Starting phenix.real_space_refine on Sat Sep 12 01:57:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tf1_25858/09_2026/7tf1_25858.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tf1_25858/09_2026/7tf1_25858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tf1_25858/09_2026/7tf1_25858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tf1_25858/09_2026/7tf1_25858.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tf1_25858/09_2026/7tf1_25858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tf1_25858/09_2026/7tf1_25858.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tf1_25858/09_2026/7tf1_25858.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tf1_25858/09_2026/7tf1_25858.cif" } resolution = 3.57 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= 0.024 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 8172 2.51 5 N 2130 2.21 5 O 2430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12786 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2103 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: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2103 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: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2103 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: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2103 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: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2103 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: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2103 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: 3.23, per 1000 atoms: 0.25 Number of scatterers: 12786 At special positions: 0 Unit cell: (110.5, 107.9, 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 2430 8.00 N 2130 7.00 C 8172 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=2.04 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=2.04 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=2.03 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=2.04 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 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: 0.87 Conformation dependent library (CDL) restraints added in 691.0 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 29 sheets defined 14.6% alpha, 23.9% 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 337 through 343 removed outlier: 3.822A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.726A 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: 3.646A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.243A 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: 3.612A 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: 3.816A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.750A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.636A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.466A 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: 3.782A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.102A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.626A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) 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: 3.614A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.822A pdb=" N TRP D 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 384 through 390 removed outlier: 3.539A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) removed outlier: 3.628A 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 removed outlier: 3.531A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 371 removed outlier: 3.763A pdb=" N SER E 371 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 removed outlier: 3.840A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.300A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) 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: 4.391A pdb=" N LEU F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 removed outlier: 4.149A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) removed outlier: 3.765A 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 Processing helix chain 'F' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.202A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.620A 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: 4.083A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 7.527A 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: 6.969A 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: 4.119A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 removed outlier: 7.110A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.276A 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 'C' and resid 325 through 328 removed outlier: 5.278A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.160A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.214A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB7, first strand: chain 'D' and resid 326 through 328 removed outlier: 5.620A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY D 566 " --> pdb=" O ASP D 574 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AB9, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.818A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AC2, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AC3, first strand: chain 'E' and resid 324 through 328 removed outlier: 4.268A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.135A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 391 through 392 Processing sheet with id=AC6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'F' and resid 325 through 328 removed outlier: 5.151A pdb=" N ASP F 574 " --> pdb=" O ILE F 587 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 354 through 358 removed outlier: 4.354A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU F 516 " --> pdb=" O ASN F 394 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'F' and resid 473 through 474 355 hydrogen bonds defined for protein. 915 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: 1.95 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4085 1.34 - 1.47: 3414 1.47 - 1.60: 5557 1.60 - 1.72: 0 1.72 - 1.85: 54 Bond restraints: 13110 Sorted by residual: bond pdb=" C1 NAG F1301 " pdb=" O5 NAG F1301 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.39e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.16e+00 bond pdb=" C1 NAG D1301 " pdb=" O5 NAG D1301 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.56e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.54e+00 ... (remaining 13105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 17650 2.86 - 5.72: 171 5.72 - 8.58: 13 8.58 - 11.44: 2 11.44 - 14.31: 2 Bond angle restraints: 17838 Sorted by residual: angle pdb=" CA CYS F 391 " pdb=" CB CYS F 391 " pdb=" SG CYS F 391 " ideal model delta sigma weight residual 114.40 125.11 -10.71 2.30e+00 1.89e-01 2.17e+01 angle pdb=" CA LEU A 517 " pdb=" CB LEU A 517 " pdb=" CG LEU A 517 " ideal model delta sigma weight residual 116.30 129.19 -12.89 3.50e+00 8.16e-02 1.36e+01 angle pdb=" CB GLU C 471 " pdb=" CG GLU C 471 " pdb=" CD GLU C 471 " ideal model delta sigma weight residual 112.60 118.04 -5.44 1.70e+00 3.46e-01 1.02e+01 angle pdb=" CG1 ILE F 410 " pdb=" CB ILE F 410 " pdb=" CG2 ILE F 410 " ideal model delta sigma weight residual 110.70 101.37 9.33 3.00e+00 1.11e-01 9.67e+00 angle pdb=" N PRO F 561 " pdb=" CA PRO F 561 " pdb=" C PRO F 561 " ideal model delta sigma weight residual 112.47 118.80 -6.33 2.06e+00 2.36e-01 9.46e+00 ... (remaining 17833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 6936 16.44 - 32.88: 644 32.88 - 49.32: 99 49.32 - 65.76: 15 65.76 - 82.20: 10 Dihedral angle restraints: 7704 sinusoidal: 3024 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 -128.15 42.15 1 1.00e+01 1.00e-02 2.48e+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 53.16 39.84 1 1.00e+01 1.00e-02 2.23e+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 -159.83 -20.17 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 7701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1631 0.074 - 0.147: 319 0.147 - 0.221: 27 0.221 - 0.295: 2 0.295 - 0.368: 1 Chirality restraints: 1980 Sorted by residual: 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 -2.03 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CB ILE F 410 " pdb=" CA ILE F 410 " pdb=" CG1 ILE F 410 " pdb=" CG2 ILE F 410 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1977 not shown) Planarity restraints: 2334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 560 " 0.045 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO B 561 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO B 521 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 520 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO D 521 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 521 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 521 " 0.035 5.00e-02 4.00e+02 ... (remaining 2331 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3864 2.82 - 3.34: 10148 3.34 - 3.86: 21155 3.86 - 4.38: 24097 4.38 - 4.90: 41249 Nonbonded interactions: 100513 Sorted by model distance: nonbonded pdb=" OD2 ASP D 578 " pdb=" OG1 THR D 581 " model vdw 2.300 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.308 3.040 nonbonded pdb=" OD2 ASP C 578 " pdb=" OG1 THR C 581 " model vdw 2.311 3.040 nonbonded pdb=" O TYR A 495 " pdb=" OH TYR A 505 " model vdw 2.320 3.040 nonbonded pdb=" O THR F 393 " pdb=" OG1 THR F 523 " model vdw 2.325 3.040 ... (remaining 100508 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.400 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.140 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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: 19.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.004 0.072 13146 Z= 0.194 Angle : 0.784 14.306 17922 Z= 0.410 Chirality : 0.056 0.368 1980 Planarity : 0.007 0.069 2322 Dihedral : 12.651 82.203 4644 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.36 % Allowed : 2.31 % Favored : 97.33 % 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: -1.40 (0.18), residues: 1596 helix: -3.41 (0.25), residues: 160 sheet: 0.10 (0.26), residues: 364 loop : -0.92 (0.16), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 577 TYR 0.023 0.002 TYR E 495 PHE 0.022 0.002 PHE F 377 TRP 0.016 0.002 TRP F 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (13110) covalent geometry : angle 0.76806 / 0.41 (17838) SS BOND : bond 0.00457 / 0.27 ( 24) SS BOND : angle 1.34623 / 0.91 ( 48) hydrogen bonds : bond 0.20526 / 13.84 ( 355) hydrogen bonds : angle 9.36537 / 6.70 ( 915) link_NAG-ASN : bond 0.00717 / 0.45 ( 12) link_NAG-ASN : angle 3.33267 / 1.94 ( 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 307 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 302 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.9083 (pt) cc_final: 0.8730 (mt) REVERT: A 584 ILE cc_start: 0.8926 (mp) cc_final: 0.8456 (mt) REVERT: B 366 SER cc_start: 0.8636 (m) cc_final: 0.8400 (p) REVERT: B 387 LEU cc_start: 0.9506 (mt) cc_final: 0.9288 (mt) REVERT: B 406 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8138 (mt-10) REVERT: B 408 ARG cc_start: 0.8482 (ptm-80) cc_final: 0.8050 (ptm-80) REVERT: B 462 LYS cc_start: 0.8843 (mttt) cc_final: 0.8496 (mppt) REVERT: B 465 GLU cc_start: 0.8064 (tt0) cc_final: 0.7540 (tt0) REVERT: B 493 GLN cc_start: 0.8583 (tp40) cc_final: 0.8056 (tm-30) REVERT: B 537 LYS cc_start: 0.8851 (mtmt) cc_final: 0.8443 (mtpp) REVERT: B 557 LYS cc_start: 0.7621 (mttp) cc_final: 0.7212 (tttm) REVERT: C 409 GLN cc_start: 0.8847 (mt0) cc_final: 0.8553 (tt0) REVERT: C 498 GLN cc_start: 0.9011 (mt0) cc_final: 0.8688 (mm-40) REVERT: D 414 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8204 (mp10) REVERT: D 468 ILE cc_start: 0.9294 (pt) cc_final: 0.8907 (mt) REVERT: D 474 GLN cc_start: 0.8784 (tt0) cc_final: 0.8467 (tp40) REVERT: E 368 LEU cc_start: 0.9371 (mt) cc_final: 0.9012 (pp) REVERT: E 386 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8314 (tttt) REVERT: E 408 ARG cc_start: 0.8738 (ptm-80) cc_final: 0.8281 (tmm-80) REVERT: E 462 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8575 (mmmt) REVERT: E 465 GLU cc_start: 0.8000 (tt0) cc_final: 0.7500 (tt0) REVERT: E 538 CYS cc_start: 0.7411 (t) cc_final: 0.7204 (t) REVERT: E 584 ILE cc_start: 0.8459 (mm) cc_final: 0.8183 (mm) REVERT: F 365 TYR cc_start: 0.8609 (m-80) cc_final: 0.8389 (m-80) REVERT: F 378 LYS cc_start: 0.8476 (mtpp) cc_final: 0.8020 (tptm) REVERT: F 380 TYR cc_start: 0.8731 (m-80) cc_final: 0.8430 (m-80) REVERT: F 409 GLN cc_start: 0.8974 (mt0) cc_final: 0.8386 (mt0) REVERT: F 434 ILE cc_start: 0.8758 (mt) cc_final: 0.8490 (mm) REVERT: F 440 ASN cc_start: 0.8125 (m110) cc_final: 0.7419 (m110) REVERT: F 457 ARG cc_start: 0.8495 (ttt-90) cc_final: 0.8274 (ttp80) REVERT: F 498 GLN cc_start: 0.8918 (mt0) cc_final: 0.8584 (mm-40) REVERT: F 568 ASP cc_start: 0.5818 (p0) cc_final: 0.5544 (p0) REVERT: F 580 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7299 (tp-100) REVERT: F 583 GLU cc_start: 0.8283 (tp30) cc_final: 0.7761 (tp30) REVERT: F 584 ILE cc_start: 0.7900 (mp) cc_final: 0.7474 (mt) outliers start: 5 outliers final: 0 residues processed: 305 average time/residue: 0.1397 time to fit residues: 58.3370 Evaluate side-chains 139 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 481 ASN F 536 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.086642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.071072 restraints weight = 40239.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.073482 restraints weight = 20671.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.075072 restraints weight = 13454.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.076149 restraints weight = 10063.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.076831 restraints weight = 8189.617| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13146 Z= 0.216 Angle : 0.620 9.116 17922 Z= 0.322 Chirality : 0.047 0.342 1980 Planarity : 0.005 0.054 2322 Dihedral : 4.574 21.715 1764 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.59 % Allowed : 9.16 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.12 (0.19), residues: 1596 helix: -2.82 (0.27), residues: 204 sheet: 0.12 (0.26), residues: 376 loop : -0.59 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 403 TYR 0.018 0.002 TYR D 365 PHE 0.017 0.002 PHE D 515 TRP 0.018 0.002 TRP E 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.22 (13110) covalent geometry : angle 0.60724 / 0.32 (17838) SS BOND : bond 0.00222 / 0.14 ( 24) SS BOND : angle 1.64664 / 1.22 ( 48) hydrogen bonds : bond 0.04129 / 2.78 ( 355) hydrogen bonds : angle 6.91372 / 4.92 ( 915) link_NAG-ASN : bond 0.00471 / 0.30 ( 12) link_NAG-ASN : angle 2.19157 / 1.27 ( 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 169 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 ILE cc_start: 0.8725 (mp) cc_final: 0.8326 (tt) REVERT: B 366 SER cc_start: 0.8602 (m) cc_final: 0.8341 (p) REVERT: B 387 LEU cc_start: 0.9533 (mt) cc_final: 0.9319 (mt) REVERT: B 406 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8250 (mt-10) REVERT: B 493 GLN cc_start: 0.8400 (tp40) cc_final: 0.8030 (tm-30) REVERT: B 528 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8142 (mtmm) REVERT: B 583 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6653 (tm-30) REVERT: C 398 ASP cc_start: 0.8974 (m-30) cc_final: 0.8497 (m-30) REVERT: D 365 TYR cc_start: 0.9126 (m-10) cc_final: 0.8912 (m-10) REVERT: D 474 GLN cc_start: 0.8584 (tt0) cc_final: 0.8276 (tt0) REVERT: E 324 GLU cc_start: 0.7878 (mp0) cc_final: 0.7433 (mp0) REVERT: E 386 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8530 (ttpt) REVERT: E 406 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8165 (mt-10) REVERT: E 455 LEU cc_start: 0.9491 (tp) cc_final: 0.9224 (tt) REVERT: F 365 TYR cc_start: 0.8529 (m-80) cc_final: 0.8256 (m-80) REVERT: F 378 LYS cc_start: 0.8244 (mtpp) cc_final: 0.7954 (tptm) REVERT: F 380 TYR cc_start: 0.8708 (m-80) cc_final: 0.8226 (m-80) REVERT: F 406 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8092 (pm20) REVERT: F 464 PHE cc_start: 0.8128 (m-80) cc_final: 0.7578 (m-80) REVERT: F 498 GLN cc_start: 0.8966 (mt0) cc_final: 0.8705 (mm-40) REVERT: F 580 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7585 (tp-100) outliers start: 22 outliers final: 16 residues processed: 164 average time/residue: 0.1039 time to fit residues: 25.8605 Evaluate side-chains 129 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 574 ASP Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 406 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 83 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 414 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 564 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.085410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.069735 restraints weight = 40370.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.072103 restraints weight = 20827.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.073681 restraints weight = 13678.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.074728 restraints weight = 10269.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.075433 restraints weight = 8408.510| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13146 Z= 0.211 Angle : 0.582 8.651 17922 Z= 0.304 Chirality : 0.047 0.333 1980 Planarity : 0.004 0.047 2322 Dihedral : 4.478 21.891 1764 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.73 % Allowed : 10.75 % Favored : 87.52 % 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: -0.94 (0.19), residues: 1596 helix: -2.75 (0.30), residues: 174 sheet: 0.17 (0.26), residues: 364 loop : -0.50 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 567 TYR 0.014 0.001 TYR D 365 PHE 0.018 0.001 PHE F 392 TRP 0.016 0.002 TRP E 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (13110) covalent geometry : angle 0.57123 / 0.30 (17838) SS BOND : bond 0.00335 / 0.23 ( 24) SS BOND : angle 1.41006 / 1.02 ( 48) hydrogen bonds : bond 0.03916 / 2.59 ( 355) hydrogen bonds : angle 6.65027 / 4.72 ( 915) link_NAG-ASN : bond 0.00462 / 0.30 ( 12) link_NAG-ASN : angle 2.09564 / 1.23 ( 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 155 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 ILE cc_start: 0.8736 (mp) cc_final: 0.8419 (tt) REVERT: B 406 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8339 (mt-10) REVERT: B 528 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.7948 (mttp) REVERT: B 583 GLU cc_start: 0.7292 (tm-30) cc_final: 0.7018 (tm-30) REVERT: D 365 TYR cc_start: 0.9124 (m-10) cc_final: 0.8906 (m-10) REVERT: D 474 GLN cc_start: 0.8523 (tt0) cc_final: 0.8070 (tt0) REVERT: D 516 GLU cc_start: 0.8528 (tt0) cc_final: 0.8158 (pp20) REVERT: E 386 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8390 (ttpt) REVERT: E 455 LEU cc_start: 0.9521 (tp) cc_final: 0.9252 (tp) REVERT: E 493 GLN cc_start: 0.8835 (tp40) cc_final: 0.8593 (mm-40) REVERT: E 554 GLU cc_start: 0.8294 (pp20) cc_final: 0.7695 (pp20) REVERT: F 340 GLU cc_start: 0.8345 (pm20) cc_final: 0.8111 (pm20) REVERT: F 365 TYR cc_start: 0.8660 (m-80) cc_final: 0.8336 (m-80) REVERT: F 378 LYS cc_start: 0.8146 (mtpp) cc_final: 0.7849 (tptm) REVERT: F 380 TYR cc_start: 0.8815 (m-80) cc_final: 0.8176 (m-80) REVERT: F 406 GLU cc_start: 0.8318 (mp0) cc_final: 0.7910 (pm20) REVERT: F 464 PHE cc_start: 0.8135 (m-80) cc_final: 0.7623 (m-80) REVERT: F 493 GLN cc_start: 0.7742 (tm-30) cc_final: 0.7473 (tm-30) REVERT: F 580 GLN cc_start: 0.8355 (mm-40) cc_final: 0.7677 (tp-100) outliers start: 24 outliers final: 21 residues processed: 149 average time/residue: 0.1001 time to fit residues: 23.1143 Evaluate side-chains 137 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 574 ASP Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 559 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 33 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.085939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.070349 restraints weight = 40592.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.072748 restraints weight = 20891.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.074335 restraints weight = 13673.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.075392 restraints weight = 10235.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.076097 restraints weight = 8352.865| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13146 Z= 0.161 Angle : 0.545 8.560 17922 Z= 0.281 Chirality : 0.046 0.327 1980 Planarity : 0.004 0.042 2322 Dihedral : 4.278 21.429 1764 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.24 % Allowed : 11.76 % Favored : 86.00 % 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: -2.62 (0.36), residues: 144 sheet: 0.19 (0.28), residues: 331 loop : -0.29 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 567 TYR 0.011 0.001 TYR D 365 PHE 0.018 0.001 PHE F 392 TRP 0.011 0.002 TRP E 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (13110) covalent geometry : angle 0.53527 / 0.28 (17838) SS BOND : bond 0.00310 / 0.21 ( 24) SS BOND : angle 1.26163 / 0.91 ( 48) hydrogen bonds : bond 0.03533 / 2.34 ( 355) hydrogen bonds : angle 6.39810 / 4.54 ( 915) link_NAG-ASN : bond 0.00459 / 0.30 ( 12) link_NAG-ASN : angle 1.98488 / 1.16 ( 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 152 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 GLU cc_start: 0.7936 (tp30) cc_final: 0.7595 (tt0) REVERT: A 584 ILE cc_start: 0.8731 (mp) cc_final: 0.8354 (tt) REVERT: B 406 GLU cc_start: 0.8574 (mt-10) cc_final: 0.7933 (mt-10) REVERT: B 528 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8068 (mttm) REVERT: B 537 LYS cc_start: 0.8391 (ttpp) cc_final: 0.8114 (tttp) REVERT: B 559 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.6344 (m-80) REVERT: D 365 TYR cc_start: 0.9118 (m-10) cc_final: 0.8861 (m-10) REVERT: E 324 GLU cc_start: 0.7816 (mp0) cc_final: 0.7607 (mp0) REVERT: E 386 LYS cc_start: 0.8610 (mtpt) cc_final: 0.8313 (tttt) REVERT: E 406 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7657 (pt0) REVERT: E 455 LEU cc_start: 0.9506 (tp) cc_final: 0.9244 (tp) REVERT: E 554 GLU cc_start: 0.8324 (pp20) cc_final: 0.7761 (pp20) REVERT: E 574 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7940 (t0) REVERT: F 340 GLU cc_start: 0.8331 (pm20) cc_final: 0.8113 (pm20) REVERT: F 365 TYR cc_start: 0.8628 (m-80) cc_final: 0.8325 (m-80) REVERT: F 378 LYS cc_start: 0.8033 (mtpp) cc_final: 0.7805 (tptm) REVERT: F 380 TYR cc_start: 0.8762 (m-80) cc_final: 0.8309 (m-80) REVERT: F 406 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7858 (pm20) REVERT: F 464 PHE cc_start: 0.8119 (m-80) cc_final: 0.7636 (m-80) REVERT: F 498 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8393 (mm-40) REVERT: F 580 GLN cc_start: 0.8350 (mm-40) cc_final: 0.7658 (tp-100) outliers start: 31 outliers final: 25 residues processed: 146 average time/residue: 0.0970 time to fit residues: 21.7788 Evaluate side-chains 140 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 574 ASP Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 559 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 110 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 88 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 65.6414 > 50:) chunk 123 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 440 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.085788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.070253 restraints weight = 40536.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.072652 restraints weight = 20763.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.074244 restraints weight = 13544.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.075293 restraints weight = 10107.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.076020 restraints weight = 8231.166| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13146 Z= 0.161 Angle : 0.549 8.496 17922 Z= 0.283 Chirality : 0.046 0.328 1980 Planarity : 0.004 0.041 2322 Dihedral : 4.246 21.236 1764 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.45 % Allowed : 12.55 % Favored : 84.99 % 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: -0.61 (0.20), residues: 1596 helix: -2.57 (0.38), residues: 144 sheet: 0.16 (0.28), residues: 331 loop : -0.24 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 328 TYR 0.010 0.001 TYR D 365 PHE 0.018 0.001 PHE F 392 TRP 0.011 0.001 TRP E 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (13110) covalent geometry : angle 0.53919 / 0.28 (17838) SS BOND : bond 0.00312 / 0.21 ( 24) SS BOND : angle 1.23803 / 0.89 ( 48) hydrogen bonds : bond 0.03475 / 2.29 ( 355) hydrogen bonds : angle 6.37530 / 4.53 ( 915) link_NAG-ASN : bond 0.00461 / 0.30 ( 12) link_NAG-ASN : angle 1.94839 / 1.15 ( 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 150 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 GLU cc_start: 0.7992 (tp30) cc_final: 0.7577 (tt0) REVERT: A 559 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.7029 (m-10) REVERT: A 584 ILE cc_start: 0.8688 (mp) cc_final: 0.8235 (mt) REVERT: B 387 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9141 (mp) REVERT: B 406 GLU cc_start: 0.8561 (mt-10) cc_final: 0.7964 (mt-10) REVERT: B 528 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8015 (mttp) REVERT: B 559 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.6551 (m-80) REVERT: B 584 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8199 (pt) REVERT: C 340 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8196 (tm-30) REVERT: C 466 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7305 (ttp80) REVERT: D 365 TYR cc_start: 0.9116 (m-10) cc_final: 0.8844 (m-10) REVERT: E 324 GLU cc_start: 0.7783 (mp0) cc_final: 0.7496 (mp0) REVERT: E 386 LYS cc_start: 0.8667 (mtpt) cc_final: 0.8321 (tttt) REVERT: E 406 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7673 (pt0) REVERT: E 455 LEU cc_start: 0.9519 (tp) cc_final: 0.9247 (tp) REVERT: E 554 GLU cc_start: 0.8266 (pp20) cc_final: 0.7638 (pp20) REVERT: E 574 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.8033 (t0) REVERT: F 340 GLU cc_start: 0.8345 (pm20) cc_final: 0.8097 (pm20) REVERT: F 378 LYS cc_start: 0.8013 (mtpp) cc_final: 0.7795 (tptm) REVERT: F 380 TYR cc_start: 0.8810 (m-80) cc_final: 0.8396 (m-80) REVERT: F 406 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7794 (pm20) REVERT: F 464 PHE cc_start: 0.8122 (m-80) cc_final: 0.7656 (m-80) REVERT: F 580 GLN cc_start: 0.8431 (mm-40) cc_final: 0.7717 (tp-100) outliers start: 34 outliers final: 25 residues processed: 145 average time/residue: 0.1057 time to fit residues: 23.3489 Evaluate side-chains 138 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 574 ASP Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 559 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 0.7980 chunk 105 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 86 optimal weight: 0.0000 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 142 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.087759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.072518 restraints weight = 39877.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.074931 restraints weight = 20213.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.076523 restraints weight = 13083.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.077590 restraints weight = 9730.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.078322 restraints weight = 7880.100| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 13146 Z= 0.098 Angle : 0.524 8.671 17922 Z= 0.269 Chirality : 0.045 0.323 1980 Planarity : 0.003 0.037 2322 Dihedral : 3.944 19.315 1764 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.02 % Allowed : 13.35 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.70 (0.38), residues: 138 sheet: 0.20 (0.27), residues: 338 loop : -0.21 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 328 TYR 0.010 0.001 TYR D 365 PHE 0.017 0.001 PHE F 392 TRP 0.008 0.001 TRP D 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (13110) covalent geometry : angle 0.51428 / 0.27 (17838) SS BOND : bond 0.00330 / 0.22 ( 24) SS BOND : angle 1.18789 / 0.85 ( 48) hydrogen bonds : bond 0.03173 / 2.12 ( 355) hydrogen bonds : angle 6.14548 / 4.35 ( 915) link_NAG-ASN : bond 0.00477 / 0.31 ( 12) link_NAG-ASN : angle 1.90657 / 1.13 ( 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 149 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 GLU cc_start: 0.7954 (tp30) cc_final: 0.7655 (tt0) REVERT: A 559 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.6770 (m-10) REVERT: A 584 ILE cc_start: 0.8599 (mp) cc_final: 0.8360 (mm) REVERT: B 406 GLU cc_start: 0.8587 (mt-10) cc_final: 0.7989 (mt-10) REVERT: B 528 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7949 (mttm) REVERT: B 537 LYS cc_start: 0.8896 (tttt) cc_final: 0.8632 (tttm) REVERT: D 365 TYR cc_start: 0.9077 (m-10) cc_final: 0.8769 (m-10) REVERT: D 471 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7739 (tm-30) REVERT: E 324 GLU cc_start: 0.7788 (mp0) cc_final: 0.7550 (mp0) REVERT: E 386 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8226 (tttt) REVERT: E 406 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7762 (pt0) REVERT: E 455 LEU cc_start: 0.9471 (tp) cc_final: 0.9222 (tp) REVERT: E 493 GLN cc_start: 0.8865 (tp40) cc_final: 0.8619 (mm-40) REVERT: E 554 GLU cc_start: 0.8256 (pp20) cc_final: 0.7606 (pp20) REVERT: F 340 GLU cc_start: 0.8300 (pm20) cc_final: 0.8013 (pm20) REVERT: F 380 TYR cc_start: 0.8802 (m-80) cc_final: 0.8385 (m-80) REVERT: F 406 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7887 (pm20) REVERT: F 580 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7567 (tp-100) REVERT: F 583 GLU cc_start: 0.8574 (tp30) cc_final: 0.8262 (tp30) outliers start: 28 outliers final: 21 residues processed: 142 average time/residue: 0.1005 time to fit residues: 22.1928 Evaluate side-chains 136 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 515 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 0.0970 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN C 414 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.087722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.072496 restraints weight = 40165.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.074896 restraints weight = 20483.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.076484 restraints weight = 13311.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.077546 restraints weight = 9934.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.078285 restraints weight = 8052.371| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13146 Z= 0.109 Angle : 0.535 8.582 17922 Z= 0.275 Chirality : 0.045 0.325 1980 Planarity : 0.003 0.036 2322 Dihedral : 3.873 19.013 1764 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.16 % Allowed : 14.07 % Favored : 83.77 % 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: -0.42 (0.21), residues: 1596 helix: -2.65 (0.40), residues: 122 sheet: 0.20 (0.27), residues: 342 loop : -0.10 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 328 TYR 0.017 0.001 TYR F 365 PHE 0.015 0.001 PHE F 392 TRP 0.008 0.001 TRP D 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (13110) covalent geometry : angle 0.52565 / 0.27 (17838) SS BOND : bond 0.00304 / 0.21 ( 24) SS BOND : angle 1.18413 / 0.84 ( 48) hydrogen bonds : bond 0.03162 / 2.10 ( 355) hydrogen bonds : angle 6.06766 / 4.29 ( 915) link_NAG-ASN : bond 0.00471 / 0.31 ( 12) link_NAG-ASN : angle 1.87226 / 1.10 ( 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 147 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.6983 (m-10) REVERT: A 584 ILE cc_start: 0.8667 (mp) cc_final: 0.8315 (mt) REVERT: B 406 GLU cc_start: 0.8656 (mt-10) cc_final: 0.7994 (mt-10) REVERT: B 528 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7978 (mttm) REVERT: B 559 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.6113 (m-80) REVERT: C 398 ASP cc_start: 0.8877 (m-30) cc_final: 0.8462 (m-30) REVERT: C 466 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7306 (ttp80) REVERT: D 365 TYR cc_start: 0.8926 (m-10) cc_final: 0.8629 (m-10) REVERT: D 471 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7757 (tm-30) REVERT: E 324 GLU cc_start: 0.7824 (mp0) cc_final: 0.7579 (mp0) REVERT: E 386 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8193 (tttt) REVERT: E 406 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7970 (pt0) REVERT: E 455 LEU cc_start: 0.9473 (tp) cc_final: 0.9211 (tp) REVERT: E 554 GLU cc_start: 0.8264 (pp20) cc_final: 0.7607 (pp20) REVERT: F 406 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: F 464 PHE cc_start: 0.7881 (m-80) cc_final: 0.7470 (m-80) REVERT: F 580 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7593 (tp-100) REVERT: F 583 GLU cc_start: 0.8605 (tp30) cc_final: 0.8328 (tp30) outliers start: 30 outliers final: 24 residues processed: 140 average time/residue: 0.0971 time to fit residues: 21.3847 Evaluate side-chains 140 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 515 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 118 optimal weight: 0.0030 chunk 63 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.087891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.072695 restraints weight = 40123.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.075106 restraints weight = 20444.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.076706 restraints weight = 13255.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.077756 restraints weight = 9847.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.078492 restraints weight = 7996.612| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13146 Z= 0.109 Angle : 0.541 8.656 17922 Z= 0.278 Chirality : 0.045 0.325 1980 Planarity : 0.003 0.035 2322 Dihedral : 3.838 18.031 1764 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.45 % Allowed : 14.65 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.39 (0.21), residues: 1596 helix: -2.66 (0.36), residues: 146 sheet: 0.26 (0.27), residues: 336 loop : -0.01 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 328 TYR 0.023 0.001 TYR F 380 PHE 0.015 0.001 PHE F 392 TRP 0.009 0.001 TRP D 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (13110) covalent geometry : angle 0.53197 / 0.28 (17838) SS BOND : bond 0.00310 / 0.21 ( 24) SS BOND : angle 1.15249 / 0.82 ( 48) hydrogen bonds : bond 0.03156 / 2.08 ( 355) hydrogen bonds : angle 6.02985 / 4.26 ( 915) link_NAG-ASN : bond 0.00466 / 0.30 ( 12) link_NAG-ASN : angle 1.87189 / 1.10 ( 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 151 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8275 (m-30) cc_final: 0.8014 (m-30) REVERT: A 559 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.6971 (m-10) REVERT: A 584 ILE cc_start: 0.8685 (mp) cc_final: 0.8298 (mt) REVERT: B 406 GLU cc_start: 0.8648 (mt-10) cc_final: 0.7976 (mt-10) REVERT: B 528 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7985 (mttm) REVERT: B 559 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.6214 (m-80) REVERT: B 584 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8084 (pt) REVERT: C 398 ASP cc_start: 0.8859 (m-30) cc_final: 0.8443 (m-30) REVERT: C 466 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7208 (ttp80) REVERT: D 471 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7898 (tm-30) REVERT: E 324 GLU cc_start: 0.7804 (mp0) cc_final: 0.7549 (mp0) REVERT: E 386 LYS cc_start: 0.8578 (mtpt) cc_final: 0.8185 (tttt) REVERT: E 406 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7993 (pt0) REVERT: E 455 LEU cc_start: 0.9462 (tp) cc_final: 0.9206 (tp) REVERT: E 554 GLU cc_start: 0.8250 (pp20) cc_final: 0.7593 (pp20) REVERT: F 406 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: F 464 PHE cc_start: 0.7843 (m-80) cc_final: 0.7501 (m-80) REVERT: F 580 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7488 (tp-100) REVERT: F 583 GLU cc_start: 0.8619 (tp30) cc_final: 0.8361 (tp30) outliers start: 34 outliers final: 25 residues processed: 144 average time/residue: 0.0941 time to fit residues: 21.3241 Evaluate side-chains 141 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 559 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 144 optimal weight: 0.2980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.086371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.071098 restraints weight = 40047.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.073497 restraints weight = 20450.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.075070 restraints weight = 13277.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.076123 restraints weight = 9895.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.076865 restraints weight = 8020.774| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13146 Z= 0.151 Angle : 0.565 8.652 17922 Z= 0.293 Chirality : 0.045 0.330 1980 Planarity : 0.004 0.036 2322 Dihedral : 4.000 17.908 1764 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.24 % Allowed : 14.86 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.48 (0.21), residues: 1596 helix: -2.80 (0.38), residues: 138 sheet: 0.19 (0.27), residues: 336 loop : -0.09 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 328 TYR 0.024 0.001 TYR D 365 PHE 0.022 0.001 PHE D 392 TRP 0.009 0.001 TRP D 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (13110) covalent geometry : angle 0.55650 / 0.29 (17838) SS BOND : bond 0.00315 / 0.21 ( 24) SS BOND : angle 1.19651 / 0.85 ( 48) hydrogen bonds : bond 0.03408 / 2.21 ( 355) hydrogen bonds : angle 6.13435 / 4.33 ( 915) link_NAG-ASN : bond 0.00461 / 0.30 ( 12) link_NAG-ASN : angle 1.88169 / 1.11 ( 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 144 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8390 (m-30) cc_final: 0.8120 (m-30) REVERT: A 559 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6921 (m-10) REVERT: A 584 ILE cc_start: 0.8677 (mp) cc_final: 0.8312 (mt) REVERT: B 406 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8030 (mt-10) REVERT: B 528 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8007 (mttm) REVERT: B 559 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.6412 (m-80) REVERT: C 466 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7283 (ttp80) REVERT: D 471 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7808 (tm-30) REVERT: E 324 GLU cc_start: 0.7850 (mp0) cc_final: 0.7584 (mp0) REVERT: E 386 LYS cc_start: 0.8606 (mtpt) cc_final: 0.8249 (tttt) REVERT: E 406 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7807 (pt0) REVERT: E 455 LEU cc_start: 0.9502 (tp) cc_final: 0.9236 (tp) REVERT: E 554 GLU cc_start: 0.8240 (pp20) cc_final: 0.7585 (pp20) REVERT: F 406 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7783 (pm20) REVERT: F 464 PHE cc_start: 0.7888 (m-80) cc_final: 0.7523 (m-80) REVERT: F 580 GLN cc_start: 0.8362 (mm-40) cc_final: 0.7695 (tp-100) REVERT: F 583 GLU cc_start: 0.8675 (tp30) cc_final: 0.8474 (tp30) outliers start: 31 outliers final: 25 residues processed: 137 average time/residue: 0.1010 time to fit residues: 21.4489 Evaluate side-chains 140 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 559 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 109 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 105 optimal weight: 0.2980 chunk 73 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 144 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.087072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.071812 restraints weight = 40072.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.074220 restraints weight = 20443.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.075815 restraints weight = 13260.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.076872 restraints weight = 9868.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.077615 restraints weight = 8002.930| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13146 Z= 0.121 Angle : 0.563 8.765 17922 Z= 0.290 Chirality : 0.045 0.328 1980 Planarity : 0.003 0.036 2322 Dihedral : 3.903 16.511 1764 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.24 % Allowed : 14.72 % Favored : 83.04 % 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: -0.45 (0.21), residues: 1596 helix: -2.77 (0.38), residues: 138 sheet: 0.19 (0.27), residues: 336 loop : -0.05 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.020 0.001 TYR D 365 PHE 0.019 0.001 PHE D 392 TRP 0.009 0.001 TRP D 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (13110) covalent geometry : angle 0.55454 / 0.29 (17838) SS BOND : bond 0.00316 / 0.22 ( 24) SS BOND : angle 1.17187 / 0.84 ( 48) hydrogen bonds : bond 0.03368 / 2.16 ( 355) hydrogen bonds : angle 6.09852 / 4.31 ( 915) link_NAG-ASN : bond 0.00466 / 0.30 ( 12) link_NAG-ASN : angle 1.88603 / 1.12 ( 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 144 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8335 (m-30) cc_final: 0.8009 (m-30) REVERT: A 559 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.6930 (m-10) REVERT: A 584 ILE cc_start: 0.8672 (mp) cc_final: 0.8308 (mt) REVERT: B 406 GLU cc_start: 0.8635 (mt-10) cc_final: 0.7997 (mt-10) REVERT: B 528 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8000 (mttm) REVERT: B 559 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.5768 (m-80) REVERT: C 398 ASP cc_start: 0.8860 (m-30) cc_final: 0.8457 (m-30) REVERT: C 466 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7231 (ttp80) REVERT: D 471 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7785 (tm-30) REVERT: E 324 GLU cc_start: 0.7837 (mp0) cc_final: 0.7582 (mp0) REVERT: E 386 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8202 (tttt) REVERT: E 406 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7850 (pt0) REVERT: E 455 LEU cc_start: 0.9489 (tp) cc_final: 0.9220 (tp) REVERT: E 554 GLU cc_start: 0.8307 (pp20) cc_final: 0.7652 (pp20) REVERT: F 406 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7765 (pm20) REVERT: F 464 PHE cc_start: 0.7862 (m-80) cc_final: 0.7515 (m-80) REVERT: F 580 GLN cc_start: 0.8319 (mm-40) cc_final: 0.7573 (tp-100) outliers start: 31 outliers final: 24 residues processed: 137 average time/residue: 0.0992 time to fit residues: 21.2091 Evaluate side-chains 140 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 559 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 134 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.086881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.071600 restraints weight = 40061.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.073992 restraints weight = 20515.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.075592 restraints weight = 13340.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.076658 restraints weight = 9924.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.077393 restraints weight = 8030.076| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13146 Z= 0.129 Angle : 0.572 11.635 17922 Z= 0.293 Chirality : 0.046 0.329 1980 Planarity : 0.003 0.037 2322 Dihedral : 3.903 16.594 1764 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.02 % Allowed : 15.01 % Favored : 82.97 % 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: -0.46 (0.21), residues: 1596 helix: -2.81 (0.38), residues: 138 sheet: 0.20 (0.27), residues: 336 loop : -0.06 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.020 0.001 TYR F 380 PHE 0.018 0.001 PHE D 392 TRP 0.009 0.001 TRP E 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (13110) covalent geometry : angle 0.56426 / 0.29 (17838) SS BOND : bond 0.00314 / 0.21 ( 24) SS BOND : angle 1.17328 / 0.84 ( 48) hydrogen bonds : bond 0.03343 / 2.17 ( 355) hydrogen bonds : angle 6.11026 / 4.31 ( 915) link_NAG-ASN : bond 0.00465 / 0.30 ( 12) link_NAG-ASN : angle 1.87393 / 1.11 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2119.10 seconds wall clock time: 37 minutes 38.45 seconds (2258.45 seconds total)