Starting phenix.real_space_refine on Thu Feb 15 16:36:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf1_25858/02_2024/7tf1_25858.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf1_25858/02_2024/7tf1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf1_25858/02_2024/7tf1_25858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf1_25858/02_2024/7tf1_25858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf1_25858/02_2024/7tf1_25858.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf1_25858/02_2024/7tf1_25858.pdb" } 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 Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.04, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 4.62 Conformation dependent library (CDL) restraints added in 2.5 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: 1.65 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: 3.81 Time building geometry restraints manager: 5.08 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: 101.37 - 108.02: 588 108.02 - 114.66: 7136 114.66 - 121.31: 6487 121.31 - 127.96: 3564 127.96 - 134.61: 63 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 2.440 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.308 2.440 nonbonded pdb=" OD2 ASP C 578 " pdb=" OG1 THR C 581 " model vdw 2.311 2.440 nonbonded pdb=" O TYR A 495 " pdb=" OH TYR A 505 " model vdw 2.320 2.440 nonbonded pdb=" O THR F 393 " pdb=" OG1 THR F 523 " model vdw 2.325 2.440 ... (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 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: 2.950 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: 13.420 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 35.180 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.790 ------------------------------------------------------------------------------- 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 13110 Z= 0.267 Angle : 0.768 14.306 17838 Z= 0.407 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 302 time to evaluate : 1.448 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: 0.2949 time to fit residues: 121.3652 Evaluate side-chains 139 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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: 0.3980 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 360 ASN B 394 ASN ** B 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13110 Z= 0.200 Angle : 0.544 8.533 17838 Z= 0.283 Chirality : 0.046 0.332 1980 Planarity : 0.005 0.053 2322 Dihedral : 5.513 57.239 2016 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.66 % Allowed : 9.24 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.07 (0.19), residues: 1596 helix: -2.73 (0.27), residues: 204 sheet: 0.21 (0.26), residues: 366 loop : -0.58 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 436 PHE 0.015 0.001 PHE D 515 TYR 0.020 0.001 TYR D 365 ARG 0.007 0.000 ARG C 403 *********************** 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 181 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.638 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: 0.8733 (mp) cc_final: 0.8337 (mt) REVERT: B 366 SER cc_start: 0.8738 (m) cc_final: 0.8472 (p) REVERT: B 387 LEU cc_start: 0.9627 (mt) cc_final: 0.9404 (mt) REVERT: B 406 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8420 (mt-10) REVERT: B 408 ARG cc_start: 0.8605 (ptm-80) cc_final: 0.8138 (ptm-80) REVERT: B 471 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8452 (pp20) REVERT: B 493 GLN cc_start: 0.8373 (tp40) cc_final: 0.7898 (tm-30) REVERT: B 537 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8237 (mtpp) REVERT: B 583 GLU cc_start: 0.7358 (tm-30) cc_final: 0.6906 (tm-30) REVERT: C 357 ARG cc_start: 0.6742 (ttt180) cc_final: 0.6507 (ttm170) REVERT: C 366 SER cc_start: 0.8912 (m) cc_final: 0.8708 (p) REVERT: C 398 ASP cc_start: 0.8900 (m-30) cc_final: 0.8588 (m-30) REVERT: C 498 GLN cc_start: 0.8989 (mt0) cc_final: 0.8737 (mm-40) REVERT: D 365 TYR cc_start: 0.9169 (m-10) cc_final: 0.8913 (m-10) REVERT: D 468 ILE cc_start: 0.9284 (pt) cc_final: 0.9031 (tp) REVERT: D 474 GLN cc_start: 0.8486 (tt0) cc_final: 0.8227 (tt0) REVERT: E 324 GLU cc_start: 0.7769 (mp0) cc_final: 0.7215 (mp0) REVERT: E 366 SER cc_start: 0.8863 (t) cc_final: 0.8287 (p) REVERT: E 386 LYS cc_start: 0.8911 (mtpt) cc_final: 0.8494 (ttpt) REVERT: E 406 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8075 (mt-10) REVERT: E 465 GLU cc_start: 0.8018 (tt0) cc_final: 0.7807 (tt0) REVERT: E 493 GLN cc_start: 0.8817 (tp40) cc_final: 0.8504 (mm110) REVERT: E 554 GLU cc_start: 0.7857 (pp20) cc_final: 0.7655 (pp20) REVERT: F 365 TYR cc_start: 0.8621 (m-80) cc_final: 0.8356 (m-80) REVERT: F 406 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7923 (pm20) REVERT: F 464 PHE cc_start: 0.8125 (m-80) cc_final: 0.7603 (m-80) REVERT: F 498 GLN cc_start: 0.9019 (mt0) cc_final: 0.8698 (mm-40) REVERT: F 577 ARG cc_start: 0.7490 (ttp80) cc_final: 0.7286 (ttm170) REVERT: F 580 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7606 (tp-100) outliers start: 23 outliers final: 16 residues processed: 173 average time/residue: 0.2332 time to fit residues: 60.0712 Evaluate side-chains 138 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 B residue 390 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 582 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 0.0570 overall best weight: 0.7900 ------------------------------------------------------------------------------- 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** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN C 414 GLN ** D 388 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13110 Z= 0.169 Angle : 0.496 7.773 17838 Z= 0.260 Chirality : 0.045 0.327 1980 Planarity : 0.004 0.043 2322 Dihedral : 4.988 58.583 2016 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.80 % Allowed : 10.75 % Favored : 87.45 % 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: -0.85 (0.19), residues: 1596 helix: -2.72 (0.31), residues: 174 sheet: 0.38 (0.26), residues: 364 loop : -0.49 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 436 PHE 0.014 0.001 PHE F 392 TYR 0.014 0.001 TYR F 380 ARG 0.004 0.000 ARG E 567 *********************** 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 161 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.502 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: 0.8693 (mp) cc_final: 0.8378 (tt) REVERT: B 366 SER cc_start: 0.8693 (m) cc_final: 0.8451 (p) REVERT: B 369 TYR cc_start: 0.7178 (t80) cc_final: 0.6934 (t80) REVERT: B 406 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8549 (mt-10) REVERT: B 414 GLN cc_start: 0.7734 (tp-100) cc_final: 0.7017 (tp-100) REVERT: B 471 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8437 (pp20) REVERT: B 537 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8303 (mtpp) REVERT: B 583 GLU cc_start: 0.7352 (tm-30) cc_final: 0.7081 (tm-30) REVERT: C 340 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8208 (tm-30) REVERT: C 364 ASP cc_start: 0.8464 (t0) cc_final: 0.8257 (t0) REVERT: C 554 GLU cc_start: 0.7670 (tp30) cc_final: 0.7451 (tp30) REVERT: D 365 TYR cc_start: 0.9140 (m-10) cc_final: 0.8887 (m-10) REVERT: E 324 GLU cc_start: 0.7763 (mp0) cc_final: 0.7495 (mp0) REVERT: E 386 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8448 (ttpt) REVERT: E 406 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7954 (mt-10) REVERT: E 465 GLU cc_start: 0.8014 (tt0) cc_final: 0.7798 (tt0) REVERT: E 554 GLU cc_start: 0.7990 (pp20) cc_final: 0.7742 (pp20) REVERT: F 365 TYR cc_start: 0.8657 (m-80) cc_final: 0.8307 (m-80) REVERT: F 406 GLU cc_start: 0.8263 (mp0) cc_final: 0.7760 (pm20) REVERT: F 440 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8530 (p0) REVERT: F 464 PHE cc_start: 0.8034 (m-80) cc_final: 0.7517 (m-80) REVERT: F 498 GLN cc_start: 0.9054 (mt0) cc_final: 0.8706 (mm-40) REVERT: F 580 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7619 (tp-100) outliers start: 25 outliers final: 21 residues processed: 153 average time/residue: 0.2342 time to fit residues: 53.4437 Evaluate side-chains 144 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain D residue 401 VAL 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 389 ASP 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 433 VAL Chi-restraints excluded: chain F residue 440 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 150 optimal weight: 0.0020 chunk 74 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 40 optimal weight: 0.0370 overall best weight: 0.5266 ------------------------------------------------------------------------------- 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** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 13110 Z= 0.136 Angle : 0.468 7.961 17838 Z= 0.245 Chirality : 0.045 0.324 1980 Planarity : 0.004 0.040 2322 Dihedral : 4.691 58.999 2016 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.02 % Allowed : 11.26 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.20), residues: 1596 helix: -2.52 (0.40), residues: 122 sheet: 0.40 (0.25), residues: 370 loop : -0.29 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 PHE 0.014 0.001 PHE D 392 TYR 0.014 0.001 TYR F 380 ARG 0.005 0.000 ARG E 403 *********************** 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 157 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 ILE cc_start: 0.8772 (mp) cc_final: 0.8352 (tt) REVERT: B 366 SER cc_start: 0.8669 (m) cc_final: 0.8426 (p) REVERT: B 369 TYR cc_start: 0.7181 (t80) cc_final: 0.6948 (t80) REVERT: B 405 ASP cc_start: 0.8888 (t0) cc_final: 0.8670 (t0) REVERT: B 406 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8386 (mt-10) REVERT: B 408 ARG cc_start: 0.8624 (ptm-80) cc_final: 0.8285 (ppt170) REVERT: B 414 GLN cc_start: 0.7718 (tp-100) cc_final: 0.6726 (tp-100) REVERT: B 528 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8021 (mtmm) REVERT: B 529 LYS cc_start: 0.9231 (mtpt) cc_final: 0.8985 (mmmt) REVERT: B 537 LYS cc_start: 0.8775 (mtmt) cc_final: 0.8320 (mtpp) REVERT: B 557 LYS cc_start: 0.7422 (mttp) cc_final: 0.7127 (tttm) REVERT: C 398 ASP cc_start: 0.8816 (m-30) cc_final: 0.8452 (m-30) REVERT: D 516 GLU cc_start: 0.8743 (pt0) cc_final: 0.8064 (pp20) REVERT: E 324 GLU cc_start: 0.7797 (mp0) cc_final: 0.7519 (mp0) REVERT: E 386 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8365 (tttt) REVERT: E 406 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8056 (mt-10) REVERT: E 455 LEU cc_start: 0.9482 (tp) cc_final: 0.9241 (tt) REVERT: E 465 GLU cc_start: 0.8032 (tt0) cc_final: 0.7808 (tt0) REVERT: E 554 GLU cc_start: 0.8058 (pp20) cc_final: 0.7768 (pp20) REVERT: F 406 GLU cc_start: 0.8305 (mp0) cc_final: 0.7807 (pm20) REVERT: F 440 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8425 (p0) REVERT: F 464 PHE cc_start: 0.7983 (m-80) cc_final: 0.7566 (m-80) REVERT: F 498 GLN cc_start: 0.9057 (mt0) cc_final: 0.8700 (mm-40) REVERT: F 580 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7619 (tp-100) REVERT: F 583 GLU cc_start: 0.8691 (tp30) cc_final: 0.8243 (tp30) outliers start: 28 outliers final: 21 residues processed: 149 average time/residue: 0.2278 time to fit residues: 51.0544 Evaluate side-chains 141 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain D residue 401 VAL 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 389 ASP Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 440 ASN Chi-restraints excluded: chain F residue 515 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 135 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13110 Z= 0.216 Angle : 0.501 8.085 17838 Z= 0.262 Chirality : 0.045 0.325 1980 Planarity : 0.003 0.039 2322 Dihedral : 4.765 57.185 2016 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.38 % Allowed : 11.76 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.45 (0.20), residues: 1596 helix: -2.56 (0.38), residues: 138 sheet: 0.51 (0.28), residues: 333 loop : -0.21 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 436 PHE 0.013 0.001 PHE F 392 TYR 0.013 0.001 TYR D 365 ARG 0.004 0.000 ARG E 403 *********************** 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 fitting. rotamer outliers: 33 poor density : 123 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 ILE cc_start: 0.8799 (mp) cc_final: 0.8422 (tt) REVERT: B 366 SER cc_start: 0.8621 (m) cc_final: 0.8357 (p) REVERT: B 406 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8426 (mt-10) REVERT: B 414 GLN cc_start: 0.7861 (tp-100) cc_final: 0.7642 (tp40) REVERT: B 528 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7923 (mtmm) REVERT: B 529 LYS cc_start: 0.9208 (mtpt) cc_final: 0.8965 (mmmt) REVERT: B 537 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8598 (ttpp) REVERT: D 516 GLU cc_start: 0.8695 (pt0) cc_final: 0.8100 (pp20) REVERT: E 324 GLU cc_start: 0.7805 (mp0) cc_final: 0.7511 (mp0) REVERT: E 386 LYS cc_start: 0.8828 (mtpt) cc_final: 0.8351 (tttt) REVERT: E 406 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8002 (mt-10) REVERT: E 455 LEU cc_start: 0.9538 (tp) cc_final: 0.9258 (tt) REVERT: E 465 GLU cc_start: 0.8032 (tt0) cc_final: 0.7809 (tt0) REVERT: E 554 GLU cc_start: 0.8276 (pp20) cc_final: 0.7914 (pp20) REVERT: F 406 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7806 (pm20) REVERT: F 464 PHE cc_start: 0.7974 (m-80) cc_final: 0.7641 (m-80) REVERT: F 498 GLN cc_start: 0.9068 (mt0) cc_final: 0.8804 (mm-40) REVERT: F 583 GLU cc_start: 0.8741 (tp30) cc_final: 0.8395 (tp30) outliers start: 33 outliers final: 27 residues processed: 146 average time/residue: 0.2193 time to fit residues: 48.5426 Evaluate side-chains 142 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain D residue 389 ASP 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 389 ASP 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 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 50 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13110 Z= 0.297 Angle : 0.541 8.331 17838 Z= 0.283 Chirality : 0.046 0.327 1980 Planarity : 0.004 0.039 2322 Dihedral : 5.047 47.334 2016 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.81 % Allowed : 11.90 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.46 (0.20), residues: 1596 helix: -2.50 (0.39), residues: 138 sheet: 0.36 (0.27), residues: 334 loop : -0.17 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 436 PHE 0.018 0.001 PHE D 392 TYR 0.016 0.001 TYR B 365 ARG 0.004 0.000 ARG E 403 *********************** 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 fitting. rotamer outliers: 39 poor density : 119 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7051 (m-10) REVERT: A 584 ILE cc_start: 0.8841 (mp) cc_final: 0.8178 (mt) REVERT: B 366 SER cc_start: 0.8571 (m) cc_final: 0.8364 (p) REVERT: B 406 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8424 (mt-10) REVERT: B 528 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7850 (mttm) REVERT: B 529 LYS cc_start: 0.9229 (mtpt) cc_final: 0.8978 (mmmt) REVERT: B 559 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.5870 (m-80) REVERT: C 378 LYS cc_start: 0.8258 (ttmm) cc_final: 0.7864 (ttmm) REVERT: D 378 LYS cc_start: 0.8913 (mmpt) cc_final: 0.8671 (mmmm) REVERT: D 471 GLU cc_start: 0.8282 (tp30) cc_final: 0.7981 (tm-30) REVERT: E 324 GLU cc_start: 0.7846 (mp0) cc_final: 0.7553 (mp0) REVERT: E 368 LEU cc_start: 0.9403 (mt) cc_final: 0.8995 (pp) REVERT: E 386 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8345 (tttt) REVERT: E 455 LEU cc_start: 0.9565 (tp) cc_final: 0.9307 (tp) REVERT: E 465 GLU cc_start: 0.8098 (tt0) cc_final: 0.7882 (tt0) REVERT: E 554 GLU cc_start: 0.8391 (pp20) cc_final: 0.7804 (pp20) REVERT: E 583 GLU cc_start: 0.7841 (tp30) cc_final: 0.7633 (tp30) REVERT: F 340 GLU cc_start: 0.8416 (pm20) cc_final: 0.8206 (pm20) REVERT: F 406 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7774 (pm20) REVERT: F 464 PHE cc_start: 0.7971 (m-80) cc_final: 0.7710 (m-80) REVERT: F 498 GLN cc_start: 0.9121 (mt0) cc_final: 0.8624 (mm-40) REVERT: F 583 GLU cc_start: 0.8889 (tp30) cc_final: 0.8591 (tp30) outliers start: 39 outliers final: 31 residues processed: 150 average time/residue: 0.2185 time to fit residues: 50.3359 Evaluate side-chains 142 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 107 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain D residue 389 ASP 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 389 ASP 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 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 145 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 0.0070 chunk 150 optimal weight: 0.0070 chunk 94 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 chunk 93 optimal weight: 0.0570 overall best weight: 0.2334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN D 474 GLN E 498 GLN ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 13110 Z= 0.130 Angle : 0.499 8.505 17838 Z= 0.260 Chirality : 0.045 0.318 1980 Planarity : 0.003 0.036 2322 Dihedral : 4.433 35.446 2016 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.24 % Allowed : 13.35 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.45 (0.20), residues: 1596 helix: -2.53 (0.34), residues: 162 sheet: 0.41 (0.27), residues: 338 loop : -0.11 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 436 PHE 0.014 0.001 PHE F 392 TYR 0.007 0.001 TYR E 365 ARG 0.003 0.000 ARG F 567 *********************** 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 159 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 ILE cc_start: 0.8610 (mp) cc_final: 0.8278 (tt) REVERT: B 366 SER cc_start: 0.8583 (m) cc_final: 0.8354 (p) REVERT: B 406 GLU cc_start: 0.8684 (mt-10) cc_final: 0.7944 (mt-10) REVERT: B 414 GLN cc_start: 0.7379 (tp40) cc_final: 0.7003 (tp40) REVERT: B 528 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7742 (mttm) REVERT: B 529 LYS cc_start: 0.9211 (mtpt) cc_final: 0.8963 (mmmt) REVERT: B 537 LYS cc_start: 0.8244 (ttpp) cc_final: 0.7914 (tttm) REVERT: D 516 GLU cc_start: 0.8546 (pt0) cc_final: 0.8283 (pp20) REVERT: E 324 GLU cc_start: 0.7914 (mp0) cc_final: 0.7641 (mp0) REVERT: E 368 LEU cc_start: 0.9379 (mt) cc_final: 0.9007 (pp) REVERT: E 386 LYS cc_start: 0.8643 (mtpt) cc_final: 0.8205 (tttt) REVERT: E 455 LEU cc_start: 0.9527 (tp) cc_final: 0.9229 (tt) REVERT: E 554 GLU cc_start: 0.8308 (pp20) cc_final: 0.7690 (pp20) REVERT: E 583 GLU cc_start: 0.7762 (tp30) cc_final: 0.7547 (tp30) REVERT: F 376 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.7797 (p) REVERT: F 406 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: F 464 PHE cc_start: 0.7860 (m-80) cc_final: 0.7551 (m-80) REVERT: F 466 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7607 (mtp85) REVERT: F 498 GLN cc_start: 0.9025 (mt0) cc_final: 0.8754 (mm-40) REVERT: F 583 GLU cc_start: 0.8778 (tp30) cc_final: 0.8442 (tp30) outliers start: 31 outliers final: 24 residues processed: 148 average time/residue: 0.2334 time to fit residues: 52.2232 Evaluate side-chains 145 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 466 ARG Chi-restraints excluded: chain F residue 515 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 144 optimal weight: 0.0570 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN E 498 GLN ** E 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13110 Z= 0.213 Angle : 0.520 8.713 17838 Z= 0.273 Chirality : 0.045 0.325 1980 Planarity : 0.003 0.037 2322 Dihedral : 4.511 36.743 2016 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.38 % Allowed : 14.29 % Favored : 83.33 % 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: -0.39 (0.20), residues: 1596 helix: -2.43 (0.40), residues: 138 sheet: 0.36 (0.27), residues: 336 loop : -0.10 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 436 PHE 0.021 0.001 PHE D 392 TYR 0.015 0.001 TYR B 365 ARG 0.004 0.000 ARG E 403 *********************** 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 148 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 ILE cc_start: 0.8741 (mp) cc_final: 0.8221 (tt) REVERT: B 366 SER cc_start: 0.8611 (m) cc_final: 0.8360 (p) REVERT: B 406 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8083 (mt-10) REVERT: B 414 GLN cc_start: 0.7548 (tp40) cc_final: 0.7312 (tp40) REVERT: B 529 LYS cc_start: 0.9221 (mtpt) cc_final: 0.8978 (mmmt) REVERT: B 559 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.5998 (m-80) REVERT: D 516 GLU cc_start: 0.8656 (pt0) cc_final: 0.8303 (pp20) REVERT: E 324 GLU cc_start: 0.7918 (mp0) cc_final: 0.7622 (mp0) REVERT: E 368 LEU cc_start: 0.9380 (mt) cc_final: 0.9009 (pp) REVERT: E 386 LYS cc_start: 0.8732 (mtpt) cc_final: 0.8289 (tttt) REVERT: E 455 LEU cc_start: 0.9553 (tp) cc_final: 0.9283 (tp) REVERT: E 554 GLU cc_start: 0.8308 (pp20) cc_final: 0.7618 (pp20) REVERT: F 406 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7691 (pm20) REVERT: F 464 PHE cc_start: 0.7885 (m-80) cc_final: 0.7618 (m-80) REVERT: F 466 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7638 (mtp85) REVERT: F 498 GLN cc_start: 0.9100 (mt0) cc_final: 0.8617 (mm-40) REVERT: F 583 GLU cc_start: 0.8907 (tp30) cc_final: 0.8661 (tp30) outliers start: 33 outliers final: 27 residues processed: 138 average time/residue: 0.2637 time to fit residues: 54.3398 Evaluate side-chains 142 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 112 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 401 VAL 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 389 ASP Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain F residue 324 GLU 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 466 ARG Chi-restraints excluded: chain F residue 515 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.3980 chunk 140 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 92 optimal weight: 0.0170 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN E 544 ASN F 440 ASN ** F 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13110 Z= 0.180 Angle : 0.512 8.807 17838 Z= 0.267 Chirality : 0.045 0.323 1980 Planarity : 0.003 0.037 2322 Dihedral : 4.392 36.136 2016 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.24 % Allowed : 14.57 % Favored : 83.19 % 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: -0.36 (0.21), residues: 1596 helix: -2.46 (0.40), residues: 138 sheet: 0.37 (0.27), residues: 336 loop : -0.08 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 436 PHE 0.016 0.001 PHE D 392 TYR 0.010 0.001 TYR A 369 ARG 0.005 0.000 ARG E 403 *********************** 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 146 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.6731 (m-10) REVERT: A 584 ILE cc_start: 0.8537 (mp) cc_final: 0.8289 (mm) REVERT: B 366 SER cc_start: 0.8610 (m) cc_final: 0.8360 (p) REVERT: B 406 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8091 (mt-10) REVERT: B 414 GLN cc_start: 0.7559 (tp40) cc_final: 0.7305 (tp40) REVERT: B 529 LYS cc_start: 0.9225 (mtpt) cc_final: 0.8999 (mmmt) REVERT: D 471 GLU cc_start: 0.8419 (tp30) cc_final: 0.8200 (tm-30) REVERT: D 516 GLU cc_start: 0.8602 (pt0) cc_final: 0.8331 (pp20) REVERT: E 324 GLU cc_start: 0.8003 (mp0) cc_final: 0.7723 (mp0) REVERT: E 368 LEU cc_start: 0.9365 (mt) cc_final: 0.8998 (pp) REVERT: E 386 LYS cc_start: 0.8722 (mtpt) cc_final: 0.8269 (tttt) REVERT: E 455 LEU cc_start: 0.9547 (tp) cc_final: 0.9291 (tp) REVERT: E 554 GLU cc_start: 0.8280 (pp20) cc_final: 0.7604 (pp20) REVERT: F 406 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7782 (pm20) REVERT: F 440 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8387 (p0) REVERT: F 464 PHE cc_start: 0.7933 (m-80) cc_final: 0.7629 (m-80) REVERT: F 466 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7657 (mtp85) REVERT: F 498 GLN cc_start: 0.9083 (mt0) cc_final: 0.8605 (mm-40) REVERT: F 583 GLU cc_start: 0.8919 (tp30) cc_final: 0.8653 (tp30) outliers start: 31 outliers final: 26 residues processed: 137 average time/residue: 0.2269 time to fit residues: 46.9933 Evaluate side-chains 139 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain F residue 324 GLU 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 440 ASN Chi-restraints excluded: chain F residue 466 ARG Chi-restraints excluded: chain F residue 515 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 123 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13110 Z= 0.286 Angle : 0.564 9.647 17838 Z= 0.296 Chirality : 0.046 0.329 1980 Planarity : 0.004 0.038 2322 Dihedral : 4.733 38.562 2016 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.45 % Allowed : 14.65 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.44 (0.21), residues: 1596 helix: -2.49 (0.40), residues: 138 sheet: 0.28 (0.27), residues: 338 loop : -0.13 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 436 PHE 0.017 0.001 PHE D 392 TYR 0.010 0.001 TYR C 365 ARG 0.005 0.000 ARG E 403 ********************** 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 145 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 111 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 559 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7061 (m-10) REVERT: A 584 ILE cc_start: 0.8810 (mp) cc_final: 0.8353 (mt) REVERT: B 366 SER cc_start: 0.8636 (m) cc_final: 0.8381 (p) REVERT: B 406 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8059 (mt-10) REVERT: B 529 LYS cc_start: 0.9236 (mtpt) cc_final: 0.9008 (mmmt) REVERT: B 559 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.6063 (m-80) REVERT: D 471 GLU cc_start: 0.8451 (tp30) cc_final: 0.8203 (tm-30) REVERT: D 516 GLU cc_start: 0.8704 (pt0) cc_final: 0.8376 (pp20) REVERT: E 324 GLU cc_start: 0.7981 (mp0) cc_final: 0.7684 (mp0) REVERT: E 368 LEU cc_start: 0.9374 (mt) cc_final: 0.8996 (pp) REVERT: E 386 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8275 (tttt) REVERT: E 455 LEU cc_start: 0.9566 (tp) cc_final: 0.9306 (tp) REVERT: E 554 GLU cc_start: 0.8413 (pp20) cc_final: 0.7758 (pp20) REVERT: F 340 GLU cc_start: 0.8394 (pm20) cc_final: 0.8157 (pm20) REVERT: F 406 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7743 (pm20) REVERT: F 464 PHE cc_start: 0.7980 (m-80) cc_final: 0.7713 (m-80) REVERT: F 498 GLN cc_start: 0.9098 (mt0) cc_final: 0.8624 (mm-40) REVERT: F 583 GLU cc_start: 0.8839 (tp30) cc_final: 0.8535 (tp30) outliers start: 34 outliers final: 27 residues processed: 136 average time/residue: 0.2155 time to fit residues: 44.8736 Evaluate side-chains 138 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 391 CYS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 559 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.0370 chunk 37 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 0.1980 chunk 123 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN D 474 GLN ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3577 r_free = 0.3577 target = 0.087153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.072033 restraints weight = 40339.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.074412 restraints weight = 20751.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.075987 restraints weight = 13520.703| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13110 Z= 0.182 Angle : 0.525 8.956 17838 Z= 0.274 Chirality : 0.046 0.324 1980 Planarity : 0.003 0.037 2322 Dihedral : 4.523 37.578 2016 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.09 % Allowed : 15.01 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.42 (0.21), residues: 1596 helix: -2.50 (0.40), residues: 138 sheet: 0.31 (0.27), residues: 346 loop : -0.12 (0.19), residues: 1112 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 0.008 0.001 TYR C 365 ARG 0.005 0.000 ARG E 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2537.52 seconds wall clock time: 47 minutes 8.24 seconds (2828.24 seconds total)