Starting phenix.real_space_refine on Sat Feb 17 12:28:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpf_16151/02_2024/8bpf_16151.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpf_16151/02_2024/8bpf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpf_16151/02_2024/8bpf_16151.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpf_16151/02_2024/8bpf_16151.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpf_16151/02_2024/8bpf_16151.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpf_16151/02_2024/8bpf_16151.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Residue "A GLU 468": "OE1" <-> "OE2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B ARG 461": "NH1" <-> "NH2" Residue "B ARG 514": "NH1" <-> "NH2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 508": "OE1" <-> "OE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "E TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 415": "OE1" <-> "OE2" Residue "F GLU 508": "OE1" <-> "OE2" Residue "H PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 525": "OE1" <-> "OE2" Residue "H GLU 541": "OE1" <-> "OE2" Residue "I GLU 22": "OE1" <-> "OE2" Residue "I GLU 51": "OE1" <-> "OE2" Residue "I TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 111": "OD1" <-> "OD2" Residue "J ASP 9": "OD1" <-> "OD2" Residue "J ASP 66": "OD1" <-> "OD2" Residue "L GLU 462": "OE1" <-> "OE2" Residue "L GLU 468": "OE1" <-> "OE2" Residue "L GLU 532": "OE1" <-> "OE2" Residue "L GLU 549": "OE1" <-> "OE2" Residue "L ARG 550": "NH1" <-> "NH2" Residue "L TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.19, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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: 6.96 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 2.10 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: 6.16 Time building geometry restraints manager: 7.55 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: 99.87 - 106.76: 855 106.76 - 113.65: 10851 113.65 - 120.54: 6899 120.54 - 127.43: 7219 127.43 - 134.32: 238 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: 10719 17.97 - 35.94: 844 35.94 - 53.91: 147 53.91 - 71.88: 27 71.88 - 89.85: 20 Dihedral angle restraints: 11757 sinusoidal: 4793 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 11754 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 2.440 nonbonded pdb=" O LEU H 372 " pdb=" OG1 THR H 404 " model vdw 2.283 2.440 nonbonded pdb=" OG SER L 469 " pdb=" O VAL L 523 " model vdw 2.287 2.440 nonbonded pdb=" OG1 THR K 379 " pdb=" OG1 THR K 429 " model vdw 2.304 2.440 nonbonded pdb=" O ILE J 5 " pdb=" OG1 THR J 18 " model vdw 2.309 2.440 ... (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 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 568 or resid 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 568 or resid 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 568 or resid 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 568 or resid 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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.660 Check model and map are aligned: 0.270 Set scattering table: 0.190 Process input model: 49.240 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 0.006 0.049 19049 Z= 0.409 Angle : 0.850 7.967 26062 Z= 0.555 Chirality : 0.062 0.812 3095 Planarity : 0.006 0.124 3327 Dihedral : 13.399 89.850 7134 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (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 TRP 0.020 0.001 TRP C 418 HIS 0.007 0.001 HIS A 450 PHE 0.028 0.002 PHE F 354 TYR 0.020 0.001 TYR F 500 ARG 0.005 0.000 ARG L 467 *********************** 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 fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 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: 0.7657 (tmtt) REVERT: I 121 ASN cc_start: 0.8569 (m110) cc_final: 0.8061 (m110) REVERT: J 22 ILE cc_start: 0.8427 (pt) cc_final: 0.8064 (pt) REVERT: J 31 ASP cc_start: 0.8731 (m-30) cc_final: 0.8482 (m-30) REVERT: K 506 MET cc_start: 0.7214 (mtt) cc_final: 0.7005 (mtt) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.4200 time to fit residues: 202.0984 Evaluate side-chains 198 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 118 optimal weight: 0.9990 chunk 93 optimal weight: 0.4980 chunk 181 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 210 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 ASN ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** H 395 ASN H 490 GLN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19049 Z= 0.227 Angle : 0.664 8.804 26062 Z= 0.344 Chirality : 0.047 0.204 3095 Planarity : 0.005 0.054 3327 Dihedral : 4.502 30.864 2801 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.49 % Favored : 91.42 % Rotamer: Outliers : 1.80 % Allowed : 10.60 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.17), residues: 2344 helix: -1.25 (0.31), residues: 236 sheet: 0.29 (0.18), residues: 832 loop : -1.85 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 418 HIS 0.007 0.001 HIS B 430 PHE 0.029 0.002 PHE L 479 TYR 0.027 0.001 TYR H 562 ARG 0.009 0.001 ARG H 491 *********************** 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 253 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 215 time to evaluate : 2.661 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.8359 (pttt) cc_final: 0.7355 (mmtt) REVERT: A 445 LYS cc_start: 0.8168 (mttt) cc_final: 0.7950 (mtmm) REVERT: B 376 ASP cc_start: 0.8169 (p0) cc_final: 0.7768 (p0) REVERT: C 373 THR cc_start: 0.6358 (t) cc_final: 0.4871 (p) REVERT: I 121 ASN cc_start: 0.8534 (m110) cc_final: 0.8026 (t0) REVERT: J 31 ASP cc_start: 0.8796 (m-30) cc_final: 0.8488 (m-30) REVERT: K 364 LYS cc_start: 0.7851 (ptpp) cc_final: 0.5816 (ptpp) REVERT: L 527 GLU cc_start: 0.8866 (mp0) cc_final: 0.8531 (mp0) REVERT: L 534 TYR cc_start: 0.8365 (m-10) cc_final: 0.7812 (m-10) outliers start: 38 outliers final: 24 residues processed: 236 average time/residue: 0.3812 time to fit residues: 130.2235 Evaluate side-chains 202 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 2.037 ------------------------------------------------------------------------------- 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 400 HIS Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain E residue 491 ARG 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 483 ASP Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 36 LYS 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 Chi-restraints excluded: chain K residue 570 ASP Chi-restraints excluded: chain L residue 525 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 175 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 228 optimal weight: 0.6980 chunk 187 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 169 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 HIS F 490 GLN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 395 ASN ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 439 GLN ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19049 Z= 0.211 Angle : 0.630 11.740 26062 Z= 0.322 Chirality : 0.046 0.171 3095 Planarity : 0.004 0.049 3327 Dihedral : 4.368 27.934 2801 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.45 % Favored : 91.47 % Rotamer: Outliers : 1.66 % Allowed : 13.77 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.17), residues: 2344 helix: -0.98 (0.31), residues: 235 sheet: 0.29 (0.18), residues: 840 loop : -1.80 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 528 HIS 0.008 0.001 HIS K 400 PHE 0.025 0.002 PHE L 479 TYR 0.011 0.001 TYR K 375 ARG 0.008 0.000 ARG H 491 *********************** 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 228 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 193 time to evaluate : 2.354 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: 0.8373 (pttt) cc_final: 0.7387 (mmtt) REVERT: A 423 ARG cc_start: 0.8354 (ptp-110) cc_final: 0.7566 (tmm160) REVERT: A 445 LYS cc_start: 0.8042 (mttt) cc_final: 0.7831 (mtmm) REVERT: B 376 ASP cc_start: 0.8219 (p0) cc_final: 0.7813 (p0) REVERT: G 375 TYR cc_start: 0.7743 (m-80) cc_final: 0.7532 (m-80) REVERT: H 568 MET cc_start: 0.6951 (mtt) cc_final: 0.6737 (tmm) REVERT: J 31 ASP cc_start: 0.8760 (m-30) cc_final: 0.8459 (m-30) REVERT: L 534 TYR cc_start: 0.8598 (m-10) cc_final: 0.7969 (m-10) outliers start: 35 outliers final: 23 residues processed: 210 average time/residue: 0.3531 time to fit residues: 108.7170 Evaluate side-chains 197 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 523 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 538 VAL Chi-restraints excluded: chain H residue 395 ASN Chi-restraints excluded: chain H residue 405 PHE Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 104 ASP 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 K residue 570 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 400 HIS H 490 GLN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19049 Z= 0.233 Angle : 0.620 9.310 26062 Z= 0.318 Chirality : 0.046 0.171 3095 Planarity : 0.004 0.045 3327 Dihedral : 4.388 26.443 2801 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.75 % Favored : 91.17 % Rotamer: Outliers : 2.51 % Allowed : 16.13 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.17), residues: 2344 helix: -0.86 (0.32), residues: 236 sheet: 0.28 (0.18), residues: 852 loop : -1.78 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 528 HIS 0.008 0.001 HIS K 400 PHE 0.022 0.002 PHE L 479 TYR 0.027 0.001 TYR H 562 ARG 0.008 0.000 ARG H 491 *********************** 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 237 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 184 time to evaluate : 2.334 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.8400 (pttt) cc_final: 0.7661 (mmmt) REVERT: B 376 ASP cc_start: 0.8164 (p0) cc_final: 0.7767 (p0) REVERT: G 375 TYR cc_start: 0.7727 (m-80) cc_final: 0.7451 (m-80) REVERT: J 31 ASP cc_start: 0.8752 (m-30) cc_final: 0.8457 (m-30) REVERT: K 467 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7396 (tpt90) REVERT: L 534 TYR cc_start: 0.8655 (m-10) cc_final: 0.7974 (m-10) outliers start: 53 outliers final: 34 residues processed: 218 average time/residue: 0.3464 time to fit residues: 110.9040 Evaluate side-chains 208 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 173 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 489 MET Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain E residue 364 LYS 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 499 LYS Chi-restraints excluded: chain G 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 483 ASP 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 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 K residue 570 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 4.9990 chunk 127 optimal weight: 0.0010 chunk 3 optimal weight: 20.0000 chunk 166 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 GLN ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 395 ASN ** I 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19049 Z= 0.178 Angle : 0.596 8.847 26062 Z= 0.303 Chirality : 0.045 0.158 3095 Planarity : 0.004 0.045 3327 Dihedral : 4.223 23.837 2801 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.11 % Favored : 91.85 % Rotamer: Outliers : 2.60 % Allowed : 17.03 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.17), residues: 2344 helix: -0.81 (0.32), residues: 236 sheet: 0.30 (0.18), residues: 857 loop : -1.72 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 528 HIS 0.009 0.001 HIS K 400 PHE 0.022 0.001 PHE L 479 TYR 0.012 0.001 TYR H 562 ARG 0.005 0.000 ARG A 423 *********************** 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 237 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 182 time to evaluate : 2.461 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.8366 (pttt) cc_final: 0.7368 (mmtt) REVERT: B 376 ASP cc_start: 0.8230 (p0) cc_final: 0.7829 (p0) REVERT: D 445 LYS cc_start: 0.7237 (mmtt) cc_final: 0.6821 (mmtt) REVERT: G 375 TYR cc_start: 0.7817 (m-80) cc_final: 0.7484 (m-80) REVERT: J 31 ASP cc_start: 0.8792 (m-30) cc_final: 0.8526 (m-30) REVERT: L 534 TYR cc_start: 0.8636 (m-10) cc_final: 0.8059 (m-10) outliers start: 55 outliers final: 38 residues processed: 220 average time/residue: 0.3488 time to fit residues: 113.3804 Evaluate side-chains 201 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 456 LEU 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 C residue 350 ILE 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 400 HIS 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 364 LYS Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 523 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 347 VAL Chi-restraints excluded: chain G residue 499 LYS Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 395 ASN Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 520 ILE 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 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 570 ASP 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 75 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 224 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 545 ASN ** I 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19049 Z= 0.296 Angle : 0.655 16.000 26062 Z= 0.334 Chirality : 0.046 0.153 3095 Planarity : 0.005 0.051 3327 Dihedral : 4.483 25.773 2801 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.75 % Favored : 91.13 % Rotamer: Outliers : 2.89 % Allowed : 18.02 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2344 helix: -0.72 (0.33), residues: 234 sheet: 0.17 (0.18), residues: 859 loop : -1.76 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 488 HIS 0.007 0.001 HIS L 518 PHE 0.025 0.002 PHE D 479 TYR 0.014 0.002 TYR C 562 ARG 0.012 0.001 ARG H 491 *********************** 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 231 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 170 time to evaluate : 2.148 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: 0.8502 (pttt) cc_final: 0.7683 (mmmt) REVERT: B 376 ASP cc_start: 0.8221 (p0) cc_final: 0.7830 (p0) REVERT: D 445 LYS cc_start: 0.7405 (mmtt) cc_final: 0.7132 (mmtm) REVERT: E 491 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7255 (ptt-90) REVERT: G 375 TYR cc_start: 0.7855 (m-80) cc_final: 0.7496 (m-80) REVERT: H 441 ILE cc_start: 0.3616 (pt) cc_final: 0.3258 (tp) REVERT: J 31 ASP cc_start: 0.8763 (m-30) cc_final: 0.8498 (m-30) REVERT: L 534 TYR cc_start: 0.8816 (m-10) cc_final: 0.8107 (m-10) outliers start: 61 outliers final: 51 residues processed: 214 average time/residue: 0.3486 time to fit residues: 110.9609 Evaluate side-chains 212 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 160 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 456 LEU 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 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 443 ARG Chi-restraints excluded: chain C residue 473 THR 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 394 THR Chi-restraints excluded: chain D residue 400 HIS 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 360 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 364 LYS 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 388 GLU 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 F residue 538 VAL Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 499 LYS Chi-restraints excluded: chain G residue 521 LEU 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 453 ASP Chi-restraints excluded: chain H residue 483 ASP 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 121 ASN 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 K residue 466 LEU Chi-restraints excluded: chain K residue 570 ASP Chi-restraints excluded: chain L residue 515 TYR 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 216 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 127 optimal weight: 0.3980 chunk 163 optimal weight: 8.9990 chunk 188 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19049 Z= 0.288 Angle : 0.654 12.343 26062 Z= 0.334 Chirality : 0.046 0.151 3095 Planarity : 0.005 0.045 3327 Dihedral : 4.610 26.752 2801 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.75 % Favored : 91.13 % Rotamer: Outliers : 3.41 % Allowed : 18.21 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.17), residues: 2344 helix: -0.77 (0.32), residues: 240 sheet: 0.14 (0.18), residues: 856 loop : -1.80 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 488 HIS 0.006 0.001 HIS E 518 PHE 0.023 0.002 PHE D 479 TYR 0.013 0.002 TYR H 562 ARG 0.006 0.001 ARG E 514 *********************** 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 237 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 165 time to evaluate : 2.241 Fit side-chains 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: A 364 LYS cc_start: 0.8584 (pttt) cc_final: 0.7796 (mmmt) REVERT: B 376 ASP cc_start: 0.8307 (p0) cc_final: 0.7906 (p0) REVERT: B 419 ASN cc_start: 0.9419 (t0) cc_final: 0.9177 (t0) REVERT: E 358 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7648 (m-80) REVERT: G 375 TYR cc_start: 0.7976 (m-80) cc_final: 0.7539 (m-80) REVERT: J 31 ASP cc_start: 0.8743 (m-30) cc_final: 0.8244 (m-30) REVERT: K 364 LYS cc_start: 0.8026 (ptpp) cc_final: 0.7749 (mtmt) REVERT: L 524 SER cc_start: 0.8631 (m) cc_final: 0.8170 (t) REVERT: L 534 TYR cc_start: 0.8864 (m-10) cc_final: 0.8235 (m-10) outliers start: 72 outliers final: 60 residues processed: 220 average time/residue: 0.3293 time to fit residues: 107.8156 Evaluate side-chains 216 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 155 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 533 THR 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 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 C residue 350 ILE Chi-restraints excluded: chain C residue 443 ARG Chi-restraints excluded: chain C residue 473 THR 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 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 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 364 LYS Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 388 GLU 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 537 VAL Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 499 LYS Chi-restraints excluded: chain G residue 521 LEU 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 453 ASP Chi-restraints excluded: chain H residue 483 ASP 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 121 ASN 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 365 LEU Chi-restraints excluded: chain K residue 432 ASP Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 570 ASP Chi-restraints excluded: chain L residue 515 TYR 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 89 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 203 optimal weight: 0.2980 chunk 214 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 ASN F 430 HIS I 123 HIS ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19049 Z= 0.297 Angle : 0.673 12.986 26062 Z= 0.341 Chirality : 0.046 0.154 3095 Planarity : 0.005 0.048 3327 Dihedral : 4.710 27.937 2801 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.34 % Favored : 90.53 % Rotamer: Outliers : 3.41 % Allowed : 18.87 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2344 helix: -0.76 (0.32), residues: 240 sheet: 0.05 (0.18), residues: 872 loop : -1.78 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 488 HIS 0.006 0.001 HIS E 518 PHE 0.024 0.002 PHE D 479 TYR 0.021 0.002 TYR E 375 ARG 0.008 0.001 ARG I 83 *********************** 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 232 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 160 time to evaluate : 2.359 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: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.8643 (pttt) cc_final: 0.7772 (mmmt) REVERT: B 376 ASP cc_start: 0.8332 (p0) cc_final: 0.7941 (p0) REVERT: B 419 ASN cc_start: 0.9382 (t0) cc_final: 0.9099 (t0) REVERT: D 445 LYS cc_start: 0.7490 (mmtt) cc_final: 0.6653 (mmtt) REVERT: E 358 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7654 (m-80) REVERT: G 375 TYR cc_start: 0.8096 (m-80) cc_final: 0.7682 (m-80) REVERT: I 121 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.7858 (t0) REVERT: J 31 ASP cc_start: 0.8763 (m-30) cc_final: 0.8319 (m-30) REVERT: L 524 SER cc_start: 0.8574 (m) cc_final: 0.8137 (t) REVERT: L 534 TYR cc_start: 0.8939 (m-10) cc_final: 0.8397 (m-10) outliers start: 72 outliers final: 62 residues processed: 213 average time/residue: 0.3333 time to fit residues: 105.6755 Evaluate side-chains 215 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 151 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 533 THR 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 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 C residue 443 ARG Chi-restraints excluded: chain C residue 473 THR 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 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 364 LYS Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 506 MET Chi-restraints excluded: chain E residue 523 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 537 VAL Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 499 LYS Chi-restraints excluded: chain G residue 521 LEU 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 441 ILE Chi-restraints excluded: chain H residue 453 ASP Chi-restraints excluded: chain H residue 483 ASP 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 121 ASN Chi-restraints excluded: chain I residue 123 HIS 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 365 LEU Chi-restraints excluded: chain K residue 432 ASP Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 570 ASP Chi-restraints excluded: chain L residue 515 TYR 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 195 optimal weight: 0.9980 chunk 208 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 chunk 125 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 63 optimal weight: 0.4980 chunk 188 optimal weight: 0.9980 chunk 197 optimal weight: 10.0000 chunk 207 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19049 Z= 0.195 Angle : 0.628 11.604 26062 Z= 0.318 Chirality : 0.045 0.168 3095 Planarity : 0.004 0.049 3327 Dihedral : 4.500 25.990 2801 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.28 % Favored : 91.60 % Rotamer: Outliers : 2.89 % Allowed : 19.30 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.17), residues: 2344 helix: -0.59 (0.32), residues: 239 sheet: 0.15 (0.18), residues: 868 loop : -1.69 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 528 HIS 0.007 0.001 HIS I 123 PHE 0.022 0.001 PHE L 479 TYR 0.016 0.001 TYR E 375 ARG 0.005 0.000 ARG H 491 *********************** 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 223 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 162 time to evaluate : 2.380 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: symmetry clash REVERT: A 364 LYS cc_start: 0.8516 (pttt) cc_final: 0.7474 (mmtt) REVERT: B 376 ASP cc_start: 0.8332 (p0) cc_final: 0.7936 (p0) REVERT: B 419 ASN cc_start: 0.9378 (t0) cc_final: 0.9118 (t0) REVERT: D 445 LYS cc_start: 0.7513 (mmtt) cc_final: 0.6716 (mmtt) REVERT: E 358 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7586 (m-80) REVERT: G 375 TYR cc_start: 0.8117 (m-80) cc_final: 0.7692 (m-80) REVERT: J 31 ASP cc_start: 0.8734 (m-30) cc_final: 0.8271 (m-30) REVERT: L 524 SER cc_start: 0.8566 (m) cc_final: 0.8184 (t) REVERT: L 534 TYR cc_start: 0.8875 (m-10) cc_final: 0.8327 (m-10) outliers start: 61 outliers final: 56 residues processed: 210 average time/residue: 0.3225 time to fit residues: 102.3681 Evaluate side-chains 208 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 151 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain C residue 443 ARG Chi-restraints excluded: chain C residue 477 THR 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 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 364 LYS Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 523 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 506 MET Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 499 LYS 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 483 ASP 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 121 ASN 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 365 LEU Chi-restraints excluded: chain K residue 432 ASP Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain K residue 570 ASP Chi-restraints excluded: chain L residue 515 TYR 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 220 optimal weight: 0.0000 chunk 134 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 153 optimal weight: 0.0270 chunk 231 optimal weight: 0.8980 chunk 212 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 142 optimal weight: 20.0000 chunk 112 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 overall best weight: 0.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 430 HIS ** I 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19049 Z= 0.171 Angle : 0.626 10.336 26062 Z= 0.316 Chirality : 0.045 0.187 3095 Planarity : 0.004 0.049 3327 Dihedral : 4.292 22.490 2801 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.94 % Favored : 91.94 % Rotamer: Outliers : 2.41 % Allowed : 20.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.17), residues: 2344 helix: -0.46 (0.33), residues: 236 sheet: 0.31 (0.18), residues: 863 loop : -1.61 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 418 HIS 0.004 0.001 HIS C 400 PHE 0.022 0.001 PHE L 479 TYR 0.014 0.001 TYR E 375 ARG 0.007 0.000 ARG I 83 ********************** 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 fitting. rotamer outliers: 51 poor density : 173 time to evaluate : 2.380 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: 0.8415 (pttt) cc_final: 0.7413 (mmtt) REVERT: B 376 ASP cc_start: 0.8325 (p0) cc_final: 0.7932 (p0) REVERT: B 419 ASN cc_start: 0.9367 (t0) cc_final: 0.9109 (t0) REVERT: D 405 PHE cc_start: 0.6543 (t80) cc_final: 0.6096 (t80) REVERT: E 358 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: G 375 TYR cc_start: 0.8189 (m-80) cc_final: 0.7797 (m-80) REVERT: I 121 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.7760 (t0) REVERT: J 31 ASP cc_start: 0.8720 (m-30) cc_final: 0.8172 (m-30) REVERT: K 364 LYS cc_start: 0.7232 (mtmt) cc_final: 0.6812 (mtmm) REVERT: L 524 SER cc_start: 0.8633 (m) cc_final: 0.8277 (t) REVERT: L 534 TYR cc_start: 0.8786 (m-10) cc_final: 0.8238 (m-10) outliers start: 51 outliers final: 47 residues processed: 209 average time/residue: 0.3453 time to fit residues: 107.7102 Evaluate side-chains 208 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 159 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain C residue 477 THR 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 394 THR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 533 THR 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 364 LYS Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 523 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 499 LYS 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 483 ASP 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 121 ASN Chi-restraints excluded: chain I residue 123 HIS 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 365 LEU Chi-restraints excluded: chain K residue 432 ASP Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain K residue 570 ASP Chi-restraints excluded: chain L residue 515 TYR 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 196 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 169 optimal weight: 0.5980 chunk 27 optimal weight: 0.0270 chunk 51 optimal weight: 20.0000 chunk 184 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 33 optimal weight: 0.0040 chunk 161 optimal weight: 2.9990 overall best weight: 0.4050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.091702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.060858 restraints weight = 66607.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.063973 restraints weight = 42044.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.064246 restraints weight = 25926.564| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19049 Z= 0.166 Angle : 0.612 10.184 26062 Z= 0.311 Chirality : 0.045 0.197 3095 Planarity : 0.004 0.048 3327 Dihedral : 4.171 22.208 2801 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.68 % Favored : 92.19 % Rotamer: Outliers : 2.60 % Allowed : 20.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2344 helix: -0.32 (0.33), residues: 235 sheet: 0.42 (0.18), residues: 870 loop : -1.56 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 418 HIS 0.010 0.001 HIS K 400 PHE 0.022 0.001 PHE L 479 TYR 0.014 0.001 TYR E 375 ARG 0.006 0.000 ARG I 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3861.50 seconds wall clock time: 71 minutes 14.97 seconds (4274.97 seconds total)