Starting phenix.real_space_refine on Wed Jun 11 16:00:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tf1_25858/06_2025/7tf1_25858.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tf1_25858/06_2025/7tf1_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tf1_25858/06_2025/7tf1_25858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tf1_25858/06_2025/7tf1_25858.map" model { file = "/net/cci-nas-00/data/ceres_data/7tf1_25858/06_2025/7tf1_25858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tf1_25858/06_2025/7tf1_25858.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'ASP:plan': 1, 'HIS: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, 'ASP:plan': 1, 'HIS: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, 'ASP:plan': 1, 'HIS: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, 'ASP:plan': 1, 'HIS: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, 'ASP:plan': 1, 'HIS: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, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.44, per 1000 atoms: 0.74 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: 3.03 Conformation dependent library (CDL) restraints added in 1.8 seconds 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2988 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 29 sheets defined 14.6% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 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: 3.61 Time building geometry restraints manager: 3.63 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.320 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.490 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (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 TRP 0.016 0.002 TRP F 353 PHE 0.022 0.002 PHE F 377 TYR 0.023 0.002 TYR E 495 ARG 0.009 0.001 ARG F 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00717 ( 12) link_NAG-ASN : angle 3.33267 ( 36) hydrogen bonds : bond 0.20526 ( 355) hydrogen bonds : angle 9.36537 ( 915) SS BOND : bond 0.00457 ( 24) SS BOND : angle 1.34623 ( 48) covalent geometry : bond 0.00414 (13110) covalent geometry : angle 0.76806 (17838) *********************** 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 : 1.593 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: 0.8850 (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: 0.8496 (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: 0.3109 time to fit residues: 127.9422 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 : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 536 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.085884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.070309 restraints weight = 40142.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.072689 restraints weight = 20704.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.074289 restraints weight = 13542.601| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 13146 Z= 0.238 Angle : 0.637 9.379 17922 Z= 0.331 Chirality : 0.047 0.338 1980 Planarity : 0.005 0.054 2322 Dihedral : 5.825 57.372 2016 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.59 % Allowed : 9.38 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 1596 helix: -2.83 (0.27), residues: 204 sheet: 0.09 (0.26), residues: 376 loop : -0.59 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 436 PHE 0.017 0.002 PHE D 515 TYR 0.018 0.002 TYR D 365 ARG 0.012 0.001 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 12) link_NAG-ASN : angle 2.24599 ( 36) hydrogen bonds : bond 0.04162 ( 355) hydrogen bonds : angle 6.94219 ( 915) SS BOND : bond 0.00312 ( 24) SS BOND : angle 1.59128 ( 48) covalent geometry : bond 0.00530 (13110) covalent geometry : angle 0.62494 (17838) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 1.424 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: 0.8740 (mp) cc_final: 0.8353 (tt) REVERT: B 366 SER cc_start: 0.8630 (m) cc_final: 0.8366 (p) REVERT: B 387 LEU cc_start: 0.9559 (mt) cc_final: 0.9334 (mt) REVERT: B 406 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8249 (mt-10) REVERT: B 493 GLN cc_start: 0.8459 (tp40) cc_final: 0.8099 (tm-30) REVERT: B 528 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8143 (mtmm) REVERT: B 583 GLU cc_start: 0.7205 (tm-30) cc_final: 0.6682 (tm-30) REVERT: C 398 ASP cc_start: 0.8969 (m-30) cc_final: 0.8519 (m-30) REVERT: D 365 TYR cc_start: 0.9161 (m-10) cc_final: 0.8837 (m-10) REVERT: D 474 GLN cc_start: 0.8611 (tt0) cc_final: 0.8287 (tt0) REVERT: E 324 GLU cc_start: 0.7926 (mp0) cc_final: 0.7461 (mp0) REVERT: E 386 LYS cc_start: 0.8827 (mtpt) cc_final: 0.8567 (ttpt) REVERT: E 406 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8207 (mt-10) REVERT: E 455 LEU cc_start: 0.9501 (tp) cc_final: 0.9225 (tp) REVERT: F 340 GLU cc_start: 0.8411 (pm20) cc_final: 0.8206 (pm20) REVERT: F 365 TYR cc_start: 0.8604 (m-80) cc_final: 0.8311 (m-80) REVERT: F 378 LYS cc_start: 0.8246 (mtpp) cc_final: 0.7938 (tptm) REVERT: F 380 TYR cc_start: 0.8736 (m-80) cc_final: 0.8232 (m-80) REVERT: F 406 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7982 (pm20) REVERT: F 464 PHE cc_start: 0.8181 (m-80) cc_final: 0.7638 (m-80) REVERT: F 511 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8517 (m) REVERT: F 580 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7590 (tp-100) outliers start: 22 outliers final: 15 residues processed: 165 average time/residue: 0.2291 time to fit residues: 56.2397 Evaluate side-chains 130 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 142 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 61 optimal weight: 0.0070 chunk 84 optimal weight: 0.7980 chunk 24 optimal weight: 0.0270 overall best weight: 0.5056 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.088531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.072971 restraints weight = 39847.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.075397 restraints weight = 20268.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.077024 restraints weight = 13163.010| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 13146 Z= 0.103 Angle : 0.529 8.871 17922 Z= 0.273 Chirality : 0.046 0.327 1980 Planarity : 0.004 0.042 2322 Dihedral : 4.915 50.027 2016 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.37 % Allowed : 10.75 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.19), residues: 1596 helix: -2.89 (0.29), residues: 174 sheet: 0.32 (0.28), residues: 324 loop : -0.46 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 436 PHE 0.016 0.001 PHE F 392 TYR 0.014 0.001 TYR E 365 ARG 0.005 0.000 ARG E 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 12) link_NAG-ASN : angle 2.13196 ( 36) hydrogen bonds : bond 0.03546 ( 355) hydrogen bonds : angle 6.48200 ( 915) SS BOND : bond 0.00386 ( 24) SS BOND : angle 1.52212 ( 48) covalent geometry : bond 0.00230 (13110) covalent geometry : angle 0.51547 (17838) *********************** 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 167 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.454 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 584 ILE cc_start: 0.8677 (mp) cc_final: 0.8204 (tt) REVERT: B 366 SER cc_start: 0.8615 (m) cc_final: 0.8411 (p) REVERT: B 369 TYR cc_start: 0.7082 (t80) cc_final: 0.6855 (t80) REVERT: B 406 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8418 (mt-10) REVERT: B 408 ARG cc_start: 0.8549 (ptm-80) cc_final: 0.8219 (ppt170) REVERT: B 414 GLN cc_start: 0.7287 (tp40) cc_final: 0.6756 (tp-100) REVERT: B 528 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7993 (mttm) REVERT: B 583 GLU cc_start: 0.7345 (tm-30) cc_final: 0.7118 (tm-30) REVERT: C 398 ASP cc_start: 0.8904 (m-30) cc_final: 0.8418 (m-30) REVERT: D 474 GLN cc_start: 0.8564 (tt0) cc_final: 0.8213 (tt0) REVERT: D 516 GLU cc_start: 0.8476 (tt0) cc_final: 0.8141 (pp20) REVERT: E 386 LYS cc_start: 0.8816 (mtpt) cc_final: 0.8411 (ttpt) REVERT: E 455 LEU cc_start: 0.9428 (tp) cc_final: 0.9222 (tt) REVERT: E 493 GLN cc_start: 0.8827 (tp40) cc_final: 0.8527 (mm-40) REVERT: E 554 GLU cc_start: 0.8162 (pp20) cc_final: 0.7846 (pp20) REVERT: F 365 TYR cc_start: 0.8598 (m-80) cc_final: 0.8315 (m-80) REVERT: F 378 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7811 (tptm) REVERT: F 380 TYR cc_start: 0.8821 (m-80) cc_final: 0.8220 (m-80) REVERT: F 406 GLU cc_start: 0.8213 (mp0) cc_final: 0.7780 (pm20) REVERT: F 464 PHE cc_start: 0.8000 (m-80) cc_final: 0.7512 (m-80) REVERT: F 498 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8417 (mm-40) REVERT: F 580 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7472 (tp-100) outliers start: 19 outliers final: 17 residues processed: 162 average time/residue: 0.2349 time to fit residues: 57.5731 Evaluate side-chains 145 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.897 ------------------------------------------------------------------------------- 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 B residue 390 LEU Chi-restraints excluded: chain B residue 480 CYS 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 401 VAL Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 574 ASP Chi-restraints excluded: chain F residue 387 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 37 optimal weight: 4.9990 chunk 142 optimal weight: 0.0970 chunk 141 optimal weight: 8.9990 chunk 150 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 481 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.086347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.070677 restraints weight = 40335.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.073087 restraints weight = 20880.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.074667 restraints weight = 13700.586| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3395 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= 0.178 Angle : 0.547 8.571 17922 Z= 0.286 Chirality : 0.046 0.329 1980 Planarity : 0.004 0.042 2322 Dihedral : 4.873 38.541 2016 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.16 % Allowed : 11.47 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.20), residues: 1596 helix: -2.73 (0.35), residues: 144 sheet: 0.27 (0.28), residues: 331 loop : -0.31 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 436 PHE 0.015 0.001 PHE F 392 TYR 0.022 0.001 TYR D 365 ARG 0.003 0.000 ARG E 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 12) link_NAG-ASN : angle 2.08126 ( 36) hydrogen bonds : bond 0.03561 ( 355) hydrogen bonds : angle 6.39108 ( 915) SS BOND : bond 0.00311 ( 24) SS BOND : angle 1.32916 ( 48) covalent geometry : bond 0.00402 (13110) covalent geometry : angle 0.53558 (17838) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 GLU cc_start: 0.8080 (tp30) cc_final: 0.7606 (tt0) REVERT: A 584 ILE cc_start: 0.8626 (mp) cc_final: 0.8275 (tt) REVERT: B 366 SER cc_start: 0.8649 (m) cc_final: 0.8438 (p) REVERT: B 406 GLU cc_start: 0.8604 (mt-10) cc_final: 0.7975 (mt-10) REVERT: B 493 GLN cc_start: 0.8248 (tp-100) cc_final: 0.7998 (tp-100) REVERT: B 528 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7937 (mttm) REVERT: B 584 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.7990 (pt) REVERT: D 516 GLU cc_start: 0.8398 (tt0) cc_final: 0.8136 (pp20) REVERT: E 368 LEU cc_start: 0.9380 (mt) cc_final: 0.8990 (pp) REVERT: E 386 LYS cc_start: 0.8666 (mtpt) cc_final: 0.8397 (tttt) REVERT: E 455 LEU cc_start: 0.9496 (tp) cc_final: 0.9239 (tp) REVERT: E 554 GLU cc_start: 0.8285 (pp20) cc_final: 0.7866 (pp20) REVERT: F 365 TYR cc_start: 0.8707 (m-80) cc_final: 0.8328 (m-80) REVERT: F 378 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7781 (tptm) REVERT: F 380 TYR cc_start: 0.8853 (m-80) cc_final: 0.8404 (m-80) REVERT: F 406 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7840 (pm20) REVERT: F 464 PHE cc_start: 0.8132 (m-80) cc_final: 0.7603 (m-80) REVERT: F 498 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8374 (mm-40) REVERT: F 580 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7550 (tp-100) REVERT: F 583 GLU cc_start: 0.8551 (tp30) cc_final: 0.8238 (tp30) outliers start: 30 outliers final: 24 residues processed: 146 average time/residue: 0.2100 time to fit residues: 47.0558 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 : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain 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 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 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 406 GLU Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 559 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 87 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.086276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.070579 restraints weight = 40292.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.072982 restraints weight = 20872.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.074555 restraints weight = 13697.371| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13146 Z= 0.167 Angle : 0.552 9.533 17922 Z= 0.285 Chirality : 0.046 0.328 1980 Planarity : 0.004 0.040 2322 Dihedral : 4.806 38.123 2016 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.31 % Allowed : 12.12 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.20), residues: 1596 helix: -2.74 (0.37), residues: 138 sheet: 0.19 (0.27), residues: 338 loop : -0.29 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 436 PHE 0.017 0.001 PHE F 392 TYR 0.019 0.001 TYR D 365 ARG 0.003 0.000 ARG F 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 12) link_NAG-ASN : angle 2.05711 ( 36) hydrogen bonds : bond 0.03486 ( 355) hydrogen bonds : angle 6.37397 ( 915) SS BOND : bond 0.00318 ( 24) SS BOND : angle 1.32176 ( 48) covalent geometry : bond 0.00377 (13110) covalent geometry : angle 0.54110 (17838) *********************** 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 156 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 ILE cc_start: 0.8624 (mp) cc_final: 0.8295 (tt) REVERT: B 366 SER cc_start: 0.8725 (m) cc_final: 0.8493 (p) REVERT: B 406 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8180 (mt-10) REVERT: B 493 GLN cc_start: 0.8335 (tp-100) cc_final: 0.8037 (tp-100) REVERT: B 528 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8025 (mttm) REVERT: B 559 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.6146 (m-80) REVERT: D 471 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7891 (tm-30) REVERT: E 324 GLU cc_start: 0.7830 (mp0) cc_final: 0.7534 (mp0) REVERT: E 368 LEU cc_start: 0.9376 (mt) cc_final: 0.8992 (pp) REVERT: E 386 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8290 (tttt) REVERT: E 455 LEU cc_start: 0.9498 (tp) cc_final: 0.9241 (tp) REVERT: E 495 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: E 554 GLU cc_start: 0.8332 (pp20) cc_final: 0.7700 (pp20) REVERT: F 340 GLU cc_start: 0.8392 (pm20) cc_final: 0.8120 (pm20) REVERT: F 365 TYR cc_start: 0.8738 (m-80) cc_final: 0.8343 (m-80) REVERT: F 378 LYS cc_start: 0.8003 (mtpp) cc_final: 0.7776 (tptm) REVERT: F 380 TYR cc_start: 0.8856 (m-80) cc_final: 0.8406 (m-80) REVERT: F 406 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: F 464 PHE cc_start: 0.8100 (m-80) cc_final: 0.7647 (m-80) REVERT: F 580 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7526 (tp-100) REVERT: F 583 GLU cc_start: 0.8605 (tp30) cc_final: 0.8364 (tp30) outliers start: 32 outliers final: 26 residues processed: 148 average time/residue: 0.2156 time to fit residues: 48.7954 Evaluate side-chains 143 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 387 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 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 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 574 ASP Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 559 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 29 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 140 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 76 optimal weight: 0.0050 chunk 64 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 13 optimal weight: 0.0570 chunk 7 optimal weight: 0.9990 overall best weight: 0.5114 ------------------------------------------------------------------------------- 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** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.088306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.072869 restraints weight = 40526.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.075316 restraints weight = 20544.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.076940 restraints weight = 13299.090| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3685 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= 0.101 Angle : 0.534 8.727 17922 Z= 0.274 Chirality : 0.046 0.323 1980 Planarity : 0.003 0.037 2322 Dihedral : 4.470 36.137 2016 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.24 % Allowed : 12.77 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1596 helix: -2.74 (0.38), residues: 138 sheet: 0.20 (0.27), residues: 338 loop : -0.19 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 436 PHE 0.015 0.001 PHE F 392 TYR 0.008 0.001 TYR D 365 ARG 0.002 0.000 ARG F 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 12) link_NAG-ASN : angle 2.01274 ( 36) hydrogen bonds : bond 0.03159 ( 355) hydrogen bonds : angle 6.15331 ( 915) SS BOND : bond 0.00298 ( 24) SS BOND : angle 1.19661 ( 48) covalent geometry : bond 0.00233 (13110) covalent geometry : angle 0.52393 (17838) *********************** 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 158 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.6791 (m-10) REVERT: A 584 ILE cc_start: 0.8604 (mp) cc_final: 0.8194 (mm) REVERT: B 387 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9072 (mp) REVERT: B 406 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8034 (mt-10) REVERT: B 493 GLN cc_start: 0.8295 (tp-100) cc_final: 0.8042 (tp-100) REVERT: B 528 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7906 (mttm) REVERT: B 584 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8144 (pt) REVERT: C 398 ASP cc_start: 0.8886 (m-30) cc_final: 0.8448 (m-30) REVERT: C 466 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7256 (ttp80) REVERT: D 471 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7879 (tm-30) REVERT: E 324 GLU cc_start: 0.7836 (mp0) cc_final: 0.7561 (mp0) REVERT: E 368 LEU cc_start: 0.9359 (mt) cc_final: 0.9008 (pp) REVERT: E 386 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8262 (tttt) REVERT: E 455 LEU cc_start: 0.9448 (tp) cc_final: 0.9208 (tp) REVERT: E 495 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7391 (m-80) REVERT: E 554 GLU cc_start: 0.8244 (pp20) cc_final: 0.7849 (pp20) REVERT: E 574 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7928 (t0) REVERT: F 340 GLU cc_start: 0.8362 (pm20) cc_final: 0.8076 (pm20) REVERT: F 378 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7740 (tptm) REVERT: F 380 TYR cc_start: 0.8833 (m-80) cc_final: 0.8406 (m-80) REVERT: F 406 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: F 464 PHE cc_start: 0.7930 (m-80) cc_final: 0.7480 (m-80) REVERT: F 583 GLU cc_start: 0.8568 (tp30) cc_final: 0.8298 (tp30) outliers start: 31 outliers final: 22 residues processed: 150 average time/residue: 0.2186 time to fit residues: 49.9007 Evaluate side-chains 142 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 387 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 584 ILE 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 D residue 362 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 574 ASP Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 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 108 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 140 optimal weight: 3.9990 chunk 72 optimal weight: 0.0470 chunk 41 optimal weight: 0.4980 chunk 132 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.087871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.072494 restraints weight = 40483.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.074913 restraints weight = 20632.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.076516 restraints weight = 13380.805| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3841 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= 0.112 Angle : 0.547 8.902 17922 Z= 0.281 Chirality : 0.046 0.329 1980 Planarity : 0.003 0.036 2322 Dihedral : 4.422 34.310 2016 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.45 % Allowed : 13.42 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1596 helix: -2.83 (0.36), residues: 138 sheet: 0.20 (0.27), residues: 336 loop : -0.15 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 436 PHE 0.015 0.001 PHE D 392 TYR 0.017 0.001 TYR F 365 ARG 0.002 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 12) link_NAG-ASN : angle 2.03856 ( 36) hydrogen bonds : bond 0.03154 ( 355) hydrogen bonds : angle 6.10588 ( 915) SS BOND : bond 0.00298 ( 24) SS BOND : angle 1.17884 ( 48) covalent geometry : bond 0.00258 (13110) covalent geometry : angle 0.53671 (17838) *********************** 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 151 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.6749 (m-10) REVERT: B 406 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8073 (mt-10) REVERT: B 493 GLN cc_start: 0.8333 (tp-100) cc_final: 0.8015 (tp-100) REVERT: B 528 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7932 (mttm) REVERT: B 559 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.6207 (m-80) REVERT: B 584 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7968 (pt) REVERT: C 398 ASP cc_start: 0.8892 (m-30) cc_final: 0.8451 (m-30) REVERT: C 466 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7186 (ttp80) REVERT: D 471 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7879 (tm-30) REVERT: E 324 GLU cc_start: 0.7820 (mp0) cc_final: 0.7538 (mp0) REVERT: E 368 LEU cc_start: 0.9361 (mt) cc_final: 0.9015 (pp) REVERT: E 386 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8248 (tttt) REVERT: E 455 LEU cc_start: 0.9459 (tp) cc_final: 0.9209 (tp) REVERT: E 493 GLN cc_start: 0.8776 (tp40) cc_final: 0.8514 (mm-40) REVERT: E 495 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7341 (m-80) REVERT: E 574 ASP cc_start: 0.8200 (t70) cc_final: 0.7982 (t0) REVERT: F 340 GLU cc_start: 0.8357 (pm20) cc_final: 0.8084 (pm20) REVERT: F 378 LYS cc_start: 0.7969 (mtpp) cc_final: 0.7764 (tptm) REVERT: F 380 TYR cc_start: 0.8834 (m-80) cc_final: 0.8388 (m-80) REVERT: F 406 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7892 (pm20) REVERT: F 464 PHE cc_start: 0.7940 (m-80) cc_final: 0.7501 (m-80) REVERT: F 583 GLU cc_start: 0.8563 (tp30) cc_final: 0.8230 (tp30) outliers start: 34 outliers final: 23 residues processed: 144 average time/residue: 0.2148 time to fit residues: 46.9299 Evaluate side-chains 140 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 495 TYR 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 121 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 99 optimal weight: 0.0470 chunk 11 optimal weight: 0.8980 chunk 102 optimal weight: 0.2980 chunk 153 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.088242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.072935 restraints weight = 40236.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.075355 restraints weight = 20546.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.076954 restraints weight = 13334.168| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3917 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 : 0.547 8.854 17922 Z= 0.283 Chirality : 0.045 0.330 1980 Planarity : 0.003 0.036 2322 Dihedral : 4.317 32.616 2016 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.24 % Allowed : 13.56 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1596 helix: -2.76 (0.39), residues: 122 sheet: 0.22 (0.27), residues: 336 loop : -0.06 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 PHE 0.013 0.001 PHE F 392 TYR 0.007 0.001 TYR D 369 ARG 0.002 0.000 ARG F 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 12) link_NAG-ASN : angle 2.02020 ( 36) hydrogen bonds : bond 0.03234 ( 355) hydrogen bonds : angle 6.06959 ( 915) SS BOND : bond 0.00302 ( 24) SS BOND : angle 1.16341 ( 48) covalent geometry : bond 0.00257 (13110) covalent geometry : angle 0.53754 (17838) *********************** 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 154 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 PHE cc_start: 0.4806 (OUTLIER) cc_final: 0.4554 (m-10) REVERT: B 406 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8134 (mt-10) REVERT: B 493 GLN cc_start: 0.8314 (tp-100) cc_final: 0.7978 (tp-100) REVERT: B 528 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8007 (mtmm) REVERT: B 559 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.6074 (m-80) REVERT: C 398 ASP cc_start: 0.8868 (m-30) cc_final: 0.8434 (m-30) REVERT: C 466 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7154 (ttp80) REVERT: D 471 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7789 (tm-30) REVERT: E 324 GLU cc_start: 0.7891 (mp0) cc_final: 0.7629 (mp0) REVERT: E 368 LEU cc_start: 0.9355 (mt) cc_final: 0.9014 (pp) REVERT: E 386 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8245 (tttt) REVERT: E 455 LEU cc_start: 0.9454 (tp) cc_final: 0.9200 (tp) REVERT: E 495 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: F 340 GLU cc_start: 0.8317 (pm20) cc_final: 0.8055 (pm20) REVERT: F 378 LYS cc_start: 0.7993 (mtpp) cc_final: 0.7773 (tptm) REVERT: F 380 TYR cc_start: 0.8823 (m-80) cc_final: 0.8366 (m-80) REVERT: F 406 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7904 (pm20) REVERT: F 464 PHE cc_start: 0.7904 (m-80) cc_final: 0.7535 (m-80) REVERT: F 583 GLU cc_start: 0.8531 (tp30) cc_final: 0.8253 (tp30) outliers start: 31 outliers final: 21 residues processed: 146 average time/residue: 0.2184 time to fit residues: 48.4861 Evaluate side-chains 144 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 495 TYR 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 153 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.086486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070953 restraints weight = 40178.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.073325 restraints weight = 20675.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.074908 restraints weight = 13514.886| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13146 Z= 0.179 Angle : 0.598 8.635 17922 Z= 0.311 Chirality : 0.046 0.334 1980 Planarity : 0.004 0.038 2322 Dihedral : 4.642 34.565 2016 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.31 % Allowed : 14.00 % Favored : 83.69 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1596 helix: -2.87 (0.36), residues: 138 sheet: 0.14 (0.27), residues: 336 loop : -0.15 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 436 PHE 0.024 0.001 PHE D 392 TYR 0.013 0.001 TYR D 369 ARG 0.004 0.000 ARG F 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 12) link_NAG-ASN : angle 2.04333 ( 36) hydrogen bonds : bond 0.03591 ( 355) hydrogen bonds : angle 6.21902 ( 915) SS BOND : bond 0.00312 ( 24) SS BOND : angle 1.24677 ( 48) covalent geometry : bond 0.00408 (13110) covalent geometry : angle 0.58851 (17838) *********************** 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 153 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 PHE cc_start: 0.4182 (OUTLIER) cc_final: 0.3728 (m-10) REVERT: B 406 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8119 (mt-10) REVERT: B 414 GLN cc_start: 0.7490 (tp40) cc_final: 0.7164 (tp-100) REVERT: B 493 GLN cc_start: 0.8418 (tp-100) cc_final: 0.8062 (tp-100) REVERT: B 528 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7929 (mtmm) REVERT: B 559 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.5966 (m-80) REVERT: C 466 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7330 (ttp80) REVERT: D 471 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7765 (tm-30) REVERT: D 516 GLU cc_start: 0.8494 (pt0) cc_final: 0.8129 (pp20) REVERT: E 324 GLU cc_start: 0.7954 (mp0) cc_final: 0.7615 (mp0) REVERT: E 368 LEU cc_start: 0.9367 (mt) cc_final: 0.9016 (pp) REVERT: E 386 LYS cc_start: 0.8663 (mtpt) cc_final: 0.8300 (tttt) REVERT: E 455 LEU cc_start: 0.9508 (tp) cc_final: 0.9223 (tp) REVERT: E 495 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.7404 (m-80) REVERT: E 554 GLU cc_start: 0.8013 (pp20) cc_final: 0.7697 (pp20) REVERT: F 340 GLU cc_start: 0.8409 (pm20) cc_final: 0.8145 (pm20) REVERT: F 378 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7767 (tptm) REVERT: F 380 TYR cc_start: 0.8845 (m-80) cc_final: 0.8409 (m-80) REVERT: F 406 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7829 (pm20) REVERT: F 464 PHE cc_start: 0.7958 (m-80) cc_final: 0.7559 (m-80) outliers start: 32 outliers final: 24 residues processed: 144 average time/residue: 0.2224 time to fit residues: 48.5941 Evaluate side-chains 147 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 495 TYR 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 495 TYR Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 559 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 135 optimal weight: 3.9990 chunk 36 optimal weight: 0.0870 chunk 131 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.9360 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.088191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.072697 restraints weight = 40796.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.075117 restraints weight = 20799.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.076715 restraints weight = 13486.237| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13146 Z= 0.138 Angle : 0.588 8.821 17922 Z= 0.305 Chirality : 0.046 0.330 1980 Planarity : 0.004 0.037 2322 Dihedral : 4.580 34.103 2016 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1596 helix: -2.85 (0.36), residues: 138 sheet: 0.14 (0.27), residues: 336 loop : -0.14 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 PHE 0.019 0.001 PHE D 392 TYR 0.015 0.001 TYR D 365 ARG 0.005 0.000 ARG F 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 12) link_NAG-ASN : angle 2.05651 ( 36) hydrogen bonds : bond 0.03460 ( 355) hydrogen bonds : angle 6.21542 ( 915) SS BOND : bond 0.00365 ( 24) SS BOND : angle 1.52103 ( 48) covalent geometry : bond 0.00320 (13110) covalent geometry : angle 0.57641 (17838) ********************** 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 146 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 PHE cc_start: 0.4312 (OUTLIER) cc_final: 0.3641 (m-10) REVERT: B 406 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8116 (mt-10) REVERT: B 414 GLN cc_start: 0.7460 (tp40) cc_final: 0.7122 (tp-100) REVERT: B 493 GLN cc_start: 0.8393 (tp-100) cc_final: 0.8053 (tp-100) REVERT: B 528 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7923 (mtmm) REVERT: B 559 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.5565 (m-80) REVERT: C 398 ASP cc_start: 0.8864 (m-30) cc_final: 0.8479 (m-30) REVERT: C 466 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7221 (ttp80) REVERT: D 471 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7862 (tm-30) REVERT: D 516 GLU cc_start: 0.8447 (pt0) cc_final: 0.8109 (pp20) REVERT: E 324 GLU cc_start: 0.7952 (mp0) cc_final: 0.7620 (mp0) REVERT: E 368 LEU cc_start: 0.9370 (mt) cc_final: 0.9031 (pp) REVERT: E 386 LYS cc_start: 0.8627 (mtpt) cc_final: 0.8275 (tttt) REVERT: E 455 LEU cc_start: 0.9484 (tp) cc_final: 0.9222 (tp) REVERT: E 493 GLN cc_start: 0.8772 (tp40) cc_final: 0.8508 (mm-40) REVERT: E 495 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: E 554 GLU cc_start: 0.8110 (pp20) cc_final: 0.7907 (pp20) REVERT: F 340 GLU cc_start: 0.8381 (pm20) cc_final: 0.8142 (pm20) REVERT: F 378 LYS cc_start: 0.8006 (mtpp) cc_final: 0.7780 (tptm) REVERT: F 380 TYR cc_start: 0.8829 (m-80) cc_final: 0.8412 (m-80) REVERT: F 406 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7785 (pm20) REVERT: F 464 PHE cc_start: 0.7950 (m-80) cc_final: 0.7567 (m-80) outliers start: 29 outliers final: 23 residues processed: 139 average time/residue: 0.2663 time to fit residues: 56.8609 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 : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 559 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 121 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 126 optimal weight: 0.0020 chunk 123 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.9392 ------------------------------------------------------------------------------- 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 439 ASN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.085112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.069674 restraints weight = 40457.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.072011 restraints weight = 20948.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.073547 restraints weight = 13750.946| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13146 Z= 0.233 Angle : 0.638 8.723 17922 Z= 0.331 Chirality : 0.047 0.342 1980 Planarity : 0.004 0.040 2322 Dihedral : 5.089 38.817 2016 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.16 % Allowed : 13.85 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.21), residues: 1596 helix: -2.94 (0.35), residues: 138 sheet: 0.07 (0.27), residues: 338 loop : -0.21 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 436 PHE 0.020 0.001 PHE D 392 TYR 0.018 0.002 TYR C 365 ARG 0.005 0.001 ARG F 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 12) link_NAG-ASN : angle 2.13052 ( 36) hydrogen bonds : bond 0.03838 ( 355) hydrogen bonds : angle 6.46209 ( 915) SS BOND : bond 0.00333 ( 24) SS BOND : angle 1.67537 ( 48) covalent geometry : bond 0.00531 (13110) covalent geometry : angle 0.62656 (17838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3965.48 seconds wall clock time: 69 minutes 55.71 seconds (4195.71 seconds total)