Starting phenix.real_space_refine on Sat Jul 4 05:28:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bpf_16151/07_2026/8bpf_16151.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bpf_16151/07_2026/8bpf_16151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bpf_16151/07_2026/8bpf_16151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bpf_16151/07_2026/8bpf_16151.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8bpf_16151/07_2026/8bpf_16151.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bpf_16151/07_2026/8bpf_16151.cif" model { file = "/net/cci-nas-00/data/ceres_data/8bpf_16151/07_2026/8bpf_16151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bpf_16151/07_2026/8bpf_16151.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 94 5.16 5 C 11697 2.51 5 N 3148 2.21 5 O 3654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18593 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1790 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 212} Chain: "B" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1756 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 207} Chain: "C" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1740 Classifications: {'peptide': 224} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "F" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1742 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1757 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 207} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 805 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "J" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 827 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain breaks: 1 Chain: "K" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1778 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Chain: "L" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 115} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.21, per 1000 atoms: 0.23 Number of scatterers: 18593 At special positions: 0 Unit cell: (189, 100.44, 170.64, 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 94 16.00 O 3654 8.00 N 3148 7.00 C 11697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS J 68 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 414 " - pdb=" SG CYS C 414 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.04 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.04 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.03 Simple disulfide: pdb=" SG CYS D 414 " - pdb=" SG CYS E 414 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.04 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 426 " distance=2.03 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.03 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 414 " - pdb=" SG CYS G 414 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.04 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.04 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 414 " - pdb=" SG CYS K 414 " distance=2.03 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.04 Simple disulfide: pdb=" SG CYS I 37 " - pdb=" SG CYS I 104 " distance=2.03 Simple disulfide: pdb=" SG CYS I 49 " - pdb=" SG CYS I 58 " distance=1.58 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.04 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS L 575 " distance=2.04 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.03 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.04 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 601 " - " ASN A 563 " " NAG B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 563 " " NAG E 601 " - " ASN E 563 " " NAG F 601 " - " ASN F 563 " " NAG G 601 " - " ASN G 563 " " NAG H 601 " - " ASN H 563 " " NAG K 601 " - " ASN K 563 " " NAG L 601 " - " ASN L 563 " " NAG M 1 " - " ASN J 48 " Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 630.8 milliseconds 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4536 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 58 sheets defined 12.2% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.792A pdb=" N LEU A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.610A pdb=" N LEU A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.689A pdb=" N LEU B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 removed outlier: 3.855A pdb=" N TRP B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 466 removed outlier: 3.650A pdb=" N ASN B 465 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 531 removed outlier: 3.576A pdb=" N GLY B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 496 through 498 No H-bonds generated for 'chain 'C' and resid 496 through 498' Processing helix chain 'C' and resid 524 through 529 Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.908A pdb=" N TRP D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 466 removed outlier: 4.248A pdb=" N LEU D 466 " --> pdb=" O GLU D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 531 Processing helix chain 'E' and resid 353 through 361 removed outlier: 3.821A pdb=" N THR E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.815A pdb=" N GLY E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 466 removed outlier: 3.710A pdb=" N ASN E 465 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E 466 " --> pdb=" O GLN E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 531 Processing helix chain 'E' and resid 553 through 557 removed outlier: 3.553A pdb=" N THR E 556 " --> pdb=" O ASP E 553 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY E 557 " --> pdb=" O LYS E 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 553 through 557' Processing helix chain 'F' and resid 353 through 361 removed outlier: 3.687A pdb=" N THR F 360 " --> pdb=" O SER F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 removed outlier: 4.001A pdb=" N TRP F 418 " --> pdb=" O CYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 466 removed outlier: 3.545A pdb=" N ASN F 465 " --> pdb=" O GLU F 462 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU F 466 " --> pdb=" O GLN F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 498 No H-bonds generated for 'chain 'F' and resid 496 through 498' Processing helix chain 'F' and resid 524 through 529 Processing helix chain 'F' and resid 553 through 558 removed outlier: 3.562A pdb=" N GLY F 557 " --> pdb=" O LYS F 554 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS F 558 " --> pdb=" O SER F 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 361 removed outlier: 3.958A pdb=" N THR G 360 " --> pdb=" O SER G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 Processing helix chain 'G' and resid 525 through 529 Processing helix chain 'H' and resid 353 through 360 Processing helix chain 'H' and resid 414 through 419 Processing helix chain 'H' and resid 524 through 529 Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 116 through 120 Processing helix chain 'K' and resid 353 through 360 removed outlier: 3.538A pdb=" N LEU K 359 " --> pdb=" O ALA K 355 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR K 360 " --> pdb=" O SER K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 421 removed outlier: 3.807A pdb=" N TRP K 418 " --> pdb=" O CYS K 414 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY K 421 " --> pdb=" O ASP K 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 466 removed outlier: 3.536A pdb=" N LEU K 466 " --> pdb=" O GLU K 462 " (cutoff:3.500A) Processing helix chain 'K' and resid 496 through 500 Processing helix chain 'K' and resid 524 through 529 Processing helix chain 'L' and resid 526 through 530 removed outlier: 3.947A pdb=" N ASN L 529 " --> pdb=" O GLU L 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA2, first strand: chain 'A' and resid 380 through 384 Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 457 Processing sheet with id=AA4, first strand: chain 'A' and resid 453 through 457 removed outlier: 5.142A pdb=" N THR A 477 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA A 517 " --> pdb=" O THR A 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.688A pdb=" N MET A 489 " --> pdb=" O THR A 535 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.688A pdb=" N MET A 489 " --> pdb=" O THR A 535 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 534 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 563 removed outlier: 7.201A pdb=" N TYR A 562 " --> pdb=" O ASN B 563 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 565 through 569 Processing sheet with id=AA9, first strand: chain 'B' and resid 379 through 383 Processing sheet with id=AB1, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.503A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.503A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 493 through 494 removed outlier: 3.821A pdb=" N TYR B 534 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 552 " --> pdb=" O TYR B 534 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 347 through 350 removed outlier: 4.292A pdb=" N ASP C 371 " --> pdb=" O PHE C 405 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE C 405 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 379 through 383 removed outlier: 3.611A pdb=" N THR C 379 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C 424 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 428 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 437 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N HIS C 430 " --> pdb=" O SER C 435 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER C 435 " --> pdb=" O HIS C 430 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 455 through 457 removed outlier: 3.680A pdb=" N THR C 473 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER C 519 " --> pdb=" O CYS C 474 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE C 520 " --> pdb=" O VAL C 501 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 455 through 457 removed outlier: 3.680A pdb=" N THR C 473 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 476 " --> pdb=" O ALA C 517 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 493 through 494 removed outlier: 3.566A pdb=" N MET C 489 " --> pdb=" O THR C 535 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.972A pdb=" N THR D 366 " --> pdb=" O ILE D 350 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 365 " --> pdb=" O ALA D 411 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 411 " --> pdb=" O LEU D 365 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 379 through 383 removed outlier: 4.253A pdb=" N THR D 379 " --> pdb=" O THR D 429 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.529A pdb=" N THR D 473 " --> pdb=" O LEU D 457 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.529A pdb=" N THR D 473 " --> pdb=" O LEU D 457 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 493 through 494 Processing sheet with id=AC5, first strand: chain 'D' and resid 565 through 567 removed outlier: 3.683A pdb=" N LEU D 566 " --> pdb=" O SER E 565 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL E 567 " --> pdb=" O LEU D 566 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 346 through 350 removed outlier: 3.591A pdb=" N ILE E 350 " --> pdb=" O THR E 366 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR E 366 " --> pdb=" O ILE E 350 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU E 368 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLY E 409 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR E 370 " --> pdb=" O ALA E 407 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ALA E 407 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU E 372 " --> pdb=" O PHE E 405 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 379 through 383 Processing sheet with id=AC8, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.505A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AD1, first strand: chain 'F' and resid 346 through 350 removed outlier: 4.093A pdb=" N ARG F 346 " --> pdb=" O THR F 370 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR F 370 " --> pdb=" O ARG F 346 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR F 366 " --> pdb=" O ILE F 350 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 380 through 383 removed outlier: 4.061A pdb=" N PHE F 424 " --> pdb=" O ILE F 441 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE F 441 " --> pdb=" O PHE F 424 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 453 through 457 removed outlier: 3.825A pdb=" N VAL F 476 " --> pdb=" O ALA F 517 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 453 through 457 removed outlier: 3.825A pdb=" N VAL F 476 " --> pdb=" O ALA F 517 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 493 through 494 Processing sheet with id=AD6, first strand: chain 'F' and resid 566 through 567 Processing sheet with id=AD7, first strand: chain 'G' and resid 347 through 350 removed outlier: 3.749A pdb=" N THR G 366 " --> pdb=" O ILE G 350 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 379 through 381 Processing sheet with id=AD9, first strand: chain 'G' and resid 399 through 400 removed outlier: 3.742A pdb=" N THR G 404 " --> pdb=" O HIS G 400 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.619A pdb=" N THR G 473 " --> pdb=" O LEU G 457 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 469 through 471 Processing sheet with id=AE3, first strand: chain 'G' and resid 485 through 489 Processing sheet with id=AE4, first strand: chain 'H' and resid 347 through 350 removed outlier: 3.534A pdb=" N THR H 366 " --> pdb=" O ILE H 350 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR H 370 " --> pdb=" O ALA H 407 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ALA H 407 " --> pdb=" O THR H 370 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU H 372 " --> pdb=" O PHE H 405 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 379 through 383 removed outlier: 4.351A pdb=" N THR H 379 " --> pdb=" O THR H 429 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR H 429 " --> pdb=" O THR H 379 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS H 426 " --> pdb=" O GLN H 439 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN H 439 " --> pdb=" O CYS H 426 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.654A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER H 519 " --> pdb=" O CYS H 474 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL H 501 " --> pdb=" O ILE H 520 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.654A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 493 through 494 Processing sheet with id=AE9, first strand: chain 'H' and resid 562 through 564 removed outlier: 6.214A pdb=" N ASN H 563 " --> pdb=" O VAL K 564 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'I' and resid 32 through 38 removed outlier: 3.681A pdb=" N CYS I 37 " --> pdb=" O PHE I 87 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 100 through 105 removed outlier: 3.590A pdb=" N CYS I 104 " --> pdb=" O GLN I 116 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN I 116 " --> pdb=" O CYS I 104 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.806A pdb=" N ARG J 20 " --> pdb=" O GLU J 34 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ASN L 563 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG J 35 " --> pdb=" O ASN L 563 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 40 through 41 Processing sheet with id=AF5, first strand: chain 'J' and resid 103 through 104 removed outlier: 6.677A pdb=" N TYR J 103 " --> pdb=" O CYS L 575 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'J' and resid 110 through 115 Processing sheet with id=AF7, first strand: chain 'K' and resid 347 through 350 removed outlier: 4.377A pdb=" N THR K 366 " --> pdb=" O ILE K 350 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU K 365 " --> pdb=" O ALA K 411 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA K 411 " --> pdb=" O LEU K 365 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 379 through 383 removed outlier: 3.574A pdb=" N THR K 379 " --> pdb=" O THR K 429 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR K 425 " --> pdb=" O THR K 383 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.524A pdb=" N TYR K 455 " --> pdb=" O LEU K 475 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER K 519 " --> pdb=" O CYS K 474 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 487 through 489 removed outlier: 3.583A pdb=" N MET K 489 " --> pdb=" O THR K 535 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR K 535 " --> pdb=" O MET K 489 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 454 through 457 removed outlier: 3.923A pdb=" N ILE L 520 " --> pdb=" O VAL L 501 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 454 through 457 Processing sheet with id=AG4, first strand: chain 'L' and resid 489 through 490 557 hydrogen bonds defined for protein. 1383 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: 2.16 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5614 1.34 - 1.46: 4144 1.46 - 1.58: 9163 1.58 - 1.71: 0 1.71 - 1.83: 128 Bond restraints: 19049 Sorted by residual: bond pdb=" C MET B 568 " pdb=" N SER B 569 " ideal model delta sigma weight residual 1.331 1.380 -0.049 1.33e-02 5.65e+03 1.34e+01 bond pdb=" N VAL A 552 " pdb=" CA VAL A 552 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.25e+01 bond pdb=" N VAL L 552 " pdb=" CA VAL L 552 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.18e+01 bond pdb=" N VAL C 390 " pdb=" CA VAL C 390 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.15e-02 7.56e+03 1.13e+01 bond pdb=" N VAL A 538 " pdb=" CA VAL A 538 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.11e-02 8.12e+03 1.11e+01 ... (remaining 19044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 24012 1.59 - 3.19: 1798 3.19 - 4.78: 226 4.78 - 6.37: 21 6.37 - 7.97: 5 Bond angle restraints: 26062 Sorted by residual: angle pdb=" CA ARG L 546 " pdb=" CB ARG L 546 " pdb=" CG ARG L 546 " ideal model delta sigma weight residual 114.10 122.07 -7.97 2.00e+00 2.50e-01 1.59e+01 angle pdb=" N LEU C 466 " pdb=" CA LEU C 466 " pdb=" C LEU C 466 " ideal model delta sigma weight residual 114.62 110.14 4.48 1.14e+00 7.69e-01 1.55e+01 angle pdb=" N ASN A 545 " pdb=" CA ASN A 545 " pdb=" C ASN A 545 " ideal model delta sigma weight residual 113.16 108.32 4.84 1.24e+00 6.50e-01 1.52e+01 angle pdb=" CA ALA F 482 " pdb=" C ALA F 482 " pdb=" O ALA F 482 " ideal model delta sigma weight residual 122.37 117.94 4.43 1.15e+00 7.56e-01 1.48e+01 angle pdb=" CA ASP I 111 " pdb=" C ASP I 111 " pdb=" O ASP I 111 " ideal model delta sigma weight residual 121.36 116.82 4.54 1.20e+00 6.94e-01 1.43e+01 ... (remaining 26057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10477 17.97 - 35.94: 834 35.94 - 53.91: 147 53.91 - 71.88: 27 71.88 - 89.85: 20 Dihedral angle restraints: 11505 sinusoidal: 4541 harmonic: 6964 Sorted by residual: dihedral pdb=" CB CYS A 367 " pdb=" SG CYS A 367 " pdb=" SG CYS A 426 " pdb=" CB CYS A 426 " ideal model delta sinusoidal sigma weight residual -86.00 -173.30 87.30 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS J 14 " pdb=" SG CYS J 14 " pdb=" SG CYS L 575 " pdb=" CB CYS L 575 " ideal model delta sinusoidal sigma weight residual 93.00 174.02 -81.02 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CB CYS J 12 " pdb=" SG CYS J 12 " pdb=" SG CYS J 100 " pdb=" CB CYS J 100 " ideal model delta sinusoidal sigma weight residual 93.00 156.85 -63.85 1 1.00e+01 1.00e-02 5.37e+01 ... (remaining 11502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.162: 3041 0.162 - 0.325: 50 0.325 - 0.487: 3 0.487 - 0.650: 0 0.650 - 0.812: 1 Chirality restraints: 3095 Sorted by residual: chirality pdb=" C1 NAG F 601 " pdb=" ND2 ASN F 563 " pdb=" C2 NAG F 601 " pdb=" O5 NAG F 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.59 -0.81 2.00e-01 2.50e+01 1.65e+01 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 563 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" C1 NAG K 601 " pdb=" ND2 ASN K 563 " pdb=" C2 NAG K 601 " pdb=" O5 NAG K 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.77 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 3092 not shown) Planarity restraints: 3338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 563 " -0.054 2.00e-02 2.50e+03 6.90e-02 5.95e+01 pdb=" CG ASN A 563 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 563 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 563 " 0.119 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 563 " 0.041 2.00e-02 2.50e+03 4.55e-02 2.59e+01 pdb=" CG ASN E 563 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN E 563 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN E 563 " -0.073 2.00e-02 2.50e+03 pdb=" C1 NAG E 601 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 563 " -0.042 2.00e-02 2.50e+03 4.48e-02 2.50e+01 pdb=" CG ASN K 563 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN K 563 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN K 563 " 0.071 2.00e-02 2.50e+03 pdb=" C1 NAG K 601 " -0.054 2.00e-02 2.50e+03 ... (remaining 3335 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4069 2.79 - 3.32: 17185 3.32 - 3.85: 28108 3.85 - 4.37: 31808 4.37 - 4.90: 55395 Nonbonded interactions: 136565 Sorted by model distance: nonbonded pdb=" OD1 ASN D 402 " pdb=" OG1 THR D 404 " model vdw 2.267 3.040 nonbonded pdb=" O LEU H 372 " pdb=" OG1 THR H 404 " model vdw 2.283 3.040 nonbonded pdb=" OG SER L 469 " pdb=" O VAL L 523 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR K 379 " pdb=" OG1 THR K 429 " model vdw 2.304 3.040 nonbonded pdb=" O ILE J 5 " pdb=" OG1 THR J 18 " model vdw 2.309 3.040 ... (remaining 136560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568 or resid 601)) selection = (chain 'B' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568 or resid 601)) selection = (chain 'C' and (resid 346 through 568 or resid 601)) selection = (chain 'D' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 601)) selection = (chain 'E' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 601)) selection = (chain 'F' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 601)) selection = (chain 'G' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 601)) selection = (chain 'H' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568 or resid 601)) selection = (chain 'K' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568 or resid 601)) } 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=0.00 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: 6.420 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.320 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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 : 0.007 0.453 19090 Z= 0.468 Angle : 0.900 22.834 26156 Z= 0.567 Chirality : 0.062 0.812 3095 Planarity : 0.006 0.124 3327 Dihedral : 13.559 89.850 6882 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.17), residues: 2344 helix: -1.45 (0.32), residues: 221 sheet: 0.04 (0.18), residues: 842 loop : -1.98 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 467 TYR 0.020 0.001 TYR F 500 PHE 0.028 0.002 PHE F 354 TRP 0.020 0.001 TRP C 418 HIS 0.007 0.001 HIS A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.44 (19049) covalent geometry : angle 0.85044 / 0.56 (26062) SS BOND : bond 0.08429 / 6.29 ( 29) SS BOND : angle 4.05289 / 3.21 ( 58) hydrogen bonds : bond 0.27200 / 18.37 ( 482) hydrogen bonds : angle 9.38645 / 6.62 ( 1383) link_BETA1-4 : bond 0.02201 / 1.16 ( 1) link_BETA1-4 : angle 4.43257 / 2.33 ( 3) link_NAG-ASN : bond 0.01810 / 1.18 ( 11) link_NAG-ASN : angle 6.36976 / 4.23 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.657 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 TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.8486 (pttt) cc_final: 0.7472 (mmtt) REVERT: A 445 LYS cc_start: 0.8064 (mttt) cc_final: 0.7862 (mtmm) REVERT: A 466 LEU cc_start: 0.8594 (mp) cc_final: 0.8347 (mm) REVERT: B 376 ASP cc_start: 0.8158 (p0) cc_final: 0.7834 (p0) REVERT: H 391 LYS cc_start: 0.8123 (tptt) cc_final: 0.7656 (tmtt) REVERT: I 121 ASN cc_start: 0.8569 (m110) cc_final: 0.8062 (m110) REVERT: J 22 ILE cc_start: 0.8427 (pt) cc_final: 0.8063 (pt) REVERT: J 31 ASP cc_start: 0.8731 (m-30) cc_final: 0.8483 (m-30) REVERT: K 506 MET cc_start: 0.7214 (mtt) cc_final: 0.7007 (mtt) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.1669 time to fit residues: 81.5635 Evaluate side-chains 198 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 ASN ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 GLN ** F 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 463 GLN G 510 GLN H 395 ASN J 45 ASN ** K 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 430 HIS K 439 GLN ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 463 GLN ** L 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.094069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.062653 restraints weight = 66546.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.064762 restraints weight = 36502.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.066016 restraints weight = 26096.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.066866 restraints weight = 21453.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.067402 restraints weight = 19088.501| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19090 Z= 0.170 Angle : 0.689 9.049 26156 Z= 0.360 Chirality : 0.048 0.204 3095 Planarity : 0.005 0.056 3327 Dihedral : 4.336 18.121 2549 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.83 % Favored : 91.13 % Rotamer: Outliers : 1.56 % Allowed : 10.26 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.17), residues: 2344 helix: -1.45 (0.30), residues: 235 sheet: 0.26 (0.18), residues: 831 loop : -1.85 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 514 TYR 0.033 0.002 TYR H 562 PHE 0.028 0.002 PHE L 479 TRP 0.018 0.002 TRP K 418 HIS 0.012 0.001 HIS L 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (19049) covalent geometry : angle 0.68168 / 0.36 (26062) SS BOND : bond 0.00584 / 0.37 ( 29) SS BOND : angle 1.43682 / 1.01 ( 58) hydrogen bonds : bond 0.05106 / 3.47 ( 482) hydrogen bonds : angle 6.70560 / 4.70 ( 1383) link_BETA1-4 : bond 0.00890 / 0.47 ( 1) link_BETA1-4 : angle 2.03145 / 1.07 ( 3) link_NAG-ASN : bond 0.00266 / 0.17 ( 11) link_NAG-ASN : angle 2.34429 / 1.69 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. 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: symmetry clash REVERT: A 364 LYS cc_start: 0.8240 (pttt) cc_final: 0.7540 (mmmt) REVERT: A 423 ARG cc_start: 0.7911 (mtm110) cc_final: 0.7229 (tmm160) REVERT: A 445 LYS cc_start: 0.8241 (mttt) cc_final: 0.7942 (mtmm) REVERT: B 376 ASP cc_start: 0.8404 (p0) cc_final: 0.8051 (p0) REVERT: C 373 THR cc_start: 0.6926 (t) cc_final: 0.5782 (p) REVERT: G 375 TYR cc_start: 0.8087 (m-10) cc_final: 0.7770 (m-80) REVERT: G 376 ASP cc_start: 0.7168 (p0) cc_final: 0.6686 (p0) REVERT: G 553 ASP cc_start: 0.7827 (t0) cc_final: 0.7445 (t70) REVERT: H 391 LYS cc_start: 0.8145 (tptt) cc_final: 0.7929 (tptp) REVERT: H 568 MET cc_start: 0.6806 (mtm) cc_final: 0.6387 (tmm) REVERT: I 121 ASN cc_start: 0.8570 (m110) cc_final: 0.8028 (t0) REVERT: J 31 ASP cc_start: 0.8700 (m-30) cc_final: 0.8385 (m-30) REVERT: J 134 TYR cc_start: 0.6893 (m-10) cc_final: 0.6669 (m-10) REVERT: K 364 LYS cc_start: 0.7673 (ptpp) cc_final: 0.5937 (ptpp) REVERT: K 506 MET cc_start: 0.7835 (mtt) cc_final: 0.7494 (mtt) REVERT: L 515 TYR cc_start: 0.7275 (m-80) cc_final: 0.6891 (m-80) REVERT: L 534 TYR cc_start: 0.8467 (m-10) cc_final: 0.7966 (m-10) outliers start: 33 outliers final: 18 residues processed: 234 average time/residue: 0.1386 time to fit residues: 47.2963 Evaluate side-chains 194 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 545 ASN Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 405 PHE Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 467 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 98 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 204 optimal weight: 3.9990 chunk 199 optimal weight: 30.0000 chunk 225 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 490 GLN F 430 HIS ** F 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 510 GLN H 395 ASN ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 490 GLN H 545 ASN I 85 ASN ** K 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.092112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.060593 restraints weight = 67162.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.062607 restraints weight = 36996.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.063802 restraints weight = 26711.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.064563 restraints weight = 22111.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.065098 restraints weight = 19772.876| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19090 Z= 0.195 Angle : 0.686 11.047 26156 Z= 0.353 Chirality : 0.048 0.169 3095 Planarity : 0.005 0.053 3327 Dihedral : 4.475 18.446 2549 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.09 % Favored : 90.83 % Rotamer: Outliers : 1.80 % Allowed : 14.33 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.17), residues: 2344 helix: -1.39 (0.30), residues: 236 sheet: 0.22 (0.18), residues: 833 loop : -1.86 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 491 TYR 0.022 0.002 TYR H 562 PHE 0.024 0.002 PHE D 479 TRP 0.013 0.002 TRP C 528 HIS 0.007 0.001 HIS K 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (19049) covalent geometry : angle 0.68113 / 0.35 (26062) SS BOND : bond 0.00574 / 0.37 ( 29) SS BOND : angle 1.31225 / 0.90 ( 58) hydrogen bonds : bond 0.04419 / 3.01 ( 482) hydrogen bonds : angle 6.21615 / 4.37 ( 1383) link_BETA1-4 : bond 0.00460 / 0.24 ( 1) link_BETA1-4 : angle 1.80142 / 0.94 ( 3) link_NAG-ASN : bond 0.00414 / 0.25 ( 11) link_NAG-ASN : angle 1.93158 / 1.30 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. 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 364 LYS cc_start: 0.8357 (pttt) cc_final: 0.7665 (mmmt) REVERT: A 445 LYS cc_start: 0.8159 (mttt) cc_final: 0.7866 (mtmm) REVERT: B 376 ASP cc_start: 0.8410 (p0) cc_final: 0.8063 (p0) REVERT: G 375 TYR cc_start: 0.8106 (m-10) cc_final: 0.7689 (m-10) REVERT: G 376 ASP cc_start: 0.7285 (p0) cc_final: 0.6833 (p0) REVERT: G 553 ASP cc_start: 0.7874 (t0) cc_final: 0.7600 (t70) REVERT: H 391 LYS cc_start: 0.8174 (tptt) cc_final: 0.7951 (tptp) REVERT: I 71 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7768 (tm-30) REVERT: I 121 ASN cc_start: 0.8636 (m110) cc_final: 0.8101 (t0) REVERT: J 31 ASP cc_start: 0.8728 (m-30) cc_final: 0.8452 (m-30) REVERT: L 515 TYR cc_start: 0.7555 (m-80) cc_final: 0.6956 (m-80) REVERT: L 534 TYR cc_start: 0.8659 (m-10) cc_final: 0.8213 (m-10) outliers start: 38 outliers final: 23 residues processed: 212 average time/residue: 0.1384 time to fit residues: 42.8419 Evaluate side-chains 197 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 395 ASN Chi-restraints excluded: chain H residue 405 PHE Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain K residue 467 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 115 optimal weight: 20.0000 chunk 201 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 199 optimal weight: 30.0000 chunk 106 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 GLN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 490 GLN ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 123 HIS ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 540 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.088896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.057504 restraints weight = 68136.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.059161 restraints weight = 41186.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.060131 restraints weight = 31070.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.060796 restraints weight = 26394.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.061057 restraints weight = 23864.385| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 19090 Z= 0.303 Angle : 0.773 13.960 26156 Z= 0.400 Chirality : 0.050 0.221 3095 Planarity : 0.006 0.052 3327 Dihedral : 4.978 19.284 2549 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.20 % Favored : 89.72 % Rotamer: Outliers : 3.26 % Allowed : 16.46 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.17), residues: 2344 helix: -1.72 (0.28), residues: 248 sheet: -0.06 (0.18), residues: 842 loop : -2.05 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 514 TYR 0.018 0.002 TYR B 515 PHE 0.035 0.003 PHE D 479 TRP 0.019 0.002 TRP G 488 HIS 0.010 0.002 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00714 / 0.30 (19049) covalent geometry : angle 0.76522 / 0.40 (26062) SS BOND : bond 0.00806 / 0.53 ( 29) SS BOND : angle 1.71468 / 1.15 ( 58) hydrogen bonds : bond 0.04716 / 3.21 ( 482) hydrogen bonds : angle 6.15263 / 4.32 ( 1383) link_BETA1-4 : bond 0.00235 / 0.12 ( 1) link_BETA1-4 : angle 1.46380 / 0.75 ( 3) link_NAG-ASN : bond 0.00800 / 0.50 ( 11) link_NAG-ASN : angle 2.31311 / 1.53 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 178 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. 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 359 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8599 (tt) REVERT: A 364 LYS cc_start: 0.8567 (pttt) cc_final: 0.7781 (mmmt) REVERT: A 445 LYS cc_start: 0.8213 (mttt) cc_final: 0.7894 (mtmm) REVERT: A 456 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8172 (mp) REVERT: A 465 ASN cc_start: 0.8931 (m-40) cc_final: 0.8712 (m-40) REVERT: A 506 MET cc_start: 0.8085 (mtp) cc_final: 0.7856 (mtm) REVERT: B 376 ASP cc_start: 0.8434 (p0) cc_final: 0.8106 (p0) REVERT: C 348 PHE cc_start: 0.8648 (m-80) cc_final: 0.8444 (m-80) REVERT: E 521 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8606 (tp) REVERT: F 568 MET cc_start: 0.6840 (tpp) cc_final: 0.5770 (tpt) REVERT: G 510 GLN cc_start: 0.8326 (tp-100) cc_final: 0.8079 (tp-100) REVERT: H 391 LYS cc_start: 0.8291 (tptt) cc_final: 0.8033 (tptp) REVERT: H 466 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9105 (pp) REVERT: H 568 MET cc_start: 0.7545 (mtm) cc_final: 0.6764 (tmm) REVERT: J 31 ASP cc_start: 0.8807 (m-30) cc_final: 0.8339 (m-30) REVERT: K 467 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7557 (tpt90) REVERT: L 515 TYR cc_start: 0.7743 (m-80) cc_final: 0.7045 (m-80) REVERT: L 534 TYR cc_start: 0.8844 (m-10) cc_final: 0.8435 (m-10) outliers start: 69 outliers final: 49 residues processed: 234 average time/residue: 0.1356 time to fit residues: 47.0714 Evaluate side-chains 214 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 160 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 521 LEU Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 405 PHE Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain K residue 467 ARG Chi-restraints excluded: chain L residue 520 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 164 optimal weight: 5.9990 chunk 168 optimal weight: 0.4980 chunk 80 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 180 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 199 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 GLN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 490 GLN G 463 GLN H 400 HIS I 123 HIS K 493 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.091107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.059961 restraints weight = 66402.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.061744 restraints weight = 39669.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.062761 restraints weight = 29533.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.063444 restraints weight = 24959.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.063940 restraints weight = 22500.789| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19090 Z= 0.128 Angle : 0.645 11.457 26156 Z= 0.329 Chirality : 0.046 0.156 3095 Planarity : 0.005 0.068 3327 Dihedral : 4.526 18.269 2549 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.45 % Favored : 91.47 % Rotamer: Outliers : 2.32 % Allowed : 18.07 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.17), residues: 2344 helix: -1.40 (0.30), residues: 242 sheet: 0.12 (0.18), residues: 836 loop : -1.89 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 443 TYR 0.012 0.001 TYR E 375 PHE 0.022 0.001 PHE L 479 TRP 0.012 0.001 TRP C 528 HIS 0.019 0.001 HIS I 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (19049) covalent geometry : angle 0.64237 / 0.33 (26062) SS BOND : bond 0.00493 / 0.31 ( 29) SS BOND : angle 0.99326 / 0.66 ( 58) hydrogen bonds : bond 0.03446 / 2.37 ( 482) hydrogen bonds : angle 5.70346 / 4.03 ( 1383) link_BETA1-4 : bond 0.00636 / 0.33 ( 1) link_BETA1-4 : angle 1.24140 / 0.64 ( 3) link_NAG-ASN : bond 0.00205 / 0.13 ( 11) link_NAG-ASN : angle 1.44597 / 0.99 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 178 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. 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 364 LYS cc_start: 0.8418 (pttt) cc_final: 0.7662 (mmmt) REVERT: A 445 LYS cc_start: 0.8147 (mttt) cc_final: 0.7880 (mtmm) REVERT: A 465 ASN cc_start: 0.8764 (m-40) cc_final: 0.8535 (m-40) REVERT: B 376 ASP cc_start: 0.8388 (p0) cc_final: 0.8062 (p0) REVERT: C 348 PHE cc_start: 0.8509 (m-80) cc_final: 0.8270 (m-80) REVERT: G 375 TYR cc_start: 0.8317 (m-80) cc_final: 0.7907 (m-10) REVERT: G 553 ASP cc_start: 0.7974 (t0) cc_final: 0.7677 (t70) REVERT: H 391 LYS cc_start: 0.8177 (tptt) cc_final: 0.7945 (tptp) REVERT: H 568 MET cc_start: 0.7267 (mtm) cc_final: 0.6881 (tmm) REVERT: I 121 ASN cc_start: 0.8765 (m110) cc_final: 0.7877 (t0) REVERT: J 31 ASP cc_start: 0.8728 (m-30) cc_final: 0.8260 (m-30) REVERT: K 558 LYS cc_start: 0.5978 (mppt) cc_final: 0.5621 (mppt) REVERT: L 506 MET cc_start: 0.8214 (mpp) cc_final: 0.7981 (mpp) REVERT: L 515 TYR cc_start: 0.7783 (m-80) cc_final: 0.7285 (m-10) REVERT: L 534 TYR cc_start: 0.8799 (m-10) cc_final: 0.8364 (m-10) outliers start: 49 outliers final: 32 residues processed: 215 average time/residue: 0.1403 time to fit residues: 44.1286 Evaluate side-chains 188 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 491 ARG Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain L residue 520 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 197 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 216 optimal weight: 0.2980 chunk 185 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 GLN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 395 ASN ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.089249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.057873 restraints weight = 66865.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.059493 restraints weight = 40469.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.060573 restraints weight = 30498.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.061160 restraints weight = 25907.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.061418 restraints weight = 23510.539| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19090 Z= 0.216 Angle : 0.710 13.953 26156 Z= 0.361 Chirality : 0.047 0.162 3095 Planarity : 0.005 0.051 3327 Dihedral : 4.704 19.930 2549 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.73 % Favored : 90.19 % Rotamer: Outliers : 3.45 % Allowed : 18.21 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.17), residues: 2344 helix: -1.40 (0.30), residues: 250 sheet: 0.02 (0.18), residues: 827 loop : -1.92 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 491 TYR 0.023 0.002 TYR F 375 PHE 0.026 0.002 PHE D 479 TRP 0.014 0.002 TRP E 488 HIS 0.007 0.002 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (19049) covalent geometry : angle 0.70502 / 0.36 (26062) SS BOND : bond 0.00613 / 0.40 ( 29) SS BOND : angle 1.34240 / 0.91 ( 58) hydrogen bonds : bond 0.03962 / 2.71 ( 482) hydrogen bonds : angle 5.79286 / 4.10 ( 1383) link_BETA1-4 : bond 0.00128 / 0.07 ( 1) link_BETA1-4 : angle 1.38361 / 0.71 ( 3) link_NAG-ASN : bond 0.00571 / 0.35 ( 11) link_NAG-ASN : angle 1.95044 / 1.28 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 167 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.8493 (pttt) cc_final: 0.7752 (mmmt) REVERT: A 404 THR cc_start: 0.5893 (OUTLIER) cc_final: 0.5617 (t) REVERT: A 445 LYS cc_start: 0.8245 (mttt) cc_final: 0.7921 (mtmm) REVERT: B 376 ASP cc_start: 0.8482 (p0) cc_final: 0.8156 (p0) REVERT: E 358 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7719 (m-80) REVERT: E 521 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8624 (tp) REVERT: G 385 GLN cc_start: 0.4931 (mm-40) cc_final: 0.4538 (mm-40) REVERT: H 391 LYS cc_start: 0.8247 (tptt) cc_final: 0.8002 (tptp) REVERT: J 31 ASP cc_start: 0.8744 (m-30) cc_final: 0.8321 (m-30) REVERT: K 364 LYS cc_start: 0.7140 (mtmt) cc_final: 0.6921 (mtmm) REVERT: L 506 MET cc_start: 0.8254 (mpp) cc_final: 0.8036 (mpp) REVERT: L 515 TYR cc_start: 0.7936 (m-80) cc_final: 0.7243 (m-80) REVERT: L 534 TYR cc_start: 0.8923 (m-10) cc_final: 0.8515 (m-10) outliers start: 73 outliers final: 56 residues processed: 226 average time/residue: 0.1320 time to fit residues: 44.6933 Evaluate side-chains 211 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 152 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 491 ARG Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 521 LEU Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 395 ASN Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain L residue 520 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 47 optimal weight: 7.9990 chunk 201 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 126 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 GLN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN C 545 ASN F 430 HIS H 395 ASN ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 493 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.090648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.059063 restraints weight = 67442.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.061080 restraints weight = 37045.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.062314 restraints weight = 26574.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.063077 restraints weight = 21998.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.063370 restraints weight = 19694.186| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19090 Z= 0.134 Angle : 0.668 16.351 26156 Z= 0.335 Chirality : 0.046 0.147 3095 Planarity : 0.005 0.055 3327 Dihedral : 4.515 20.372 2549 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.19 % Favored : 91.68 % Rotamer: Outliers : 3.17 % Allowed : 19.30 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.17), residues: 2344 helix: -1.26 (0.30), residues: 250 sheet: 0.15 (0.18), residues: 824 loop : -1.82 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 491 TYR 0.020 0.001 TYR F 375 PHE 0.021 0.001 PHE L 479 TRP 0.011 0.001 TRP C 528 HIS 0.007 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (19049) covalent geometry : angle 0.66561 / 0.33 (26062) SS BOND : bond 0.00486 / 0.31 ( 29) SS BOND : angle 0.99457 / 0.68 ( 58) hydrogen bonds : bond 0.03325 / 2.28 ( 482) hydrogen bonds : angle 5.55373 / 3.93 ( 1383) link_BETA1-4 : bond 0.00051 / 0.03 ( 1) link_BETA1-4 : angle 1.21226 / 0.62 ( 3) link_NAG-ASN : bond 0.00212 / 0.13 ( 11) link_NAG-ASN : angle 1.46159 / 1.00 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 166 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.8408 (pttt) cc_final: 0.7629 (mmmt) REVERT: A 404 THR cc_start: 0.5863 (OUTLIER) cc_final: 0.5583 (t) REVERT: A 445 LYS cc_start: 0.8247 (mttt) cc_final: 0.7951 (mtmm) REVERT: B 364 LYS cc_start: 0.8850 (ptpt) cc_final: 0.8475 (ptpp) REVERT: B 376 ASP cc_start: 0.8450 (p0) cc_final: 0.8121 (p0) REVERT: C 371 ASP cc_start: 0.7266 (t0) cc_final: 0.6730 (p0) REVERT: C 439 GLN cc_start: 0.5124 (OUTLIER) cc_final: 0.4837 (pm20) REVERT: C 441 ILE cc_start: 0.4522 (OUTLIER) cc_final: 0.4319 (pt) REVERT: E 358 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: E 364 LYS cc_start: 0.9050 (mtmm) cc_final: 0.8633 (mmtp) REVERT: E 489 MET cc_start: 0.7645 (tpp) cc_final: 0.7349 (mmp) REVERT: G 375 TYR cc_start: 0.8395 (m-80) cc_final: 0.8009 (m-10) REVERT: G 385 GLN cc_start: 0.4838 (mm-40) cc_final: 0.4454 (mm-40) REVERT: G 553 ASP cc_start: 0.7989 (t70) cc_final: 0.7664 (t70) REVERT: H 391 LYS cc_start: 0.8203 (tptt) cc_final: 0.7966 (tptp) REVERT: H 568 MET cc_start: 0.7348 (mtm) cc_final: 0.6724 (tmm) REVERT: J 31 ASP cc_start: 0.8682 (m-30) cc_final: 0.8257 (m-30) REVERT: L 506 MET cc_start: 0.8232 (mpp) cc_final: 0.8019 (mpp) REVERT: L 515 TYR cc_start: 0.7914 (m-80) cc_final: 0.7428 (m-10) REVERT: L 524 SER cc_start: 0.8560 (m) cc_final: 0.8123 (t) REVERT: L 534 TYR cc_start: 0.8844 (m-10) cc_final: 0.8471 (m-10) outliers start: 67 outliers final: 49 residues processed: 221 average time/residue: 0.1280 time to fit residues: 43.0032 Evaluate side-chains 210 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 157 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 491 ARG Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain L residue 520 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 86 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 221 optimal weight: 0.5980 chunk 184 optimal weight: 0.6980 chunk 145 optimal weight: 0.5980 chunk 154 optimal weight: 0.0670 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 GLN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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 = 0.4034 r_free = 0.4034 target = 0.090381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.058884 restraints weight = 66764.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.060856 restraints weight = 36923.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.062047 restraints weight = 26664.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.062810 restraints weight = 22187.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.063191 restraints weight = 19956.510| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 19090 Z= 0.144 Angle : 0.655 12.589 26156 Z= 0.331 Chirality : 0.046 0.160 3095 Planarity : 0.005 0.049 3327 Dihedral : 4.446 19.810 2549 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.58 % Favored : 91.30 % Rotamer: Outliers : 3.07 % Allowed : 19.49 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.17), residues: 2344 helix: -1.18 (0.30), residues: 250 sheet: 0.19 (0.18), residues: 820 loop : -1.79 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 491 TYR 0.019 0.001 TYR F 375 PHE 0.021 0.001 PHE L 479 TRP 0.010 0.001 TRP C 528 HIS 0.006 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (19049) covalent geometry : angle 0.65178 / 0.33 (26062) SS BOND : bond 0.00516 / 0.34 ( 29) SS BOND : angle 1.22068 / 0.88 ( 58) hydrogen bonds : bond 0.03290 / 2.26 ( 482) hydrogen bonds : angle 5.49375 / 3.89 ( 1383) link_BETA1-4 : bond 0.00181 / 0.10 ( 1) link_BETA1-4 : angle 1.20322 / 0.62 ( 3) link_NAG-ASN : bond 0.00240 / 0.15 ( 11) link_NAG-ASN : angle 1.47932 / 0.99 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 159 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.8370 (pttt) cc_final: 0.7568 (mmmt) REVERT: A 404 THR cc_start: 0.5874 (OUTLIER) cc_final: 0.5585 (t) REVERT: A 439 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6491 (pm20) REVERT: A 445 LYS cc_start: 0.8246 (mttt) cc_final: 0.7969 (mtmm) REVERT: B 359 LEU cc_start: 0.9032 (tp) cc_final: 0.8796 (pp) REVERT: B 376 ASP cc_start: 0.8411 (p0) cc_final: 0.8076 (p0) REVERT: B 514 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.8011 (mtt90) REVERT: C 439 GLN cc_start: 0.5070 (OUTLIER) cc_final: 0.4660 (pm20) REVERT: D 445 LYS cc_start: 0.7531 (mmtm) cc_final: 0.7163 (mmtt) REVERT: E 358 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7633 (m-80) REVERT: E 364 LYS cc_start: 0.9006 (mtmm) cc_final: 0.8573 (mmtm) REVERT: E 473 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8463 (p) REVERT: E 489 MET cc_start: 0.7661 (tpp) cc_final: 0.7408 (mmp) REVERT: G 375 TYR cc_start: 0.8357 (m-80) cc_final: 0.7949 (m-10) REVERT: G 385 GLN cc_start: 0.5124 (mm-40) cc_final: 0.4790 (mm-40) REVERT: H 391 LYS cc_start: 0.8225 (tptt) cc_final: 0.7983 (tptp) REVERT: H 568 MET cc_start: 0.7209 (mtm) cc_final: 0.6573 (tmm) REVERT: J 31 ASP cc_start: 0.8662 (m-30) cc_final: 0.8226 (m-30) REVERT: L 506 MET cc_start: 0.8158 (mpp) cc_final: 0.7927 (mpp) REVERT: L 515 TYR cc_start: 0.7975 (m-80) cc_final: 0.7318 (m-80) REVERT: L 524 SER cc_start: 0.8619 (m) cc_final: 0.8184 (t) REVERT: L 534 TYR cc_start: 0.8860 (m-10) cc_final: 0.8468 (m-10) outliers start: 65 outliers final: 52 residues processed: 213 average time/residue: 0.1434 time to fit residues: 45.7697 Evaluate side-chains 214 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 156 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 491 ARG Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain L residue 520 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 88 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 161 optimal weight: 30.0000 chunk 135 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 105 optimal weight: 0.0570 chunk 49 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 GLN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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 = 0.3989 r_free = 0.3989 target = 0.088069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.056710 restraints weight = 67623.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.058332 restraints weight = 40967.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.059284 restraints weight = 30965.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.059986 restraints weight = 26356.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.060322 restraints weight = 23865.941| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 19090 Z= 0.265 Angle : 0.741 15.290 26156 Z= 0.379 Chirality : 0.048 0.174 3095 Planarity : 0.005 0.049 3327 Dihedral : 4.817 19.691 2549 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.28 % Favored : 89.59 % Rotamer: Outliers : 3.41 % Allowed : 19.39 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.17), residues: 2344 helix: -1.31 (0.30), residues: 249 sheet: -0.10 (0.18), residues: 841 loop : -1.88 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 514 TYR 0.017 0.002 TYR F 375 PHE 0.032 0.002 PHE D 479 TRP 0.015 0.002 TRP B 488 HIS 0.009 0.002 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.27 (19049) covalent geometry : angle 0.73494 / 0.38 (26062) SS BOND : bond 0.00688 / 0.46 ( 29) SS BOND : angle 1.61628 / 1.13 ( 58) hydrogen bonds : bond 0.04098 / 2.79 ( 482) hydrogen bonds : angle 5.78276 / 4.09 ( 1383) link_BETA1-4 : bond 0.00118 / 0.06 ( 1) link_BETA1-4 : angle 1.39987 / 0.72 ( 3) link_NAG-ASN : bond 0.00652 / 0.42 ( 11) link_NAG-ASN : angle 2.04132 / 1.33 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 160 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.8524 (pttt) cc_final: 0.7712 (mmmt) REVERT: A 404 THR cc_start: 0.5950 (OUTLIER) cc_final: 0.5666 (t) REVERT: A 439 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.6561 (pm20) REVERT: A 445 LYS cc_start: 0.8262 (mttt) cc_final: 0.7922 (mtmm) REVERT: A 456 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7996 (mp) REVERT: A 553 ASP cc_start: 0.7425 (t0) cc_final: 0.7142 (t0) REVERT: B 376 ASP cc_start: 0.8310 (p0) cc_final: 0.7977 (p0) REVERT: B 419 ASN cc_start: 0.9507 (t0) cc_final: 0.9303 (t0) REVERT: B 514 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8066 (mtt90) REVERT: C 439 GLN cc_start: 0.5670 (OUTLIER) cc_final: 0.5435 (mp10) REVERT: D 445 LYS cc_start: 0.7642 (mmtm) cc_final: 0.7372 (mmtt) REVERT: E 358 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: E 364 LYS cc_start: 0.9075 (mtmm) cc_final: 0.8665 (mmtm) REVERT: E 473 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8473 (p) REVERT: G 375 TYR cc_start: 0.8460 (m-80) cc_final: 0.7721 (m-80) REVERT: H 391 LYS cc_start: 0.8284 (tptt) cc_final: 0.8032 (tptp) REVERT: H 568 MET cc_start: 0.7350 (mtm) cc_final: 0.7031 (tmm) REVERT: I 121 ASN cc_start: 0.8955 (OUTLIER) cc_final: 0.8104 (t0) REVERT: J 31 ASP cc_start: 0.8697 (m-30) cc_final: 0.8331 (m-30) REVERT: L 506 MET cc_start: 0.8204 (mpp) cc_final: 0.7974 (mpp) REVERT: L 515 TYR cc_start: 0.7892 (m-80) cc_final: 0.7252 (m-80) REVERT: L 524 SER cc_start: 0.8529 (m) cc_final: 0.8085 (t) REVERT: L 534 TYR cc_start: 0.8980 (m-10) cc_final: 0.8681 (m-10) outliers start: 72 outliers final: 55 residues processed: 220 average time/residue: 0.1439 time to fit residues: 47.3828 Evaluate side-chains 218 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 155 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 491 ARG Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain L residue 520 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 13 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 182 optimal weight: 0.5980 chunk 214 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 171 optimal weight: 0.0020 chunk 124 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 GLN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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 = 0.4028 r_free = 0.4028 target = 0.090061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.058961 restraints weight = 66566.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.060700 restraints weight = 39782.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.061807 restraints weight = 29659.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.062423 restraints weight = 25058.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.062834 restraints weight = 22674.799| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19090 Z= 0.127 Angle : 0.683 13.209 26156 Z= 0.343 Chirality : 0.046 0.148 3095 Planarity : 0.005 0.123 3327 Dihedral : 4.534 20.466 2549 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.98 % Favored : 91.89 % Rotamer: Outliers : 2.84 % Allowed : 20.10 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.17), residues: 2344 helix: -1.10 (0.31), residues: 244 sheet: 0.17 (0.18), residues: 821 loop : -1.71 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 491 TYR 0.015 0.001 TYR F 375 PHE 0.021 0.001 PHE L 479 TRP 0.015 0.001 TRP C 382 HIS 0.006 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (19049) covalent geometry : angle 0.68042 / 0.34 (26062) SS BOND : bond 0.00480 / 0.30 ( 29) SS BOND : angle 1.06515 / 0.75 ( 58) hydrogen bonds : bond 0.03196 / 2.18 ( 482) hydrogen bonds : angle 5.45290 / 3.85 ( 1383) link_BETA1-4 : bond 0.00265 / 0.14 ( 1) link_BETA1-4 : angle 1.10680 / 0.57 ( 3) link_NAG-ASN : bond 0.00177 / 0.11 ( 11) link_NAG-ASN : angle 1.38408 / 0.95 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 164 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.8414 (pttt) cc_final: 0.7434 (mmtt) REVERT: A 404 THR cc_start: 0.5581 (OUTLIER) cc_final: 0.5302 (t) REVERT: A 439 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.6611 (pm20) REVERT: A 445 LYS cc_start: 0.8257 (mttt) cc_final: 0.7956 (mtmm) REVERT: A 456 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7876 (mp) REVERT: B 376 ASP cc_start: 0.8304 (p0) cc_final: 0.7971 (p0) REVERT: B 514 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7956 (mtt90) REVERT: C 371 ASP cc_start: 0.7451 (t0) cc_final: 0.6893 (p0) REVERT: D 445 LYS cc_start: 0.7481 (mmtm) cc_final: 0.7214 (mmtt) REVERT: E 358 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7693 (m-80) REVERT: E 364 LYS cc_start: 0.9076 (mtmm) cc_final: 0.8720 (mmtm) REVERT: E 473 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8460 (p) REVERT: E 489 MET cc_start: 0.7658 (tpp) cc_final: 0.7432 (mmp) REVERT: G 375 TYR cc_start: 0.8396 (m-80) cc_final: 0.7640 (m-80) REVERT: G 385 GLN cc_start: 0.4824 (mm-40) cc_final: 0.4443 (mm-40) REVERT: H 391 LYS cc_start: 0.8181 (tptt) cc_final: 0.7956 (tptp) REVERT: I 121 ASN cc_start: 0.8949 (m110) cc_final: 0.8161 (t0) REVERT: J 31 ASP cc_start: 0.8633 (m-30) cc_final: 0.8210 (m-30) REVERT: L 506 MET cc_start: 0.8162 (mpp) cc_final: 0.7935 (mpp) REVERT: L 515 TYR cc_start: 0.7863 (m-80) cc_final: 0.7397 (m-10) REVERT: L 524 SER cc_start: 0.8669 (m) cc_final: 0.8293 (t) REVERT: L 534 TYR cc_start: 0.8888 (m-10) cc_final: 0.8520 (m-10) outliers start: 60 outliers final: 52 residues processed: 215 average time/residue: 0.1432 time to fit residues: 46.6527 Evaluate side-chains 215 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 157 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 491 ARG Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain G residue 392 THR Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 364 LYS Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain L residue 520 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 83 optimal weight: 0.0370 chunk 46 optimal weight: 0.0000 chunk 111 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 224 optimal weight: 2.9990 chunk 229 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 overall best weight: 1.3866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 GLN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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 = 0.4011 r_free = 0.4011 target = 0.089175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.057934 restraints weight = 67326.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.059621 restraints weight = 40532.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.060709 restraints weight = 30419.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.061283 restraints weight = 25657.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.061706 restraints weight = 23310.416| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19090 Z= 0.173 Angle : 0.699 13.048 26156 Z= 0.352 Chirality : 0.047 0.159 3095 Planarity : 0.005 0.065 3327 Dihedral : 4.553 20.035 2549 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.26 % Favored : 90.61 % Rotamer: Outliers : 2.98 % Allowed : 20.25 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.17), residues: 2344 helix: -1.08 (0.31), residues: 248 sheet: 0.11 (0.18), residues: 834 loop : -1.78 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 491 TYR 0.017 0.002 TYR C 562 PHE 0.023 0.002 PHE D 479 TRP 0.010 0.002 TRP C 528 HIS 0.006 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 (19049) covalent geometry : angle 0.69511 / 0.35 (26062) SS BOND : bond 0.00534 / 0.35 ( 29) SS BOND : angle 1.23739 / 0.87 ( 58) hydrogen bonds : bond 0.03458 / 2.34 ( 482) hydrogen bonds : angle 5.49497 / 3.88 ( 1383) link_BETA1-4 : bond 0.00143 / 0.08 ( 1) link_BETA1-4 : angle 1.26992 / 0.65 ( 3) link_NAG-ASN : bond 0.00345 / 0.22 ( 11) link_NAG-ASN : angle 1.62685 / 1.07 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3980.70 seconds wall clock time: 69 minutes 15.43 seconds (4155.43 seconds total)