645 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 : 0.491 ------------------------------------------------------------------------------- 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 406 GLU Chi-restraints excluded: chain F residue 498 GLN 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: 6.9990 chunk 152 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 132 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3604 r_free = 0.3604 target = 0.095259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.076000 restraints weight = 30629.185| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.29 r_work: 0.3129 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13152 Z= 0.206 Angle : 0.554 11.150 17928 Z= 0.282 Chirality : 0.046 0.297 1974 Planarity : 0.004 0.052 2328 Dihedral : 4.407 26.033 2016 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.44 % Allowed : 10.68 % Favored : 87.88 % 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: -0.64 (0.20), residues: 1596 helix: -2.28 (0.49), residues: 102 sheet: -0.13 (0.27), residues: 364 loop : -0.30 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 357 TYR 0.009 0.001 TYR A 473 PHE 0.012 0.001 PHE F 347 TRP 0.012 0.001 TRP B 436 Details of bonding type rmsd covalent geometry : bond 0.00480 (13116) covalent geometry : angle 0.54466 (17844) SS BOND : bond 0.00240 ( 24) SS BOND : angle 0.99075 ( 48) hydrogen bonds : bond 0.03508 ( 353) hydrogen bonds : angle 6.56114 ( 906) link_NAG-ASN : bond 0.00551 ( 12) link_NAG-ASN : angle 2.06920 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2555.73 seconds wall clock time: 44 minutes 39.07 seconds (2679.07 seconds total)