Starting phenix.real_space_refine on Wed Mar 4 10:42:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tf1_25858/03_2026/7tf1_25858.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tf1_25858/03_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_25858/03_2026/7tf1_25858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tf1_25858/03_2026/7tf1_25858.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tf1_25858/03_2026/7tf1_25858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tf1_25858/03_2026/7tf1_25858.map" } 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-dev-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.83, per 1000 atoms: 0.22 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: 0.95 Conformation dependent library (CDL) restraints added in 494.5 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: 0.46 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: 1.72 Time building geometry restraints manager: 1.25 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: 7154 16.44 - 32.88: 663 32.88 - 49.32: 109 49.32 - 65.76: 20 65.76 - 82.20: 10 Dihedral angle restraints: 7956 sinusoidal: 3276 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 7953 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: 4.090 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.520 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 : 12.708 82.203 4896 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 covalent geometry : bond 0.00414 (13110) covalent geometry : angle 0.76806 (17838) SS BOND : bond 0.00457 ( 24) SS BOND : angle 1.34623 ( 48) hydrogen bonds : bond 0.20526 ( 355) hydrogen bonds : angle 9.36537 ( 915) link_NAG-ASN : bond 0.00717 ( 12) link_NAG-ASN : angle 3.33267 ( 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 : 0.477 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: 0.1400 time to fit residues: 57.9234 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 : 0.417 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 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 = 0.3568 r_free = 0.3568 target = 0.086794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.071188 restraints weight = 40334.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.073601 restraints weight = 20766.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.075210 restraints weight = 13555.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.076279 restraints weight = 10116.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.077015 restraints weight = 8242.031| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13146 Z= 0.215 Angle : 0.618 9.109 17922 Z= 0.320 Chirality : 0.047 0.343 1980 Planarity : 0.005 0.053 2322 Dihedral : 5.791 58.736 2016 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.52 % Allowed : 9.16 % Favored : 89.32 % 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: -2.81 (0.27), residues: 204 sheet: 0.11 (0.26), residues: 376 loop : -0.59 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 403 TYR 0.018 0.002 TYR D 365 PHE 0.015 0.002 PHE D 515 TRP 0.018 0.002 TRP E 436 Details of bonding type rmsd covalent geometry : bond 0.00480 (13110) covalent geometry : angle 0.60617 (17838) SS BOND : bond 0.00357 ( 24) SS BOND : angle 1.46664 ( 48) hydrogen bonds : bond 0.04112 ( 355) hydrogen bonds : angle 6.91899 ( 915) link_NAG-ASN : bond 0.00460 ( 12) link_NAG-ASN : angle 2.26605 ( 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 170 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.480 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: 0.8723 (mp) cc_final: 0.8313 (tt) REVERT: B 366 SER cc_start: 0.8602 (m) cc_final: 0.8336 (p) REVERT: B 387 LEU cc_start: 0.9529 (mt) cc_final: 0.9314 (mt) REVERT: B 406 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8258 (mt-10) REVERT: B 493 GLN cc_start: 0.8427 (tp40) cc_final: 0.8025 (tm-30) REVERT: B 528 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8165 (mtmm) REVERT: B 583 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6665 (tm-30) REVERT: C 398 ASP cc_start: 0.8968 (m-30) cc_final: 0.8493 (m-30) REVERT: D 365 TYR cc_start: 0.9135 (m-10) cc_final: 0.8895 (m-10) REVERT: D 474 GLN cc_start: 0.8585 (tt0) cc_final: 0.8278 (tt0) REVERT: E 324 GLU cc_start: 0.7878 (mp0) cc_final: 0.7430 (mp0) REVERT: E 386 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8560 (ttpt) REVERT: E 455 LEU cc_start: 0.9492 (tp) cc_final: 0.9229 (tt) REVERT: F 365 TYR cc_start: 0.8508 (m-80) cc_final: 0.8239 (m-80) REVERT: F 378 LYS cc_start: 0.8254 (mtpp) cc_final: 0.7964 (tptm) REVERT: F 380 TYR cc_start: 0.8720 (m-80) cc_final: 0.8307 (m-80) REVERT: F 406 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8084 (pm20) REVERT: F 464 PHE cc_start: 0.8121 (m-80) cc_final: 0.7576 (m-80) REVERT: F 498 GLN cc_start: 0.8963 (mt0) cc_final: 0.8705 (mm-40) REVERT: F 580 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7572 (tp-100) outliers start: 21 outliers final: 15 residues processed: 166 average time/residue: 0.0920 time to fit residues: 23.1141 Evaluate side-chains 129 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 58 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** F 493 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 = 0.3553 r_free = 0.3553 target = 0.085989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.070302 restraints weight = 40315.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.072694 restraints weight = 20754.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.074266 restraints weight = 13608.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.075324 restraints weight = 10215.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.076054 restraints weight = 8344.521| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3174 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= 0.187 Angle : 0.568 8.653 17922 Z= 0.295 Chirality : 0.046 0.332 1980 Planarity : 0.004 0.046 2322 Dihedral : 5.205 47.924 2016 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.95 % Allowed : 10.46 % Favored : 87.59 % 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: -2.74 (0.31), residues: 174 sheet: 0.18 (0.26), residues: 366 loop : -0.51 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 567 TYR 0.013 0.001 TYR D 365 PHE 0.017 0.001 PHE F 392 TRP 0.014 0.002 TRP E 436 Details of bonding type rmsd covalent geometry : bond 0.00422 (13110) covalent geometry : angle 0.55614 (17838) SS BOND : bond 0.00322 ( 24) SS BOND : angle 1.38697 ( 48) hydrogen bonds : bond 0.03840 ( 355) hydrogen bonds : angle 6.62391 ( 915) link_NAG-ASN : bond 0.00474 ( 12) link_NAG-ASN : angle 2.16132 ( 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 162 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.333 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: 0.8698 (mp) cc_final: 0.8367 (tt) REVERT: B 406 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8344 (mt-10) REVERT: B 528 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.7935 (mttp) REVERT: B 583 GLU cc_start: 0.7311 (tm-30) cc_final: 0.7038 (tm-30) REVERT: D 365 TYR cc_start: 0.9112 (m-10) cc_final: 0.8867 (m-10) REVERT: D 474 GLN cc_start: 0.8528 (tt0) cc_final: 0.8068 (tt0) REVERT: D 516 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8036 (pp20) REVERT: E 368 LEU cc_start: 0.9372 (mt) cc_final: 0.8994 (pp) REVERT: E 386 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8470 (ttpt) REVERT: E 406 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7676 (pt0) REVERT: E 455 LEU cc_start: 0.9511 (tp) cc_final: 0.9242 (tp) REVERT: E 493 GLN cc_start: 0.8805 (tp40) cc_final: 0.8563 (mm-40) REVERT: E 554 GLU cc_start: 0.8309 (pp20) cc_final: 0.7669 (pp20) REVERT: F 340 GLU cc_start: 0.8320 (pm20) cc_final: 0.8101 (pm20) REVERT: F 365 TYR cc_start: 0.8615 (m-80) cc_final: 0.8309 (m-80) REVERT: F 378 LYS cc_start: 0.8137 (mtpp) cc_final: 0.7853 (tptm) REVERT: F 380 TYR cc_start: 0.8802 (m-80) cc_final: 0.8163 (m-80) REVERT: F 406 GLU cc_start: 0.8290 (mp0) cc_final: 0.7899 (pm20) REVERT: F 440 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8553 (p0) REVERT: F 464 PHE cc_start: 0.8111 (m-80) cc_final: 0.7595 (m-80) REVERT: F 580 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7589 (tp-100) outliers start: 27 outliers final: 23 residues processed: 155 average time/residue: 0.0898 time to fit residues: 21.6338 Evaluate side-chains 144 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 A residue 534 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 503 VAL 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 516 GLU 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 440 ASN 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: 5.9990 chunk 54 optimal weight: 0.0770 chunk 91 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 147 optimal weight: 0.0270 chunk 18 optimal weight: 1.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.088438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.072998 restraints weight = 40443.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.075431 restraints weight = 20627.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.077033 restraints weight = 13398.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.078108 restraints weight = 10006.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.078815 restraints weight = 8115.239| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 13146 Z= 0.098 Angle : 0.520 8.764 17922 Z= 0.267 Chirality : 0.045 0.322 1980 Planarity : 0.004 0.040 2322 Dihedral : 4.591 36.459 2016 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.80 % Allowed : 11.47 % Favored : 86.72 % 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: -0.72 (0.20), residues: 1596 helix: -2.70 (0.31), residues: 174 sheet: 0.33 (0.28), residues: 326 loop : -0.31 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 567 TYR 0.010 0.001 TYR E 365 PHE 0.016 0.001 PHE F 392 TRP 0.009 0.001 TRP D 436 Details of bonding type rmsd covalent geometry : bond 0.00220 (13110) covalent geometry : angle 0.50917 (17838) SS BOND : bond 0.00304 ( 24) SS BOND : angle 1.20468 ( 48) hydrogen bonds : bond 0.03262 ( 355) hydrogen bonds : angle 6.24257 ( 915) link_NAG-ASN : bond 0.00488 ( 12) link_NAG-ASN : angle 2.07243 ( 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 155 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.496 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: 0.7910 (tp30) cc_final: 0.7590 (tt0) REVERT: A 584 ILE cc_start: 0.8649 (mp) cc_final: 0.8343 (tt) REVERT: B 369 TYR cc_start: 0.7097 (t80) cc_final: 0.6836 (t80) REVERT: B 406 GLU cc_start: 0.8558 (mt-10) cc_final: 0.7910 (mt-10) REVERT: B 414 GLN cc_start: 0.7311 (tp40) cc_final: 0.6969 (tp40) REVERT: B 528 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8096 (mttp) REVERT: B 537 LYS cc_start: 0.8742 (tttt) cc_final: 0.8450 (tttm) REVERT: D 365 TYR cc_start: 0.9076 (m-10) cc_final: 0.8824 (m-10) REVERT: D 474 GLN cc_start: 0.8526 (tt0) cc_final: 0.8173 (tt0) REVERT: E 386 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8308 (tttt) REVERT: E 406 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7620 (pt0) REVERT: E 455 LEU cc_start: 0.9472 (tp) cc_final: 0.9223 (tp) REVERT: E 554 GLU cc_start: 0.8175 (pp20) cc_final: 0.7817 (pp20) REVERT: F 365 TYR cc_start: 0.8540 (m-80) cc_final: 0.8246 (m-80) REVERT: F 378 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7766 (tptm) REVERT: F 380 TYR cc_start: 0.8801 (m-80) cc_final: 0.8365 (m-80) REVERT: F 406 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: F 498 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8441 (mm-40) outliers start: 25 outliers final: 21 residues processed: 147 average time/residue: 0.0885 time to fit residues: 20.2524 Evaluate side-chains 138 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 534 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 503 VAL 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 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 E residue 574 ASP 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 515 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 110 optimal weight: 3.9990 chunk 80 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 119 optimal weight: 0.0870 chunk 98 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 76 optimal weight: 0.0970 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** E 506 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 = 0.3602 r_free = 0.3602 target = 0.088573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.073246 restraints weight = 40316.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.075665 restraints weight = 20402.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.077274 restraints weight = 13207.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.078345 restraints weight = 9794.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.079081 restraints weight = 7933.931| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 13146 Z= 0.096 Angle : 0.519 8.959 17922 Z= 0.267 Chirality : 0.046 0.327 1980 Planarity : 0.003 0.037 2322 Dihedral : 4.377 33.612 2016 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.80 % Allowed : 12.55 % Favored : 85.64 % 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: -0.51 (0.20), residues: 1596 helix: -2.60 (0.37), residues: 138 sheet: 0.33 (0.27), residues: 336 loop : -0.20 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 567 TYR 0.009 0.001 TYR E 365 PHE 0.015 0.001 PHE F 392 TRP 0.008 0.001 TRP E 436 Details of bonding type rmsd covalent geometry : bond 0.00220 (13110) covalent geometry : angle 0.50824 (17838) SS BOND : bond 0.00297 ( 24) SS BOND : angle 1.17372 ( 48) hydrogen bonds : bond 0.03167 ( 355) hydrogen bonds : angle 6.07762 ( 915) link_NAG-ASN : bond 0.00470 ( 12) link_NAG-ASN : angle 2.03628 ( 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 148 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.482 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: 0.7999 (tp30) cc_final: 0.7560 (tt0) REVERT: A 584 ILE cc_start: 0.8598 (mp) cc_final: 0.8263 (tt) REVERT: B 387 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9069 (mp) REVERT: B 406 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8217 (mt-10) REVERT: B 414 GLN cc_start: 0.7205 (tp40) cc_final: 0.6932 (tp40) REVERT: B 528 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7921 (mttm) REVERT: B 537 LYS cc_start: 0.8730 (tttt) cc_final: 0.8468 (tttm) REVERT: B 584 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8244 (pt) REVERT: E 386 LYS cc_start: 0.8663 (mtpt) cc_final: 0.8268 (tttt) REVERT: E 406 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7649 (pt0) REVERT: E 455 LEU cc_start: 0.9445 (tp) cc_final: 0.9207 (tp) REVERT: E 554 GLU cc_start: 0.8221 (pp20) cc_final: 0.7804 (pp20) REVERT: E 574 ASP cc_start: 0.8154 (t70) cc_final: 0.7897 (t0) REVERT: F 378 LYS cc_start: 0.7952 (mtpp) cc_final: 0.7748 (tptm) REVERT: F 380 TYR cc_start: 0.8814 (m-80) cc_final: 0.8348 (m-80) REVERT: F 406 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7864 (pm20) REVERT: F 498 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8435 (mm-40) outliers start: 25 outliers final: 21 residues processed: 141 average time/residue: 0.0905 time to fit residues: 19.8988 Evaluate side-chains 140 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 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 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 534 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 584 ILE 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 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 515 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN ** 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 = 0.3595 r_free = 0.3595 target = 0.088090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.072778 restraints weight = 40056.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.075177 restraints weight = 20419.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.076755 restraints weight = 13271.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.077833 restraints weight = 9907.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.078578 restraints weight = 8040.332| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3611 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= 0.114 Angle : 0.529 8.902 17922 Z= 0.271 Chirality : 0.045 0.331 1980 Planarity : 0.003 0.037 2322 Dihedral : 4.316 32.702 2016 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.31 % Allowed : 12.41 % Favored : 85.28 % 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: -0.35 (0.20), residues: 1596 helix: -2.47 (0.42), residues: 122 sheet: 0.31 (0.27), residues: 338 loop : -0.08 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 328 TYR 0.028 0.001 TYR D 365 PHE 0.014 0.001 PHE F 392 TRP 0.008 0.001 TRP D 436 Details of bonding type rmsd covalent geometry : bond 0.00263 (13110) covalent geometry : angle 0.51914 (17838) SS BOND : bond 0.00298 ( 24) SS BOND : angle 1.16300 ( 48) hydrogen bonds : bond 0.03280 ( 355) hydrogen bonds : angle 6.02437 ( 915) link_NAG-ASN : bond 0.00466 ( 12) link_NAG-ASN : angle 2.02211 ( 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 153 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.6789 (m-10) REVERT: A 584 ILE cc_start: 0.8588 (mp) cc_final: 0.8265 (mm) REVERT: B 406 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8158 (mt-10) REVERT: B 414 GLN cc_start: 0.7255 (tp40) cc_final: 0.6953 (tp40) REVERT: B 528 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7962 (mttm) REVERT: B 537 LYS cc_start: 0.8739 (tttt) cc_final: 0.8466 (tttm) REVERT: B 584 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8207 (pt) REVERT: C 398 ASP cc_start: 0.8903 (m-30) cc_final: 0.8426 (m-30) REVERT: E 324 GLU cc_start: 0.7753 (mp0) cc_final: 0.7385 (mp0) REVERT: E 386 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8230 (tttt) REVERT: E 406 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7671 (pt0) REVERT: E 455 LEU cc_start: 0.9459 (tp) cc_final: 0.9212 (tp) REVERT: E 554 GLU cc_start: 0.8291 (pp20) cc_final: 0.7577 (pp20) REVERT: E 574 ASP cc_start: 0.8192 (t70) cc_final: 0.7945 (t0) REVERT: F 378 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7768 (tptm) REVERT: F 380 TYR cc_start: 0.8804 (m-80) cc_final: 0.8331 (m-80) REVERT: F 406 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7898 (pm20) REVERT: F 583 GLU cc_start: 0.8583 (tp30) cc_final: 0.8231 (tp30) outliers start: 32 outliers final: 23 residues processed: 145 average time/residue: 0.0882 time to fit residues: 20.1631 Evaluate side-chains 141 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 534 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 584 ILE 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 391 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 133 optimal weight: 0.3980 chunk 49 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** F 440 ASN ** 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 = 0.3598 r_free = 0.3598 target = 0.088215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.072955 restraints weight = 40081.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.075363 restraints weight = 20362.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.076970 restraints weight = 13199.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.078042 restraints weight = 9786.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.078767 restraints weight = 7931.615| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 : 0.003 0.056 13146 Z= 0.110 Angle : 0.535 8.888 17922 Z= 0.275 Chirality : 0.045 0.331 1980 Planarity : 0.003 0.036 2322 Dihedral : 4.262 31.430 2016 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.16 % Allowed : 13.20 % 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: -0.31 (0.21), residues: 1596 helix: -2.55 (0.41), residues: 122 sheet: 0.33 (0.27), residues: 338 loop : -0.04 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 328 TYR 0.019 0.001 TYR D 365 PHE 0.014 0.001 PHE F 392 TRP 0.009 0.001 TRP D 436 Details of bonding type rmsd covalent geometry : bond 0.00256 (13110) covalent geometry : angle 0.52467 (17838) SS BOND : bond 0.00317 ( 24) SS BOND : angle 1.20190 ( 48) hydrogen bonds : bond 0.03234 ( 355) hydrogen bonds : angle 5.97459 ( 915) link_NAG-ASN : bond 0.00470 ( 12) link_NAG-ASN : angle 2.00410 ( 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 153 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 GLU cc_start: 0.7920 (tp30) cc_final: 0.7587 (tt0) REVERT: A 559 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.6758 (m-10) REVERT: A 584 ILE cc_start: 0.8619 (mp) cc_final: 0.8307 (mm) REVERT: B 406 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8108 (mt-10) REVERT: B 528 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7936 (mttm) REVERT: B 537 LYS cc_start: 0.8728 (tttt) cc_final: 0.8435 (tttm) REVERT: C 398 ASP cc_start: 0.8874 (m-30) cc_final: 0.8412 (m-30) REVERT: C 466 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7195 (ttp80) REVERT: D 516 GLU cc_start: 0.7346 (pp20) cc_final: 0.7057 (pp20) REVERT: E 324 GLU cc_start: 0.7711 (mp0) cc_final: 0.7392 (mp0) REVERT: E 368 LEU cc_start: 0.9333 (mt) cc_final: 0.9004 (pp) REVERT: E 386 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8235 (tttt) REVERT: E 406 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7754 (pt0) REVERT: E 455 LEU cc_start: 0.9471 (tp) cc_final: 0.9217 (tp) REVERT: E 554 GLU cc_start: 0.8214 (pp20) cc_final: 0.7588 (pp20) REVERT: F 380 TYR cc_start: 0.8766 (m-80) cc_final: 0.8296 (m-80) REVERT: F 406 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7879 (pm20) REVERT: F 464 PHE cc_start: 0.7917 (m-80) cc_final: 0.7460 (m-80) REVERT: F 583 GLU cc_start: 0.8569 (tp30) cc_final: 0.8224 (tp30) outliers start: 30 outliers final: 24 residues processed: 145 average time/residue: 0.0977 time to fit residues: 21.5001 Evaluate side-chains 142 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 534 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 503 VAL 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 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 515 PHE Chi-restraints excluded: chain F residue 559 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 72 optimal weight: 0.4980 chunk 18 optimal weight: 0.4980 chunk 57 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** 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** ** F 440 ASN ** 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 = 0.3598 r_free = 0.3598 target = 0.088293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.073113 restraints weight = 39974.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.075516 restraints weight = 20397.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.077102 restraints weight = 13213.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.078164 restraints weight = 9827.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.078907 restraints weight = 7965.308| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3826 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= 0.108 Angle : 0.538 8.871 17922 Z= 0.276 Chirality : 0.045 0.330 1980 Planarity : 0.003 0.035 2322 Dihedral : 4.198 29.932 2016 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.09 % Allowed : 13.28 % 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: -0.42 (0.20), residues: 1596 helix: -2.65 (0.34), residues: 162 sheet: 0.32 (0.27), residues: 336 loop : -0.02 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 403 TYR 0.014 0.001 TYR D 365 PHE 0.013 0.001 PHE F 392 TRP 0.009 0.001 TRP D 436 Details of bonding type rmsd covalent geometry : bond 0.00252 (13110) covalent geometry : angle 0.52844 (17838) SS BOND : bond 0.00309 ( 24) SS BOND : angle 1.18097 ( 48) hydrogen bonds : bond 0.03184 ( 355) hydrogen bonds : angle 5.93133 ( 915) link_NAG-ASN : bond 0.00469 ( 12) link_NAG-ASN : angle 1.99285 ( 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 149 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8268 (m-30) cc_final: 0.8017 (m-30) REVERT: A 465 GLU cc_start: 0.7932 (tp30) cc_final: 0.7645 (tt0) REVERT: A 559 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.6744 (m-10) REVERT: A 584 ILE cc_start: 0.8673 (mp) cc_final: 0.8348 (mm) REVERT: B 406 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8091 (mt-10) REVERT: B 414 GLN cc_start: 0.7220 (tp40) cc_final: 0.6835 (tp-100) REVERT: B 528 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7946 (mttm) REVERT: B 537 LYS cc_start: 0.8681 (tttt) cc_final: 0.8399 (tttm) REVERT: B 559 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.5562 (m-80) REVERT: E 324 GLU cc_start: 0.7663 (mp0) cc_final: 0.7361 (mp0) REVERT: E 368 LEU cc_start: 0.9316 (mt) cc_final: 0.8996 (pp) REVERT: E 386 LYS cc_start: 0.8552 (mtpt) cc_final: 0.8216 (tttt) REVERT: E 406 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7789 (pt0) REVERT: E 455 LEU cc_start: 0.9433 (tp) cc_final: 0.9202 (tp) REVERT: E 554 GLU cc_start: 0.8269 (pp20) cc_final: 0.7561 (pp20) REVERT: F 406 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7868 (pm20) REVERT: F 464 PHE cc_start: 0.7887 (m-80) cc_final: 0.7491 (m-80) REVERT: F 583 GLU cc_start: 0.8614 (tp30) cc_final: 0.8262 (tp30) outliers start: 29 outliers final: 23 residues processed: 143 average time/residue: 0.0897 time to fit residues: 20.4598 Evaluate side-chains 140 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 534 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 503 VAL 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 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 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: 0.8980 chunk 65 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** 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** E 544 ASN ** F 440 ASN ** 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 = 0.3566 r_free = 0.3566 target = 0.086513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.071073 restraints weight = 40194.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.073450 restraints weight = 20646.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.075027 restraints weight = 13483.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.076093 restraints weight = 10096.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.076837 restraints weight = 8191.742| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13146 Z= 0.165 Angle : 0.572 8.732 17922 Z= 0.295 Chirality : 0.046 0.333 1980 Planarity : 0.004 0.038 2322 Dihedral : 4.468 32.389 2016 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.24 % Allowed : 13.92 % Favored : 83.84 % 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: -2.78 (0.38), residues: 138 sheet: 0.21 (0.27), residues: 336 loop : -0.07 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 328 TYR 0.012 0.001 TYR D 365 PHE 0.013 0.001 PHE F 392 TRP 0.010 0.001 TRP D 436 Details of bonding type rmsd covalent geometry : bond 0.00379 (13110) covalent geometry : angle 0.56239 (17838) SS BOND : bond 0.00324 ( 24) SS BOND : angle 1.19094 ( 48) hydrogen bonds : bond 0.03398 ( 355) hydrogen bonds : angle 6.09448 ( 915) link_NAG-ASN : bond 0.00453 ( 12) link_NAG-ASN : angle 2.04521 ( 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 : 0.518 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 405 ASP cc_start: 0.8357 (m-30) cc_final: 0.8083 (m-30) REVERT: A 465 GLU cc_start: 0.7986 (tp30) cc_final: 0.7585 (tt0) REVERT: A 559 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.6774 (m-10) REVERT: A 584 ILE cc_start: 0.8694 (mp) cc_final: 0.8362 (mm) REVERT: B 406 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8093 (mt-10) REVERT: B 528 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7950 (mttm) REVERT: B 559 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.5451 (m-80) REVERT: C 466 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7277 (ttp80) REVERT: D 471 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7928 (tm-30) REVERT: E 324 GLU cc_start: 0.7812 (mp0) cc_final: 0.7471 (mp0) REVERT: E 368 LEU cc_start: 0.9333 (mt) cc_final: 0.9002 (pp) REVERT: E 386 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8268 (tttt) REVERT: E 406 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7781 (pt0) REVERT: E 455 LEU cc_start: 0.9500 (tp) cc_final: 0.9232 (tp) REVERT: E 554 GLU cc_start: 0.8346 (pp20) cc_final: 0.7735 (pp20) REVERT: F 340 GLU cc_start: 0.8319 (pm20) cc_final: 0.8055 (pm20) REVERT: F 406 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7757 (pm20) REVERT: F 464 PHE cc_start: 0.7923 (m-80) cc_final: 0.7534 (m-80) outliers start: 31 outliers final: 24 residues processed: 137 average time/residue: 0.0968 time to fit residues: 20.5804 Evaluate side-chains 137 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 534 VAL 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 C residue 336 CYS 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 465 GLU 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: 2.9990 chunk 5 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 144 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 107 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.086582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.071176 restraints weight = 40364.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.073572 restraints weight = 20705.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.075156 restraints weight = 13509.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.076217 restraints weight = 10081.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.076953 restraints weight = 8193.931| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4051 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= 0.149 Angle : 0.570 8.809 17922 Z= 0.293 Chirality : 0.045 0.331 1980 Planarity : 0.003 0.038 2322 Dihedral : 4.491 33.727 2016 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.09 % Allowed : 14.21 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.82 (0.38), residues: 138 sheet: 0.22 (0.27), residues: 336 loop : -0.08 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 328 TYR 0.011 0.001 TYR D 365 PHE 0.015 0.001 PHE F 392 TRP 0.010 0.001 TRP E 436 Details of bonding type rmsd covalent geometry : bond 0.00344 (13110) covalent geometry : angle 0.55986 (17838) SS BOND : bond 0.00309 ( 24) SS BOND : angle 1.19206 ( 48) hydrogen bonds : bond 0.03369 ( 355) hydrogen bonds : angle 6.07324 ( 915) link_NAG-ASN : bond 0.00449 ( 12) link_NAG-ASN : angle 2.06538 ( 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 141 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8270 (m-30) cc_final: 0.8004 (m-30) REVERT: A 406 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8420 (pt0) REVERT: A 465 GLU cc_start: 0.8005 (tp30) cc_final: 0.7649 (tt0) REVERT: A 559 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.6733 (m-10) REVERT: A 584 ILE cc_start: 0.8666 (mp) cc_final: 0.8335 (mm) REVERT: B 406 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8043 (mt-10) REVERT: B 528 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7981 (mtmm) REVERT: B 537 LYS cc_start: 0.8781 (tttt) cc_final: 0.8529 (tttp) REVERT: B 559 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.5368 (m-80) REVERT: C 466 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7250 (ttp80) REVERT: D 414 GLN cc_start: 0.8838 (tp40) cc_final: 0.8588 (tp40) REVERT: D 471 GLU cc_start: 0.8242 (tm-30) cc_final: 0.8011 (tm-30) REVERT: E 324 GLU cc_start: 0.7824 (mp0) cc_final: 0.7487 (mp0) REVERT: E 368 LEU cc_start: 0.9322 (mt) cc_final: 0.8986 (pp) REVERT: E 386 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8257 (tttt) REVERT: E 406 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7772 (pt0) REVERT: E 455 LEU cc_start: 0.9519 (tp) cc_final: 0.9268 (tp) REVERT: E 554 GLU cc_start: 0.8383 (pp20) cc_final: 0.7687 (pp20) REVERT: F 340 GLU cc_start: 0.8289 (pm20) cc_final: 0.8043 (pm20) REVERT: F 406 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7753 (pm20) REVERT: F 464 PHE cc_start: 0.7928 (m-80) cc_final: 0.7557 (m-80) REVERT: F 583 GLU cc_start: 0.8743 (tp30) cc_final: 0.8478 (tp30) outliers start: 29 outliers final: 24 residues processed: 135 average time/residue: 0.0946 time to fit residues: 19.8095 Evaluate side-chains 142 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 534 VAL 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 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 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: 4.9990 chunk 17 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** 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** ** F 440 ASN ** 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 = 0.3564 r_free = 0.3564 target = 0.086389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070903 restraints weight = 40254.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.073298 restraints weight = 20727.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.074874 restraints weight = 13541.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.075935 restraints weight = 10144.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.076678 restraints weight = 8250.635| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4138 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= 0.147 Angle : 0.570 8.703 17922 Z= 0.294 Chirality : 0.046 0.333 1980 Planarity : 0.004 0.037 2322 Dihedral : 4.531 35.113 2016 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.09 % Allowed : 14.65 % Favored : 83.26 % 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: -0.49 (0.21), residues: 1596 helix: -2.85 (0.38), residues: 138 sheet: 0.14 (0.27), residues: 336 loop : -0.06 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 577 TYR 0.011 0.001 TYR D 365 PHE 0.015 0.001 PHE F 392 TRP 0.009 0.001 TRP D 436 Details of bonding type rmsd covalent geometry : bond 0.00341 (13110) covalent geometry : angle 0.56015 (17838) SS BOND : bond 0.00311 ( 24) SS BOND : angle 1.19358 ( 48) hydrogen bonds : bond 0.03325 ( 355) hydrogen bonds : angle 6.11108 ( 915) link_NAG-ASN : bond 0.00455 ( 12) link_NAG-ASN : angle 2.06267 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1974.89 seconds wall clock time: 34 minutes 54.56 seconds (2094.56 seconds total)