Starting phenix.real_space_refine on Fri Jan 19 22:19:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf4_25861/01_2024/7tf4_25861.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf4_25861/01_2024/7tf4_25861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf4_25861/01_2024/7tf4_25861.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf4_25861/01_2024/7tf4_25861.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf4_25861/01_2024/7tf4_25861.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf4_25861/01_2024/7tf4_25861.pdb" } resolution = 3.01 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 8166 2.51 5 N 2136 2.21 5 O 2436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D ASP 427": "OD1" <-> "OD2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "D PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 340": "OE1" <-> "OE2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 586": "OD1" <-> "OD2" Residue "F PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 554": "OE1" <-> "OE2" Residue "F ASP 586": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12792 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2104 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 252} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2104 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 252} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2104 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 252} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2104 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 252} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2104 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 252} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2104 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 252} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, '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: 6.86, per 1000 atoms: 0.54 Number of scatterers: 12792 At special positions: 0 Unit cell: (111.8, 109.2, 139.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2436 8.00 N 2136 7.00 C 8166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.04 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.06 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 4.54 Conformation dependent library (CDL) restraints added in 2.2 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 31 sheets defined 14.5% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.707A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.676A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.565A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.803A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.967A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.641A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.742A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.085A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.710A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'D' and resid 337 through 343 removed outlier: 3.603A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.834A pdb=" N TRP D 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 371 removed outlier: 3.511A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 390 removed outlier: 4.278A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 390 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 365 through 371 removed outlier: 3.856A pdb=" N SER E 371 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 removed outlier: 3.921A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 407 No H-bonds generated for 'chain 'E' and resid 405 through 407' Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 364 through 370 removed outlier: 4.396A pdb=" N LEU F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 removed outlier: 4.074A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 411 " --> pdb=" O ARG F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'F' and resid 438 through 443 removed outlier: 3.505A pdb=" N SER F 443 " --> pdb=" O ASN F 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.220A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.694A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.963A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.304A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 removed outlier: 7.146A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AB3, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.006A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.063A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.098A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB8, first strand: chain 'D' and resid 326 through 328 removed outlier: 5.430A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY D 566 " --> pdb=" O ASP D 574 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AC1, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.548A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AC3, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AC4, first strand: chain 'E' and resid 324 through 328 removed outlier: 3.783A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL E 539 " --> pdb=" O GLY E 550 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.768A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ASN E 437 " --> pdb=" O PHE E 374 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE E 374 " --> pdb=" O ASN E 437 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'F' and resid 325 through 328 Processing sheet with id=AD1, first strand: chain 'F' and resid 354 through 358 removed outlier: 3.996A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'F' and resid 553 through 554 353 hydrogen bonds defined for protein. 906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4101 1.35 - 1.48: 3552 1.48 - 1.61: 5409 1.61 - 1.73: 0 1.73 - 1.86: 54 Bond restraints: 13116 Sorted by residual: bond pdb=" C1 NAG F1301 " pdb=" O5 NAG F1301 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CA LEU A 517 " pdb=" CB LEU A 517 " ideal model delta sigma weight residual 1.527 1.581 -0.054 1.75e-02 3.27e+03 9.45e+00 bond pdb=" C TYR D 505 " pdb=" N GLN D 506 " ideal model delta sigma weight residual 1.329 1.382 -0.053 1.86e-02 2.89e+03 8.10e+00 bond pdb=" C TYR B 505 " pdb=" N GLN B 506 " ideal model delta sigma weight residual 1.331 1.278 0.053 2.07e-02 2.33e+03 6.50e+00 bond pdb=" C TYR C 505 " pdb=" N GLN C 506 " ideal model delta sigma weight residual 1.331 1.281 0.050 2.07e-02 2.33e+03 5.89e+00 ... (remaining 13111 not shown) Histogram of bond angle deviations from ideal: 102.02 - 109.51: 1446 109.51 - 117.00: 7756 117.00 - 124.49: 8410 124.49 - 131.98: 219 131.98 - 139.47: 13 Bond angle restraints: 17844 Sorted by residual: angle pdb=" N ILE F 410 " pdb=" CA ILE F 410 " pdb=" C ILE F 410 " ideal model delta sigma weight residual 111.91 104.62 7.29 8.90e-01 1.26e+00 6.72e+01 angle pdb=" CA CYS F 391 " pdb=" CB CYS F 391 " pdb=" SG CYS F 391 " ideal model delta sigma weight residual 114.40 127.46 -13.06 2.30e+00 1.89e-01 3.22e+01 angle pdb=" C PHE F 515 " pdb=" N GLU F 516 " pdb=" CA GLU F 516 " ideal model delta sigma weight residual 122.65 114.85 7.80 1.49e+00 4.50e-01 2.74e+01 angle pdb=" CA GLN C 506 " pdb=" CB GLN C 506 " pdb=" CG GLN C 506 " ideal model delta sigma weight residual 114.10 121.77 -7.67 2.00e+00 2.50e-01 1.47e+01 angle pdb=" CB GLU C 471 " pdb=" CG GLU C 471 " pdb=" CD GLU C 471 " ideal model delta sigma weight residual 112.60 118.63 -6.03 1.70e+00 3.46e-01 1.26e+01 ... (remaining 17839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 7136 16.25 - 32.50: 687 32.50 - 48.75: 111 48.75 - 65.00: 15 65.00 - 81.25: 13 Dihedral angle restraints: 7962 sinusoidal: 3282 harmonic: 4680 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -144.12 58.12 1 1.00e+01 1.00e-02 4.53e+01 dihedral pdb=" CA CYS F 391 " pdb=" C CYS F 391 " pdb=" N PHE F 392 " pdb=" CA PHE F 392 " ideal model delta harmonic sigma weight residual 180.00 -150.67 -29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 46.97 46.03 1 1.00e+01 1.00e-02 2.93e+01 ... (remaining 7959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1555 0.062 - 0.125: 368 0.125 - 0.187: 44 0.187 - 0.249: 5 0.249 - 0.312: 2 Chirality restraints: 1974 Sorted by residual: chirality pdb=" CB ILE A 326 " pdb=" CA ILE A 326 " pdb=" CG1 ILE A 326 " pdb=" CG2 ILE A 326 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C1 NAG F1301 " pdb=" ND2 ASN F 331 " pdb=" C2 NAG F1301 " pdb=" O5 NAG F1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C1 NAG E1301 " pdb=" ND2 ASN E 331 " pdb=" C2 NAG E1301 " pdb=" O5 NAG E1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1971 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 560 " 0.054 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO B 561 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 560 " 0.052 5.00e-02 4.00e+02 7.89e-02 9.97e+00 pdb=" N PRO E 561 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO E 561 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 561 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 392 " -0.014 2.00e-02 2.50e+03 2.28e-02 9.10e+00 pdb=" CG PHE F 392 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE F 392 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE F 392 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE F 392 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 392 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 392 " 0.002 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3442 2.80 - 3.33: 10332 3.33 - 3.85: 21118 3.85 - 4.38: 24812 4.38 - 4.90: 42275 Nonbonded interactions: 101979 Sorted by model distance: nonbonded pdb=" OD2 ASP D 578 " pdb=" OG1 THR D 581 " model vdw 2.278 2.440 nonbonded pdb=" OG1 THR E 393 " pdb=" O GLU E 516 " model vdw 2.291 2.440 nonbonded pdb=" O TYR A 495 " pdb=" OH TYR A 505 " model vdw 2.292 2.440 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.305 2.440 nonbonded pdb=" O TYR E 495 " pdb=" OH TYR E 505 " model vdw 2.314 2.440 ... (remaining 101974 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 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: 13.580 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 35.680 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.100 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13116 Z= 0.316 Angle : 0.849 19.166 17844 Z= 0.477 Chirality : 0.054 0.312 1974 Planarity : 0.008 0.082 2328 Dihedral : 12.758 81.255 4902 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.60 (0.18), residues: 1596 helix: -4.07 (0.20), residues: 144 sheet: 0.08 (0.29), residues: 320 loop : -1.03 (0.16), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 353 PHE 0.051 0.002 PHE F 392 TYR 0.033 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 123 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 406 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7988 (mt-10) REVERT: F 580 GLN cc_start: 0.6631 (mm-40) cc_final: 0.5798 (tp-100) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2784 time to fit residues: 48.8579 Evaluate side-chains 85 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.483 ------------------------------------------------------------------------------- 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: 0.4980 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 79 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN E 394 ASN F 409 GLN F 414 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13116 Z= 0.155 Angle : 0.519 13.277 17844 Z= 0.262 Chirality : 0.045 0.319 1974 Planarity : 0.005 0.061 2328 Dihedral : 5.066 36.812 2016 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.51 % Allowed : 4.26 % Favored : 95.24 % 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: -1.21 (0.19), residues: 1596 helix: -3.28 (0.27), residues: 172 sheet: 0.20 (0.28), residues: 350 loop : -0.71 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 436 PHE 0.015 0.001 PHE F 392 TYR 0.011 0.001 TYR C 380 ARG 0.002 0.000 ARG F 567 *********************** 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 107 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7263 (pm20) cc_final: 0.6798 (pm20) REVERT: B 428 ASP cc_start: 0.7067 (p0) cc_final: 0.6842 (p0) REVERT: F 414 GLN cc_start: 0.7849 (tp-100) cc_final: 0.7628 (mm-40) outliers start: 7 outliers final: 6 residues processed: 104 average time/residue: 0.2959 time to fit residues: 43.6799 Evaluate side-chains 80 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 481 ASN Chi-restraints excluded: chain F residue 556 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 140 optimal weight: 0.4980 chunk 48 optimal weight: 0.3980 chunk 113 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13116 Z= 0.160 Angle : 0.488 8.992 17844 Z= 0.249 Chirality : 0.045 0.322 1974 Planarity : 0.004 0.055 2328 Dihedral : 4.413 31.355 2016 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.79 % Allowed : 6.71 % Favored : 92.50 % 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: -0.93 (0.19), residues: 1596 helix: -2.99 (0.32), residues: 162 sheet: 0.25 (0.28), residues: 350 loop : -0.50 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 436 PHE 0.010 0.001 PHE A 559 TYR 0.010 0.001 TYR C 380 ARG 0.003 0.000 ARG F 577 *********************** 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 96 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.725 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7228 (pm20) cc_final: 0.6634 (pm20) REVERT: B 414 GLN cc_start: 0.7584 (tp-100) cc_final: 0.7287 (tp-100) REVERT: F 567 ARG cc_start: 0.0954 (mtm-85) cc_final: 0.0269 (mtm-85) outliers start: 11 outliers final: 8 residues processed: 92 average time/residue: 0.2773 time to fit residues: 37.1689 Evaluate side-chains 83 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 481 ASN Chi-restraints excluded: chain F residue 556 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 134 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN E 580 GLN F 409 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 13116 Z= 0.407 Angle : 0.595 12.179 17844 Z= 0.303 Chirality : 0.047 0.288 1974 Planarity : 0.004 0.050 2328 Dihedral : 4.900 28.476 2016 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.30 % Allowed : 7.72 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.87 (0.20), residues: 1596 helix: -2.54 (0.38), residues: 134 sheet: 0.02 (0.27), residues: 360 loop : -0.50 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 436 PHE 0.026 0.002 PHE A 559 TYR 0.013 0.002 TYR A 369 ARG 0.004 0.001 ARG D 452 *********************** 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 93 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 1.539 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7296 (pm20) cc_final: 0.6703 (pm20) REVERT: E 584 ILE cc_start: 0.8130 (mm) cc_final: 0.7883 (mm) REVERT: F 567 ARG cc_start: 0.1272 (mtm-85) cc_final: 0.0381 (mtm-85) REVERT: F 584 ILE cc_start: 0.6999 (mp) cc_final: 0.6737 (mm) outliers start: 18 outliers final: 8 residues processed: 88 average time/residue: 0.2785 time to fit residues: 35.7079 Evaluate side-chains 77 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 481 ASN Chi-restraints excluded: chain F residue 556 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.0980 chunk 85 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN F 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13116 Z= 0.175 Angle : 0.495 10.324 17844 Z= 0.251 Chirality : 0.045 0.298 1974 Planarity : 0.004 0.051 2328 Dihedral : 4.402 28.750 2016 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.01 % Allowed : 8.80 % Favored : 90.19 % 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: -0.73 (0.20), residues: 1596 helix: -2.24 (0.42), residues: 122 sheet: -0.01 (0.27), residues: 362 loop : -0.41 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 436 PHE 0.011 0.001 PHE A 559 TYR 0.009 0.001 TYR C 380 ARG 0.002 0.000 ARG F 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 95 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 1.506 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7198 (pm20) cc_final: 0.6751 (pm20) REVERT: E 584 ILE cc_start: 0.8073 (mm) cc_final: 0.7813 (mm) REVERT: F 567 ARG cc_start: 0.1014 (mtm-85) cc_final: 0.0126 (mtm-85) outliers start: 14 outliers final: 11 residues processed: 90 average time/residue: 0.2694 time to fit residues: 35.4115 Evaluate side-chains 80 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 558 LYS Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 481 ASN Chi-restraints excluded: chain F residue 556 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 0.5980 chunk 125 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 0.0070 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN C 484 GLN ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13116 Z= 0.156 Angle : 0.475 9.833 17844 Z= 0.242 Chirality : 0.045 0.299 1974 Planarity : 0.004 0.051 2328 Dihedral : 4.188 27.674 2016 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.01 % Allowed : 9.96 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.20), residues: 1596 helix: -2.22 (0.47), residues: 106 sheet: 0.10 (0.27), residues: 360 loop : -0.36 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 436 PHE 0.009 0.001 PHE A 559 TYR 0.009 0.001 TYR C 380 ARG 0.002 0.000 ARG F 577 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 1.614 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7207 (pm20) cc_final: 0.6795 (pm20) REVERT: F 567 ARG cc_start: 0.1097 (mtm-85) cc_final: -0.0392 (mtt90) outliers start: 14 outliers final: 12 residues processed: 84 average time/residue: 0.3159 time to fit residues: 38.3664 Evaluate side-chains 77 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 481 ASN Chi-restraints excluded: chain F residue 556 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.0670 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 84 optimal weight: 0.0970 chunk 150 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13116 Z= 0.186 Angle : 0.484 10.679 17844 Z= 0.246 Chirality : 0.045 0.301 1974 Planarity : 0.004 0.051 2328 Dihedral : 4.151 25.737 2016 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.23 % Allowed : 10.46 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1596 helix: -2.15 (0.48), residues: 106 sheet: 0.13 (0.27), residues: 360 loop : -0.32 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 PHE 0.010 0.001 PHE A 559 TYR 0.008 0.001 TYR D 369 ARG 0.003 0.000 ARG C 357 *********************** 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 89 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7205 (pm20) cc_final: 0.6794 (pm20) REVERT: F 567 ARG cc_start: 0.0868 (mtm-85) cc_final: -0.0112 (mtm-85) outliers start: 17 outliers final: 14 residues processed: 83 average time/residue: 0.2534 time to fit residues: 31.4846 Evaluate side-chains 78 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 481 ASN Chi-restraints excluded: chain F residue 556 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.1980 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 118 optimal weight: 0.0770 chunk 136 optimal weight: 5.9990 chunk 144 optimal weight: 0.0010 overall best weight: 0.4548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13116 Z= 0.142 Angle : 0.464 10.687 17844 Z= 0.236 Chirality : 0.045 0.306 1974 Planarity : 0.004 0.051 2328 Dihedral : 3.936 24.049 2016 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.01 % Allowed : 10.89 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1596 helix: -2.52 (0.42), residues: 126 sheet: 0.30 (0.27), residues: 354 loop : -0.31 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 PHE 0.007 0.001 PHE A 559 TYR 0.009 0.001 TYR C 380 ARG 0.006 0.000 ARG C 357 *********************** 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 96 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 1.554 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7189 (pm20) cc_final: 0.6776 (pm20) REVERT: F 403 ARG cc_start: 0.7619 (ptt-90) cc_final: 0.6982 (ptt-90) outliers start: 14 outliers final: 12 residues processed: 89 average time/residue: 0.2797 time to fit residues: 36.6579 Evaluate side-chains 86 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 556 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 139 optimal weight: 0.0870 chunk 92 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13116 Z= 0.169 Angle : 0.471 10.711 17844 Z= 0.241 Chirality : 0.045 0.302 1974 Planarity : 0.004 0.051 2328 Dihedral : 3.953 22.008 2016 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.15 % Allowed : 10.97 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1596 helix: -2.46 (0.41), residues: 134 sheet: 0.33 (0.27), residues: 352 loop : -0.27 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 436 PHE 0.009 0.001 PHE A 559 TYR 0.007 0.001 TYR C 380 ARG 0.007 0.000 ARG C 357 *********************** 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 88 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 1.503 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7197 (pm20) cc_final: 0.6820 (pm20) REVERT: F 567 ARG cc_start: 0.0608 (mtm-85) cc_final: -0.0995 (mtt90) outliers start: 16 outliers final: 15 residues processed: 81 average time/residue: 0.2449 time to fit residues: 30.1967 Evaluate side-chains 87 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 481 ASN Chi-restraints excluded: chain F residue 556 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 155 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 75 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 13116 Z= 0.162 Angle : 0.467 10.777 17844 Z= 0.239 Chirality : 0.045 0.302 1974 Planarity : 0.004 0.051 2328 Dihedral : 3.892 21.762 2016 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.08 % Allowed : 11.18 % Favored : 87.73 % 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: -0.53 (0.20), residues: 1596 helix: -2.42 (0.43), residues: 122 sheet: 0.29 (0.27), residues: 352 loop : -0.28 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 PHE 0.008 0.001 PHE A 559 TYR 0.008 0.001 TYR C 380 ARG 0.006 0.000 ARG C 357 ********************** 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 87 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7193 (pm20) cc_final: 0.6820 (pm20) REVERT: F 567 ARG cc_start: 0.0604 (mtm-85) cc_final: -0.0998 (mtt90) outliers start: 15 outliers final: 14 residues processed: 80 average time/residue: 0.2463 time to fit residues: 30.2376 Evaluate side-chains 84 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 556 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.097639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.078734 restraints weight = 30438.029| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.19 r_work: 0.3181 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13116 Z= 0.189 Angle : 0.478 10.584 17844 Z= 0.244 Chirality : 0.045 0.301 1974 Planarity : 0.004 0.051 2328 Dihedral : 3.941 21.650 2016 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.44 % Allowed : 10.82 % Favored : 87.73 % 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: -0.53 (0.20), residues: 1596 helix: -2.38 (0.41), residues: 134 sheet: 0.31 (0.27), residues: 352 loop : -0.27 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 PHE 0.010 0.001 PHE A 559 TYR 0.007 0.001 TYR C 380 ARG 0.007 0.000 ARG C 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2548.53 seconds wall clock time: 47 minutes 22.61 seconds (2842.61 seconds total)