Starting phenix.real_space_refine on Sun Feb 18 10:46:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytd_34086/02_2024/7ytd_34086.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytd_34086/02_2024/7ytd_34086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytd_34086/02_2024/7ytd_34086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytd_34086/02_2024/7ytd_34086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytd_34086/02_2024/7ytd_34086.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytd_34086/02_2024/7ytd_34086.pdb" } resolution = 3.71 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= 0.006 sd= 0.030 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 116 5.16 5 C 13645 2.51 5 N 3696 2.21 5 O 4236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 526": "OE1" <-> "OE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "B TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 462": "OE1" <-> "OE2" Residue "D TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 508": "OE1" <-> "OE2" Residue "E TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 4": "NH1" <-> "NH2" Residue "J ARG 16": "NH1" <-> "NH2" Residue "J ASP 27": "OD1" <-> "OD2" Residue "J GLU 30": "OE1" <-> "OE2" Residue "J TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "S GLU 26": "OE1" <-> "OE2" Residue "S GLU 41": "OE1" <-> "OE2" Residue "S GLU 90": "OE1" <-> "OE2" Residue "S GLU 96": "OE1" <-> "OE2" Residue "U GLU 51": "OE1" <-> "OE2" Residue "U GLU 96": "OE1" <-> "OE2" Residue "V GLU 28": "OE1" <-> "OE2" Residue "V TYR 81": "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: 21693 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 18, 'TRANS': 210} Chain: "B" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1749 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 18, 'TRANS': 206} Chain: "C" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 206} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1749 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 18, 'TRANS': 206} 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: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1723 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain breaks: 1 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: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1730 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 18, 'TRANS': 203} Chain breaks: 1 Chain: "J" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 834 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain breaks: 1 Chain: "K" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1737 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain breaks: 1 Chain: "L" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1761 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 208} Chain breaks: 1 Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "S" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "U" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "V" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} 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: 11.23, per 1000 atoms: 0.52 Number of scatterers: 21693 At special positions: 0 Unit cell: (121.716, 187.128, 164.772, 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 116 16.00 O 4236 8.00 N 3696 7.00 C 13645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, 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=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.04 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.04 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.05 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=1.99 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS L 575 " distance=1.88 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 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.04 Simple disulfide: pdb=" SG CYS R 37 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 49 " - pdb=" SG CYS R 58 " distance=2.03 Simple disulfide: pdb=" SG CYS S 37 " - pdb=" SG CYS S 104 " distance=2.03 Simple disulfide: pdb=" SG CYS S 49 " - pdb=" SG CYS S 58 " distance=2.02 Simple disulfide: pdb=" SG CYS U 37 " - pdb=" SG CYS U 104 " distance=2.03 Simple disulfide: pdb=" SG CYS U 49 " - pdb=" SG CYS U 58 " distance=2.03 Simple disulfide: pdb=" SG CYS V 37 " - pdb=" SG CYS V 104 " distance=2.03 Simple disulfide: pdb=" SG CYS V 49 " - pdb=" SG CYS V 58 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG 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 " Time building additional restraints: 8.71 Conformation dependent library (CDL) restraints added in 4.0 seconds 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5284 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 65 sheets defined 11.2% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 461 through 466 removed outlier: 3.933A pdb=" N LEU A 466 " --> pdb=" O GLN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.585A pdb=" N TRP A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.678A pdb=" N LEU B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 Processing helix chain 'B' and resid 462 through 467 removed outlier: 4.111A pdb=" N LEU B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B 467 " --> pdb=" O GLN B 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 462 through 467' Processing helix chain 'B' and resid 524 through 530 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 524 through 530 removed outlier: 3.785A pdb=" N TRP C 528 " --> pdb=" O SER C 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 removed outlier: 3.817A pdb=" N THR D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 419 removed outlier: 4.103A pdb=" N TRP D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 467 removed outlier: 3.530A pdb=" N LEU D 464 " --> pdb=" O ALA D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 531 Processing helix chain 'E' and resid 353 through 360 removed outlier: 3.812A pdb=" N THR E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 419 removed outlier: 3.850A pdb=" N TRP E 418 " --> pdb=" O CYS E 414 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 414 through 419' Processing helix chain 'E' and resid 462 through 467 removed outlier: 4.193A pdb=" N LEU E 466 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG E 467 " --> pdb=" O GLN E 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 462 through 467' Processing helix chain 'E' and resid 524 through 529 Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 414 through 419 removed outlier: 4.015A pdb=" N TRP F 418 " --> pdb=" O CYS F 414 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 414 through 419' Processing helix chain 'F' and resid 462 through 466 removed outlier: 3.696A pdb=" N ASN F 465 " --> pdb=" O GLU F 462 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU F 466 " --> pdb=" O GLN F 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 462 through 466' Processing helix chain 'F' and resid 524 through 531 removed outlier: 3.546A pdb=" N TRP F 528 " --> pdb=" O SER F 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 359 removed outlier: 3.882A pdb=" N LEU G 359 " --> pdb=" O ALA G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 Processing helix chain 'G' and resid 462 through 466 removed outlier: 3.545A pdb=" N ASN G 465 " --> pdb=" O GLU G 462 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU G 466 " --> pdb=" O GLN G 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 462 through 466' Processing helix chain 'G' and resid 524 through 531 removed outlier: 3.813A pdb=" N TRP G 528 " --> pdb=" O SER G 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 553 through 557 removed outlier: 3.527A pdb=" N THR G 556 " --> pdb=" O ASP G 553 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY G 557 " --> pdb=" O LYS G 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 553 through 557' Processing helix chain 'H' and resid 353 through 361 Processing helix chain 'H' and resid 414 through 421 Processing helix chain 'H' and resid 462 through 466 removed outlier: 3.510A pdb=" N ASN H 465 " --> pdb=" O GLU H 462 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU H 466 " --> pdb=" O GLN H 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 462 through 466' Processing helix chain 'H' and resid 524 through 530 Processing helix chain 'J' and resid 65 through 69 removed outlier: 3.714A pdb=" N CYS J 68 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS J 69 " --> pdb=" O ASP J 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 65 through 69' Processing helix chain 'K' and resid 353 through 361 removed outlier: 3.706A pdb=" N LEU K 359 " --> pdb=" O ALA K 355 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR K 360 " --> pdb=" O SER K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 419 removed outlier: 3.663A pdb=" N ASN K 419 " --> pdb=" O GLU K 415 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 465 Processing helix chain 'K' and resid 496 through 498 No H-bonds generated for 'chain 'K' and resid 496 through 498' Processing helix chain 'K' and resid 525 through 531 removed outlier: 4.260A pdb=" N ASN K 529 " --> pdb=" O GLU K 525 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 558 removed outlier: 3.896A pdb=" N GLY K 557 " --> pdb=" O ASP K 553 " (cutoff:3.500A) Processing helix chain 'L' and resid 353 through 358 Processing helix chain 'L' and resid 414 through 418 removed outlier: 3.946A pdb=" N TRP L 418 " --> pdb=" O GLU L 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 465 removed outlier: 3.551A pdb=" N LEU L 464 " --> pdb=" O ALA L 460 " (cutoff:3.500A) Processing helix chain 'L' and resid 525 through 531 Processing helix chain 'R' and resid 109 through 113 Processing helix chain 'U' and resid 69 through 73 removed outlier: 3.567A pdb=" N LYS U 73 " --> pdb=" O ALA U 70 " (cutoff:3.500A) Processing helix chain 'U' and resid 109 through 113 removed outlier: 3.662A pdb=" N GLY U 113 " --> pdb=" O ASN U 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 109 through 113' Processing helix chain 'V' and resid 109 through 113 removed outlier: 3.602A pdb=" N GLY V 113 " --> pdb=" O ASN V 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 109 through 113' Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 347 removed outlier: 3.667A pdb=" N ALA A 407 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP A 371 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE A 405 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 383 removed outlier: 6.314A pdb=" N HIS A 430 " --> pdb=" O SER A 435 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N SER A 435 " --> pdb=" O HIS A 430 " (cutoff:3.500A) 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AA6, first strand: chain 'A' and resid 568 through 569 Processing sheet with id=AA7, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.777A pdb=" N THR B 366 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR B 363 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU B 365 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA B 411 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 381 through 383 removed outlier: 4.127A pdb=" N VAL B 428 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B 437 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 381 through 383 Processing sheet with id=AB1, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.549A pdb=" N GLY B 478 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.549A pdb=" N GLY B 478 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AB4, first strand: chain 'C' and resid 346 through 350 removed outlier: 5.305A pdb=" N THR C 370 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA C 407 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 404 " --> pdb=" O HIS C 400 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 346 through 350 Processing sheet with id=AB6, first strand: chain 'C' and resid 380 through 383 Processing sheet with id=AB7, first strand: chain 'C' and resid 453 through 457 removed outlier: 3.727A pdb=" N THR C 477 " --> pdb=" O ASP C 453 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER C 519 " --> pdb=" O CYS C 474 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 453 through 457 removed outlier: 3.727A pdb=" N THR C 477 " --> pdb=" O ASP C 453 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG C 514 " --> pdb=" O GLU C 508 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AC1, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.739A pdb=" N ALA D 407 " --> pdb=" O VAL D 369 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 379 through 383 removed outlier: 3.575A pdb=" N THR D 425 " --> pdb=" O THR D 383 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 453 through 457 removed outlier: 6.065A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 453 through 457 removed outlier: 6.065A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 493 through 494 Processing sheet with id=AC6, first strand: chain 'E' and resid 346 through 350 removed outlier: 5.763A pdb=" N THR E 366 " --> pdb=" O ALA E 411 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ALA E 411 " --> pdb=" O THR E 366 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU E 368 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY E 409 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N THR E 370 " --> pdb=" O ALA E 407 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ALA E 407 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 3.829A 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: 3.661A pdb=" N ASP E 453 " --> pdb=" O THR E 477 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.661A pdb=" N ASP E 453 " --> pdb=" O THR E 477 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 485 through 489 Processing sheet with id=AD2, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AD3, first strand: chain 'F' and resid 379 through 383 Processing sheet with id=AD4, first strand: chain 'F' and resid 455 through 457 removed outlier: 3.545A pdb=" N ILE F 472 " --> pdb=" O LEU F 521 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL F 476 " --> pdb=" O ALA F 517 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 455 through 457 removed outlier: 3.545A pdb=" N ILE F 472 " --> pdb=" O LEU F 521 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL F 476 " --> pdb=" O ALA F 517 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 493 through 494 Processing sheet with id=AD7, first strand: chain 'F' and resid 565 through 567 removed outlier: 6.284A pdb=" N SER F 565 " --> pdb=" O LEU G 566 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 347 through 350 removed outlier: 3.539A pdb=" N GLY G 409 " --> pdb=" O CYS G 367 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA G 407 " --> pdb=" O VAL G 369 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N PHE G 405 " --> pdb=" O ASP G 371 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 379 through 383 Processing sheet with id=AE1, first strand: chain 'G' and resid 453 through 457 removed outlier: 5.332A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 453 through 457 removed outlier: 5.332A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 493 through 494 removed outlier: 3.528A pdb=" N GLN G 493 " --> pdb=" O GLN G 490 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN G 490 " --> pdb=" O GLN G 493 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 346 through 350 Processing sheet with id=AE5, first strand: chain 'H' and resid 379 through 383 removed outlier: 3.651A pdb=" N PHE H 424 " --> pdb=" O ILE H 441 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU H 437 " --> pdb=" O VAL H 428 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 455 through 457 removed outlier: 3.647A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 493 through 494 Processing sheet with id=AE8, first strand: chain 'H' and resid 506 through 507 Processing sheet with id=AE9, first strand: chain 'J' and resid 40 through 41 removed outlier: 3.577A pdb=" N VAL J 41 " --> pdb=" O VAL L 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'J' and resid 110 through 113 Processing sheet with id=AF2, first strand: chain 'K' and resid 347 through 350 Processing sheet with id=AF3, first strand: chain 'K' and resid 378 through 384 Processing sheet with id=AF4, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.581A pdb=" N VAL K 476 " --> pdb=" O ALA K 517 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.581A pdb=" N VAL K 476 " --> pdb=" O ALA K 517 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 485 through 489 Processing sheet with id=AF7, first strand: chain 'K' and resid 564 through 565 Processing sheet with id=AF8, first strand: chain 'L' and resid 346 through 350 removed outlier: 3.823A pdb=" N ASP L 371 " --> pdb=" O PHE L 405 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE L 405 " --> pdb=" O ASP L 371 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 381 through 384 removed outlier: 3.564A pdb=" N PHE L 424 " --> pdb=" O ILE L 441 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 453 through 457 removed outlier: 3.797A pdb=" N THR L 473 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 453 through 457 removed outlier: 3.797A pdb=" N THR L 473 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 493 through 494 Processing sheet with id=AG4, first strand: chain 'R' and resid 33 through 38 Processing sheet with id=AG5, first strand: chain 'R' and resid 57 through 62 removed outlier: 6.939A pdb=" N LEU R 48 " --> pdb=" O VAL R 61 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N VAL R 101 " --> pdb=" O GLU R 51 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR R 102 " --> pdb=" O LYS R 117 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS R 117 " --> pdb=" O TYR R 102 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N CYS R 104 " --> pdb=" O THR R 115 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 33 through 38 Processing sheet with id=AG7, first strand: chain 'S' and resid 57 through 62 removed outlier: 7.069A pdb=" N LEU S 48 " --> pdb=" O VAL S 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS S 104 " --> pdb=" O GLN S 116 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN S 116 " --> pdb=" O CYS S 104 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 33 through 38 Processing sheet with id=AG9, first strand: chain 'U' and resid 57 through 63 removed outlier: 7.029A pdb=" N LEU U 48 " --> pdb=" O VAL U 61 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER U 63 " --> pdb=" O ILE U 46 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE U 46 " --> pdb=" O SER U 63 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL U 101 " --> pdb=" O GLU U 51 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR U 102 " --> pdb=" O LYS U 117 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS U 117 " --> pdb=" O TYR U 102 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS U 104 " --> pdb=" O THR U 115 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'V' and resid 33 through 38 Processing sheet with id=AH2, first strand: chain 'V' and resid 57 through 62 removed outlier: 7.071A pdb=" N LEU V 48 " --> pdb=" O VAL V 61 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS V 104 " --> pdb=" O THR V 115 " (cutoff:3.500A) 770 hydrogen bonds defined for protein. 1941 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: 7.36 Time building geometry restraints manager: 9.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3549 1.31 - 1.44: 5882 1.44 - 1.57: 12606 1.57 - 1.70: 0 1.70 - 1.83: 159 Bond restraints: 22196 Sorted by residual: bond pdb=" C ASN V 85 " pdb=" N LEU V 86 " ideal model delta sigma weight residual 1.331 1.552 -0.221 1.41e-02 5.03e+03 2.47e+02 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.541 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C THR L 574 " pdb=" N CYS L 575 " ideal model delta sigma weight residual 1.329 1.421 -0.092 1.40e-02 5.10e+03 4.28e+01 bond pdb=" C SER A 569 " pdb=" N ASP A 570 " ideal model delta sigma weight residual 1.333 1.402 -0.069 1.39e-02 5.18e+03 2.47e+01 bond pdb=" CA TYR C 455 " pdb=" C TYR C 455 " ideal model delta sigma weight residual 1.520 1.467 0.052 1.12e-02 7.97e+03 2.19e+01 ... (remaining 22191 not shown) Histogram of bond angle deviations from ideal: 97.61 - 104.92: 612 104.92 - 112.23: 11726 112.23 - 119.54: 7071 119.54 - 126.85: 10531 126.85 - 134.16: 374 Bond angle restraints: 30314 Sorted by residual: angle pdb=" C ASN V 85 " pdb=" N LEU V 86 " pdb=" CA LEU V 86 " ideal model delta sigma weight residual 122.59 99.67 22.92 1.57e+00 4.06e-01 2.13e+02 angle pdb=" C THR L 574 " pdb=" N CYS L 575 " pdb=" CA CYS L 575 " ideal model delta sigma weight residual 121.70 105.63 16.07 1.80e+00 3.09e-01 7.97e+01 angle pdb=" CA SER A 569 " pdb=" C SER A 569 " pdb=" O SER A 569 " ideal model delta sigma weight residual 121.44 111.32 10.12 1.17e+00 7.31e-01 7.48e+01 angle pdb=" N VAL V 122 " pdb=" CA VAL V 122 " pdb=" C VAL V 122 " ideal model delta sigma weight residual 110.30 118.08 -7.78 9.70e-01 1.06e+00 6.44e+01 angle pdb=" N SER A 569 " pdb=" CA SER A 569 " pdb=" C SER A 569 " ideal model delta sigma weight residual 109.52 120.57 -11.05 1.55e+00 4.16e-01 5.09e+01 ... (remaining 30309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.66: 12352 18.66 - 37.31: 995 37.31 - 55.97: 260 55.97 - 74.63: 39 74.63 - 93.28: 21 Dihedral angle restraints: 13667 sinusoidal: 5544 harmonic: 8123 Sorted by residual: dihedral pdb=" CB CYS R 49 " pdb=" SG CYS R 49 " pdb=" SG CYS R 58 " pdb=" CB CYS R 58 " ideal model delta sinusoidal sigma weight residual -86.00 -159.92 73.92 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS V 49 " pdb=" SG CYS V 49 " pdb=" SG CYS V 58 " pdb=" CB CYS V 58 " ideal model delta sinusoidal sigma weight residual -86.00 -155.64 69.64 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS U 49 " pdb=" SG CYS U 49 " pdb=" SG CYS U 58 " pdb=" CB CYS U 58 " ideal model delta sinusoidal sigma weight residual -86.00 -152.86 66.86 1 1.00e+01 1.00e-02 5.83e+01 ... (remaining 13664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.395: 3588 0.395 - 0.791: 9 0.791 - 1.186: 1 1.186 - 1.581: 0 1.581 - 1.977: 2 Chirality restraints: 3600 Sorted by residual: 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 -0.42 -1.98 2.00e-01 2.50e+01 9.77e+01 chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 563 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -0.54 -1.86 2.00e-01 2.50e+01 8.65e+01 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 563 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.22 -1.18 2.00e-01 2.50e+01 3.51e+01 ... (remaining 3597 not shown) Planarity restraints: 3873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 563 " -0.068 2.00e-02 2.50e+03 6.35e-02 5.04e+01 pdb=" CG ASN K 563 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN K 563 " 0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN K 563 " 0.092 2.00e-02 2.50e+03 pdb=" C1 NAG K 601 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET K 489 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C MET K 489 " 0.073 2.00e-02 2.50e+03 pdb=" O MET K 489 " -0.028 2.00e-02 2.50e+03 pdb=" N GLN K 490 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 563 " 0.030 2.00e-02 2.50e+03 3.51e-02 1.54e+01 pdb=" CG ASN C 563 " -0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN C 563 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN C 563 " -0.061 2.00e-02 2.50e+03 pdb=" C1 NAG C 601 " 0.039 2.00e-02 2.50e+03 ... (remaining 3870 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 30 1.93 - 2.67: 844 2.67 - 3.42: 30776 3.42 - 4.16: 51572 4.16 - 4.90: 87931 Nonbonded interactions: 171153 Sorted by model distance: nonbonded pdb=" CE1 HIS E 450 " pdb=" NH2 ARG E 514 " model vdw 1.188 3.340 nonbonded pdb=" N TYR V 81 " pdb=" O LEU V 86 " model vdw 1.252 2.520 nonbonded pdb=" O VAL U 23 " pdb=" CB LEU U 120 " model vdw 1.262 3.440 nonbonded pdb=" OG1 THR J 102 " pdb=" N CYS L 575 " model vdw 1.331 2.520 nonbonded pdb=" CD1 ILE J 17 " pdb=" CA ILE J 37 " model vdw 1.332 3.890 ... (remaining 171148 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 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'B' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'C' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 568 o \ r resid 601)) selection = (chain 'D' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'E' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'F' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'G' and (resid 345 through 444 or resid 449 through 512 or (resid 513 and \ (name N or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'H' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'K' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'L' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 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: 0.030 Extract box with map and model: 8.240 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 57.760 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.130 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.221 22196 Z= 0.338 Angle : 0.963 22.918 30314 Z= 0.558 Chirality : 0.079 1.977 3600 Planarity : 0.006 0.092 3863 Dihedral : 14.871 93.281 8281 Min Nonbonded Distance : 1.188 Molprobity Statistics. All-atom Clashscore : 29.57 Ramachandran Plot: Outliers : 0.91 % Allowed : 8.59 % Favored : 90.50 % Rotamer: Outliers : 4.37 % Allowed : 2.63 % Favored : 93.00 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.91 (0.16), residues: 2737 helix: -0.88 (0.37), residues: 180 sheet: -0.96 (0.16), residues: 1037 loop : -1.52 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 528 HIS 0.009 0.001 HIS F 518 PHE 0.019 0.002 PHE H 516 TYR 0.027 0.002 TYR B 455 ARG 0.012 0.000 ARG U 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 388 time to evaluate : 2.878 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 529 ASN cc_start: 0.9264 (m110) cc_final: 0.9026 (m110) REVERT: C 395 ASN cc_start: 0.5687 (t0) cc_final: 0.5277 (t0) REVERT: C 561 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8741 (mm) REVERT: D 424 PHE cc_start: 0.8586 (m-80) cc_final: 0.8245 (m-80) REVERT: D 510 GLN cc_start: 0.8305 (pp30) cc_final: 0.8071 (pp30) REVERT: D 534 TYR cc_start: 0.8559 (m-80) cc_final: 0.7940 (m-80) REVERT: E 461 ARG cc_start: 0.8015 (mmm160) cc_final: 0.7734 (mmm160) REVERT: F 493 GLN cc_start: 0.8285 (pp30) cc_final: 0.7886 (pp30) REVERT: H 506 MET cc_start: 0.7857 (mmp) cc_final: 0.7602 (mmm) REVERT: J 16 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6523 (tmm160) REVERT: L 520 ILE cc_start: 0.9135 (pt) cc_final: 0.8931 (pt) REVERT: R 36 LYS cc_start: 0.7196 (tptt) cc_final: 0.6964 (tppt) REVERT: R 46 ILE cc_start: 0.9213 (tp) cc_final: 0.8860 (tp) REVERT: R 52 MET cc_start: 0.8274 (tpt) cc_final: 0.8047 (tpp) REVERT: S 46 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8696 (tp) REVERT: U 26 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7648 (tp30) REVERT: U 66 ASN cc_start: 0.8082 (p0) cc_final: 0.7511 (t0) REVERT: U 87 PHE cc_start: 0.8080 (t80) cc_final: 0.7711 (t80) REVERT: U 111 ASP cc_start: 0.7822 (p0) cc_final: 0.7598 (p0) REVERT: U 112 ARG cc_start: 0.8211 (mmp80) cc_final: 0.7988 (mmp80) REVERT: V 43 HIS cc_start: 0.6836 (m-70) cc_final: 0.6610 (m-70) REVERT: V 83 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6511 (ptt-90) REVERT: V 87 PHE cc_start: 0.8110 (t80) cc_final: 0.7529 (t80) outliers start: 108 outliers final: 73 residues processed: 472 average time/residue: 0.3509 time to fit residues: 253.0336 Evaluate side-chains 360 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 282 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 562 TYR Chi-restraints excluded: chain C residue 563 ASN Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 568 MET Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 485 PHE Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 510 GLN Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 68 CYS Chi-restraints excluded: chain J residue 134 TYR Chi-restraints excluded: chain K residue 490 GLN Chi-restraints excluded: chain K residue 493 GLN Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 95 THR Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 28 GLU Chi-restraints excluded: chain S residue 41 GLU Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 98 ASP Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 114 LYS Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 23 VAL Chi-restraints excluded: chain V residue 26 GLU Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 80 GLN Chi-restraints excluded: chain V residue 81 TYR Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 84 LYS Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 96 GLU Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Chi-restraints excluded: chain V residue 124 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 113 optimal weight: 40.0000 chunk 69 optimal weight: 30.0000 chunk 138 optimal weight: 9.9990 chunk 109 optimal weight: 0.5980 chunk 211 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 157 optimal weight: 40.0000 chunk 245 optimal weight: 10.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN F 419 ASN G 463 GLN ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 400 HIS L 463 GLN U 123 HIS V 123 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 22196 Z= 0.317 Angle : 0.762 17.439 30314 Z= 0.380 Chirality : 0.051 0.610 3600 Planarity : 0.005 0.083 3863 Dihedral : 9.773 100.791 3346 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.29 % Favored : 91.63 % Rotamer: Outliers : 4.09 % Allowed : 11.97 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.93 (0.16), residues: 2737 helix: -1.17 (0.31), residues: 218 sheet: -0.97 (0.16), residues: 1051 loop : -1.50 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 528 HIS 0.008 0.001 HIS C 430 PHE 0.021 0.002 PHE B 354 TYR 0.019 0.002 TYR H 375 ARG 0.009 0.001 ARG F 514 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 299 time to evaluate : 2.835 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: B 515 TYR cc_start: 0.8035 (m-10) cc_final: 0.7816 (m-80) REVERT: C 395 ASN cc_start: 0.5610 (t0) cc_final: 0.5169 (t0) REVERT: C 561 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8028 (mm) REVERT: D 424 PHE cc_start: 0.8535 (m-80) cc_final: 0.8278 (m-80) REVERT: D 510 GLN cc_start: 0.8354 (pp30) cc_final: 0.8113 (pp30) REVERT: E 483 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8073 (t0) REVERT: F 493 GLN cc_start: 0.8301 (pp30) cc_final: 0.7981 (pp30) REVERT: J 8 VAL cc_start: 0.4639 (p) cc_final: 0.4277 (t) REVERT: J 37 ILE cc_start: 0.6836 (mm) cc_final: 0.6534 (mm) REVERT: J 66 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8155 (p0) REVERT: K 463 GLN cc_start: 0.8465 (tp-100) cc_final: 0.8222 (tp-100) REVERT: K 475 LEU cc_start: 0.9088 (tp) cc_final: 0.8818 (tp) REVERT: K 483 ASP cc_start: 0.8159 (t0) cc_final: 0.7918 (t0) REVERT: L 463 GLN cc_start: 0.8246 (pt0) cc_final: 0.7890 (pt0) REVERT: L 489 MET cc_start: 0.7614 (ttm) cc_final: 0.7234 (tpp) REVERT: R 36 LYS cc_start: 0.7283 (tptt) cc_final: 0.6920 (tppt) REVERT: S 51 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6458 (mp0) REVERT: S 94 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7500 (tp) REVERT: U 87 PHE cc_start: 0.7990 (t80) cc_final: 0.7753 (t80) REVERT: U 111 ASP cc_start: 0.7957 (p0) cc_final: 0.7438 (p0) REVERT: U 112 ARG cc_start: 0.8499 (mmp80) cc_final: 0.8204 (mmp80) REVERT: V 26 GLU cc_start: 0.6151 (OUTLIER) cc_final: 0.5885 (tt0) REVERT: V 81 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.5657 (m-80) REVERT: V 83 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6788 (mtm180) REVERT: V 87 PHE cc_start: 0.7960 (t80) cc_final: 0.7499 (t80) outliers start: 101 outliers final: 71 residues processed: 375 average time/residue: 0.3114 time to fit residues: 184.3351 Evaluate side-chains 354 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 275 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 510 GLN Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 376 ASP Chi-restraints excluded: chain K residue 493 GLN Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 95 THR Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 114 LYS Chi-restraints excluded: chain S residue 116 GLN Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 26 GLU Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 81 TYR Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 0.2980 chunk 76 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 166 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 245 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 243 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 400 HIS H 529 ASN K 463 GLN ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22196 Z= 0.242 Angle : 0.694 16.353 30314 Z= 0.344 Chirality : 0.049 0.581 3600 Planarity : 0.005 0.084 3863 Dihedral : 8.187 86.836 3278 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.67 % Favored : 92.29 % Rotamer: Outliers : 4.25 % Allowed : 14.68 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.85 (0.16), residues: 2737 helix: -0.82 (0.33), residues: 222 sheet: -0.91 (0.16), residues: 1060 loop : -1.50 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 528 HIS 0.006 0.001 HIS C 430 PHE 0.023 0.002 PHE A 354 TYR 0.022 0.002 TYR D 534 ARG 0.016 0.000 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 299 time to evaluate : 2.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 ARG cc_start: 0.8036 (mmm160) cc_final: 0.7651 (mmp-170) REVERT: B 415 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8333 (mp0) REVERT: C 395 ASN cc_start: 0.5379 (t0) cc_final: 0.4919 (t0) REVERT: C 521 LEU cc_start: 0.9138 (tt) cc_final: 0.8921 (tt) REVERT: C 568 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.6681 (pmm) REVERT: D 424 PHE cc_start: 0.8509 (m-80) cc_final: 0.8200 (m-10) REVERT: D 510 GLN cc_start: 0.8410 (pp30) cc_final: 0.8176 (pp30) REVERT: E 354 PHE cc_start: 0.8501 (t80) cc_final: 0.8204 (t80) REVERT: E 465 ASN cc_start: 0.8290 (m-40) cc_final: 0.8085 (m-40) REVERT: E 483 ASP cc_start: 0.8296 (t0) cc_final: 0.7923 (t0) REVERT: F 461 ARG cc_start: 0.8200 (mmm160) cc_final: 0.7929 (mmm-85) REVERT: J 67 LEU cc_start: 0.7278 (mp) cc_final: 0.7034 (mp) REVERT: K 463 GLN cc_start: 0.8676 (tp40) cc_final: 0.8340 (tp-100) REVERT: K 483 ASP cc_start: 0.8111 (t0) cc_final: 0.7750 (t0) REVERT: L 521 LEU cc_start: 0.7685 (tp) cc_final: 0.6823 (mt) REVERT: R 36 LYS cc_start: 0.7211 (tptt) cc_final: 0.6834 (tppt) REVERT: S 51 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6441 (mp0) REVERT: S 96 GLU cc_start: 0.8662 (tp30) cc_final: 0.8420 (tm-30) REVERT: S 108 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8700 (mmp) REVERT: S 114 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7215 (ptpt) REVERT: U 26 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: U 42 MET cc_start: 0.6988 (tpp) cc_final: 0.6733 (tpp) REVERT: U 87 PHE cc_start: 0.7986 (t80) cc_final: 0.7731 (t80) REVERT: U 123 HIS cc_start: 0.7358 (OUTLIER) cc_final: 0.7021 (t70) REVERT: V 81 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6081 (m-80) REVERT: V 83 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6781 (mtm180) REVERT: V 87 PHE cc_start: 0.7958 (t80) cc_final: 0.7470 (t80) outliers start: 105 outliers final: 70 residues processed: 381 average time/residue: 0.3077 time to fit residues: 184.7527 Evaluate side-chains 347 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 268 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 568 MET Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 510 GLN Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 95 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 114 LYS Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain U residue 123 HIS Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 81 TYR Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 8.9990 chunk 184 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 246 optimal weight: 9.9990 chunk 260 optimal weight: 40.0000 chunk 128 optimal weight: 0.9980 chunk 233 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN A 510 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22196 Z= 0.239 Angle : 0.686 13.678 30314 Z= 0.338 Chirality : 0.048 0.626 3600 Planarity : 0.004 0.083 3863 Dihedral : 7.598 79.870 3259 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.85 % Allowed : 16.18 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.76 (0.16), residues: 2737 helix: -0.71 (0.33), residues: 225 sheet: -0.81 (0.16), residues: 1051 loop : -1.49 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 528 HIS 0.005 0.001 HIS C 430 PHE 0.017 0.002 PHE H 424 TYR 0.017 0.002 TYR E 455 ARG 0.008 0.000 ARG J 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 278 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7806 (mmm160) REVERT: B 415 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: C 395 ASN cc_start: 0.5392 (t0) cc_final: 0.5069 (t0) REVERT: C 430 HIS cc_start: 0.4671 (OUTLIER) cc_final: 0.4467 (t70) REVERT: C 521 LEU cc_start: 0.9152 (tt) cc_final: 0.8877 (tt) REVERT: C 568 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7274 (ppp) REVERT: D 424 PHE cc_start: 0.8451 (m-80) cc_final: 0.8206 (m-10) REVERT: D 510 GLN cc_start: 0.8432 (pp30) cc_final: 0.8194 (pp30) REVERT: E 354 PHE cc_start: 0.8555 (t80) cc_final: 0.8262 (t80) REVERT: E 483 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7908 (t0) REVERT: F 461 ARG cc_start: 0.8222 (mmm160) cc_final: 0.7874 (mmm160) REVERT: G 483 ASP cc_start: 0.7712 (t0) cc_final: 0.7446 (t0) REVERT: J 67 LEU cc_start: 0.7369 (mp) cc_final: 0.7167 (mp) REVERT: K 463 GLN cc_start: 0.8620 (tp40) cc_final: 0.8336 (tp-100) REVERT: K 483 ASP cc_start: 0.8125 (t0) cc_final: 0.7791 (t0) REVERT: L 489 MET cc_start: 0.7619 (ttm) cc_final: 0.7297 (tpp) REVERT: R 36 LYS cc_start: 0.7242 (tptt) cc_final: 0.6864 (tppt) REVERT: S 51 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6400 (mp0) REVERT: S 52 MET cc_start: 0.7061 (pmm) cc_final: 0.6824 (pmm) REVERT: S 96 GLU cc_start: 0.8510 (tp30) cc_final: 0.8298 (tm-30) REVERT: S 114 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7436 (ptpt) REVERT: U 26 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: U 42 MET cc_start: 0.6984 (tpp) cc_final: 0.6777 (tpp) REVERT: U 87 PHE cc_start: 0.7929 (t80) cc_final: 0.7684 (t80) REVERT: U 123 HIS cc_start: 0.7319 (OUTLIER) cc_final: 0.6906 (t70) REVERT: V 87 PHE cc_start: 0.7961 (t80) cc_final: 0.7499 (t80) outliers start: 120 outliers final: 83 residues processed: 367 average time/residue: 0.3037 time to fit residues: 178.3439 Evaluate side-chains 345 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 254 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 541 GLU Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 416 ASP Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 510 GLN Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 545 ASN Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 375 TYR Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 562 TYR Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 95 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 114 LYS Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain U residue 123 HIS Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 9.9990 chunk 148 optimal weight: 0.3980 chunk 3 optimal weight: 50.0000 chunk 194 optimal weight: 40.0000 chunk 107 optimal weight: 4.9990 chunk 222 optimal weight: 7.9990 chunk 180 optimal weight: 0.5980 chunk 0 optimal weight: 60.0000 chunk 133 optimal weight: 10.0000 chunk 234 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22196 Z= 0.284 Angle : 0.691 13.576 30314 Z= 0.342 Chirality : 0.048 0.634 3600 Planarity : 0.005 0.084 3863 Dihedral : 7.322 69.221 3246 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.94 % Allowed : 17.60 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.16), residues: 2737 helix: -0.75 (0.33), residues: 224 sheet: -0.83 (0.16), residues: 1048 loop : -1.40 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 528 HIS 0.005 0.001 HIS C 430 PHE 0.016 0.002 PHE S 87 TYR 0.022 0.002 TYR K 455 ARG 0.004 0.000 ARG J 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 267 time to evaluate : 2.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 ARG cc_start: 0.8234 (mmm160) cc_final: 0.7821 (mmm160) REVERT: B 415 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8313 (mp0) REVERT: C 395 ASN cc_start: 0.5069 (t0) cc_final: 0.4706 (t0) REVERT: C 430 HIS cc_start: 0.4684 (OUTLIER) cc_final: 0.4445 (t70) REVERT: C 568 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7284 (ppp) REVERT: D 424 PHE cc_start: 0.8458 (m-80) cc_final: 0.8257 (m-80) REVERT: D 510 GLN cc_start: 0.8503 (pp30) cc_final: 0.8229 (pp30) REVERT: E 354 PHE cc_start: 0.8560 (t80) cc_final: 0.8252 (t80) REVERT: E 483 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7932 (t0) REVERT: F 461 ARG cc_start: 0.8155 (mmm160) cc_final: 0.7767 (mmm160) REVERT: G 483 ASP cc_start: 0.7725 (t0) cc_final: 0.7478 (t0) REVERT: K 347 VAL cc_start: 0.0039 (OUTLIER) cc_final: -0.0268 (m) REVERT: K 453 ASP cc_start: 0.8384 (m-30) cc_final: 0.7517 (p0) REVERT: K 463 GLN cc_start: 0.8705 (tp40) cc_final: 0.8456 (tp-100) REVERT: K 483 ASP cc_start: 0.8172 (t0) cc_final: 0.7814 (t0) REVERT: L 489 MET cc_start: 0.7661 (ttm) cc_final: 0.7310 (tpp) REVERT: L 568 MET cc_start: 0.5681 (mtt) cc_final: 0.5465 (mtm) REVERT: R 36 LYS cc_start: 0.7257 (tptt) cc_final: 0.6883 (tppt) REVERT: S 51 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6417 (mp0) REVERT: U 123 HIS cc_start: 0.7416 (OUTLIER) cc_final: 0.7019 (t70) REVERT: V 87 PHE cc_start: 0.7928 (t80) cc_final: 0.7463 (t80) outliers start: 122 outliers final: 93 residues processed: 358 average time/residue: 0.3136 time to fit residues: 177.9712 Evaluate side-chains 347 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 247 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 416 ASP Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 545 ASN Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 375 TYR Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 453 ASP Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 562 TYR Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 95 THR Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain U residue 123 HIS Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 4.9990 chunk 235 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 261 optimal weight: 20.0000 chunk 216 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 21 optimal weight: 0.0170 chunk 86 optimal weight: 4.9990 chunk 137 optimal weight: 40.0000 overall best weight: 1.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 490 GLN ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22196 Z= 0.201 Angle : 0.669 12.286 30314 Z= 0.328 Chirality : 0.048 0.624 3600 Planarity : 0.004 0.083 3863 Dihedral : 6.843 61.621 3233 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.57 % Allowed : 19.05 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.63 (0.16), residues: 2737 helix: -0.73 (0.33), residues: 232 sheet: -0.72 (0.16), residues: 1052 loop : -1.39 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 488 HIS 0.005 0.001 HIS C 430 PHE 0.027 0.002 PHE A 354 TYR 0.022 0.002 TYR K 455 ARG 0.005 0.000 ARG D 461 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 281 time to evaluate : 2.694 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: A 376 ASP cc_start: 0.6462 (t0) cc_final: 0.5988 (p0) REVERT: A 550 ARG cc_start: 0.8279 (mmm160) cc_final: 0.7810 (mmm160) REVERT: B 415 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8282 (mp0) REVERT: C 395 ASN cc_start: 0.4974 (t0) cc_final: 0.4592 (t0) REVERT: C 430 HIS cc_start: 0.4566 (OUTLIER) cc_final: 0.4329 (t70) REVERT: C 568 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7321 (ppp) REVERT: D 510 GLN cc_start: 0.8471 (pp30) cc_final: 0.8204 (pp30) REVERT: E 354 PHE cc_start: 0.8558 (t80) cc_final: 0.8261 (t80) REVERT: E 483 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7852 (t70) REVERT: F 366 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.8016 (p) REVERT: F 430 HIS cc_start: 0.1722 (OUTLIER) cc_final: 0.1066 (m-70) REVERT: F 461 ARG cc_start: 0.8162 (mmm160) cc_final: 0.7834 (mmm160) REVERT: G 483 ASP cc_start: 0.7728 (t0) cc_final: 0.7449 (t0) REVERT: J 19 SER cc_start: 0.8408 (OUTLIER) cc_final: 0.7965 (p) REVERT: J 67 LEU cc_start: 0.7036 (mp) cc_final: 0.6750 (mp) REVERT: K 347 VAL cc_start: 0.0180 (OUTLIER) cc_final: -0.0135 (m) REVERT: K 463 GLN cc_start: 0.8701 (tp40) cc_final: 0.8447 (tp-100) REVERT: K 483 ASP cc_start: 0.8136 (t0) cc_final: 0.7791 (t0) REVERT: K 506 MET cc_start: 0.7656 (mpp) cc_final: 0.7346 (mpp) REVERT: L 489 MET cc_start: 0.7677 (ttm) cc_final: 0.7325 (tpp) REVERT: L 568 MET cc_start: 0.5484 (mtt) cc_final: 0.5271 (mtm) REVERT: R 36 LYS cc_start: 0.7295 (tptt) cc_final: 0.6933 (tppt) REVERT: S 51 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6463 (mp0) REVERT: S 69 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7861 (tptp) REVERT: V 41 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7933 (tm-30) REVERT: V 83 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6855 (ptt-90) REVERT: V 87 PHE cc_start: 0.7938 (t80) cc_final: 0.7479 (t80) outliers start: 113 outliers final: 87 residues processed: 366 average time/residue: 0.3116 time to fit residues: 182.0693 Evaluate side-chains 351 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 253 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 563 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 541 GLU Chi-restraints excluded: chain F residue 553 ASP Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 416 ASP Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 375 TYR Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 562 TYR Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 69 LYS Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 chunk 148 optimal weight: 0.7980 chunk 190 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 219 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 chunk 260 optimal weight: 0.5980 chunk 162 optimal weight: 30.0000 chunk 158 optimal weight: 30.0000 chunk 120 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 HIS ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 63 HIS ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22196 Z= 0.219 Angle : 0.668 12.241 30314 Z= 0.328 Chirality : 0.048 0.634 3600 Planarity : 0.004 0.083 3863 Dihedral : 6.701 58.251 3230 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.94 % Allowed : 19.90 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.57 (0.16), residues: 2737 helix: -0.60 (0.33), residues: 232 sheet: -0.69 (0.16), residues: 1051 loop : -1.35 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 528 HIS 0.004 0.001 HIS C 430 PHE 0.031 0.002 PHE H 516 TYR 0.018 0.002 TYR G 375 ARG 0.005 0.000 ARG D 461 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 269 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 ASP cc_start: 0.6468 (t0) cc_final: 0.5988 (p0) REVERT: A 550 ARG cc_start: 0.8308 (mmm160) cc_final: 0.7787 (mmm160) REVERT: B 415 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8303 (mp0) REVERT: B 515 TYR cc_start: 0.7634 (m-80) cc_final: 0.7388 (t80) REVERT: C 395 ASN cc_start: 0.4980 (t0) cc_final: 0.4640 (m-40) REVERT: C 568 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7238 (ppp) REVERT: D 370 THR cc_start: 0.2336 (OUTLIER) cc_final: 0.1992 (m) REVERT: D 510 GLN cc_start: 0.8477 (pp30) cc_final: 0.8211 (pp30) REVERT: D 534 TYR cc_start: 0.8806 (m-80) cc_final: 0.8323 (m-80) REVERT: E 354 PHE cc_start: 0.8572 (t80) cc_final: 0.8283 (t80) REVERT: E 483 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7867 (t70) REVERT: F 366 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7985 (p) REVERT: F 430 HIS cc_start: 0.1537 (OUTLIER) cc_final: 0.1064 (m-70) REVERT: F 461 ARG cc_start: 0.8155 (mmm160) cc_final: 0.7821 (mmm160) REVERT: G 483 ASP cc_start: 0.7745 (t0) cc_final: 0.7483 (t0) REVERT: J 19 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.8081 (p) REVERT: J 67 LEU cc_start: 0.6931 (mp) cc_final: 0.6634 (mp) REVERT: K 347 VAL cc_start: 0.0087 (OUTLIER) cc_final: -0.0237 (m) REVERT: K 453 ASP cc_start: 0.8372 (m-30) cc_final: 0.7502 (p0) REVERT: K 463 GLN cc_start: 0.8744 (tp40) cc_final: 0.8508 (tp-100) REVERT: K 483 ASP cc_start: 0.8163 (t0) cc_final: 0.7812 (t0) REVERT: K 506 MET cc_start: 0.7654 (mpp) cc_final: 0.7338 (mpp) REVERT: L 489 MET cc_start: 0.7690 (ttm) cc_final: 0.7117 (tpp) REVERT: R 36 LYS cc_start: 0.7331 (tptt) cc_final: 0.6950 (tppt) REVERT: R 69 LYS cc_start: 0.8474 (mmmm) cc_final: 0.8189 (mmmm) REVERT: R 73 LYS cc_start: 0.8239 (mttt) cc_final: 0.7911 (mttm) REVERT: S 51 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6297 (mp0) REVERT: S 69 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7842 (tptp) REVERT: U 22 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7716 (tp30) REVERT: U 42 MET cc_start: 0.7004 (tpp) cc_final: 0.6589 (tpp) REVERT: V 41 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: V 87 PHE cc_start: 0.7762 (t80) cc_final: 0.7402 (t80) outliers start: 122 outliers final: 90 residues processed: 363 average time/residue: 0.3066 time to fit residues: 175.8865 Evaluate side-chains 363 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 261 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 541 GLU Chi-restraints excluded: chain F residue 553 ASP Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 416 ASP Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 545 ASN Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 375 TYR Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 562 TYR Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 69 LYS Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 chunk 177 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 204 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22196 Z= 0.258 Angle : 0.686 13.241 30314 Z= 0.338 Chirality : 0.047 0.423 3600 Planarity : 0.004 0.083 3863 Dihedral : 6.657 59.010 3229 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 4.73 % Allowed : 20.51 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.56 (0.16), residues: 2737 helix: -0.56 (0.33), residues: 232 sheet: -0.72 (0.16), residues: 1051 loop : -1.31 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 528 HIS 0.013 0.001 HIS J 63 PHE 0.028 0.002 PHE D 424 TYR 0.018 0.002 TYR K 455 ARG 0.005 0.000 ARG D 461 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 259 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 ASP cc_start: 0.6513 (t0) cc_final: 0.6038 (p0) REVERT: A 550 ARG cc_start: 0.8348 (mmm160) cc_final: 0.7821 (mmm160) REVERT: B 415 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: C 395 ASN cc_start: 0.4941 (t0) cc_final: 0.4584 (m-40) REVERT: C 568 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7251 (ppp) REVERT: D 370 THR cc_start: 0.2341 (OUTLIER) cc_final: 0.2001 (m) REVERT: D 510 GLN cc_start: 0.8510 (pp30) cc_final: 0.8220 (pp30) REVERT: D 534 TYR cc_start: 0.8814 (m-80) cc_final: 0.8327 (m-80) REVERT: E 354 PHE cc_start: 0.8584 (t80) cc_final: 0.8337 (t80) REVERT: E 483 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7880 (t0) REVERT: F 430 HIS cc_start: 0.1547 (OUTLIER) cc_final: 0.1023 (m-70) REVERT: F 461 ARG cc_start: 0.8144 (mmm160) cc_final: 0.7776 (mmm160) REVERT: G 402 ASN cc_start: 0.7273 (OUTLIER) cc_final: 0.7054 (p0) REVERT: G 483 ASP cc_start: 0.7793 (t0) cc_final: 0.7527 (t0) REVERT: J 19 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.8151 (p) REVERT: J 67 LEU cc_start: 0.7033 (mp) cc_final: 0.6734 (mp) REVERT: K 347 VAL cc_start: 0.0025 (OUTLIER) cc_final: -0.0307 (m) REVERT: K 453 ASP cc_start: 0.8397 (m-30) cc_final: 0.7481 (p0) REVERT: K 463 GLN cc_start: 0.8781 (tp40) cc_final: 0.8576 (tp-100) REVERT: K 483 ASP cc_start: 0.8186 (t0) cc_final: 0.7894 (t0) REVERT: K 506 MET cc_start: 0.7637 (mpp) cc_final: 0.7360 (mpp) REVERT: L 452 PRO cc_start: 0.8818 (Cg_exo) cc_final: 0.8330 (Cg_endo) REVERT: L 489 MET cc_start: 0.7654 (ttm) cc_final: 0.7108 (tpp) REVERT: R 36 LYS cc_start: 0.7277 (tptt) cc_final: 0.6891 (tppt) REVERT: S 51 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6328 (mp0) REVERT: S 69 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7935 (tptp) REVERT: U 22 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7695 (tp30) REVERT: V 87 PHE cc_start: 0.7825 (t80) cc_final: 0.7350 (t80) outliers start: 117 outliers final: 92 residues processed: 348 average time/residue: 0.3073 time to fit residues: 170.4120 Evaluate side-chains 355 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 252 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 553 ASP Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 545 ASN Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 375 TYR Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 475 LEU Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 562 TYR Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 95 THR Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 69 LYS Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 8.9990 chunk 249 optimal weight: 0.1980 chunk 227 optimal weight: 20.0000 chunk 242 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 219 optimal weight: 0.8980 chunk 229 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 63 HIS ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22196 Z= 0.207 Angle : 0.682 13.936 30314 Z= 0.333 Chirality : 0.047 0.464 3600 Planarity : 0.004 0.083 3863 Dihedral : 6.335 58.327 3225 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 4.09 % Allowed : 21.44 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.49 (0.16), residues: 2737 helix: -0.52 (0.33), residues: 232 sheet: -0.64 (0.16), residues: 1021 loop : -1.28 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 528 HIS 0.004 0.001 HIS C 430 PHE 0.030 0.001 PHE H 516 TYR 0.019 0.002 TYR G 375 ARG 0.005 0.000 ARG D 461 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 276 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 376 ASP cc_start: 0.6547 (t0) cc_final: 0.6064 (p0) REVERT: A 550 ARG cc_start: 0.8351 (mmm160) cc_final: 0.7815 (mmm160) REVERT: B 415 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: B 515 TYR cc_start: 0.7663 (m-80) cc_final: 0.7371 (t80) REVERT: C 395 ASN cc_start: 0.4936 (t0) cc_final: 0.4568 (m-40) REVERT: C 568 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7246 (ppp) REVERT: D 510 GLN cc_start: 0.8511 (pp30) cc_final: 0.8228 (pp30) REVERT: D 534 TYR cc_start: 0.8682 (m-80) cc_final: 0.8296 (m-80) REVERT: E 354 PHE cc_start: 0.8553 (t80) cc_final: 0.8309 (t80) REVERT: E 483 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7799 (t70) REVERT: F 430 HIS cc_start: 0.1551 (OUTLIER) cc_final: 0.1062 (m-70) REVERT: G 402 ASN cc_start: 0.7240 (OUTLIER) cc_final: 0.7039 (p0) REVERT: G 483 ASP cc_start: 0.7772 (t0) cc_final: 0.7502 (t0) REVERT: J 19 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8245 (p) REVERT: J 67 LEU cc_start: 0.6912 (mp) cc_final: 0.6608 (mp) REVERT: K 347 VAL cc_start: 0.0009 (OUTLIER) cc_final: -0.0323 (m) REVERT: K 453 ASP cc_start: 0.8348 (m-30) cc_final: 0.7440 (p0) REVERT: K 483 ASP cc_start: 0.8196 (t0) cc_final: 0.7899 (t0) REVERT: K 506 MET cc_start: 0.7664 (mpp) cc_final: 0.7443 (mpp) REVERT: L 489 MET cc_start: 0.7528 (ttm) cc_final: 0.7255 (tpp) REVERT: L 570 ASP cc_start: 0.6551 (p0) cc_final: 0.6301 (p0) REVERT: R 36 LYS cc_start: 0.7325 (tptt) cc_final: 0.6942 (tppt) REVERT: R 73 LYS cc_start: 0.8228 (mttt) cc_final: 0.7840 (mmtm) REVERT: S 51 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6224 (mp0) REVERT: S 69 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7914 (tptp) REVERT: U 22 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7646 (tp30) REVERT: V 87 PHE cc_start: 0.7793 (t80) cc_final: 0.7387 (t80) outliers start: 101 outliers final: 83 residues processed: 354 average time/residue: 0.2937 time to fit residues: 164.9303 Evaluate side-chains 349 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 256 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 553 ASP Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 545 ASN Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 375 TYR Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 475 LEU Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 562 TYR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 95 THR Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 69 LYS Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 20.0000 chunk 256 optimal weight: 8.9990 chunk 156 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 268 optimal weight: 20.0000 chunk 247 optimal weight: 30.0000 chunk 214 optimal weight: 30.0000 chunk 22 optimal weight: 40.0000 chunk 165 optimal weight: 0.4980 chunk 131 optimal weight: 0.2980 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 22196 Z= 0.344 Angle : 0.734 14.543 30314 Z= 0.364 Chirality : 0.048 0.504 3600 Planarity : 0.005 0.083 3863 Dihedral : 6.495 57.813 3221 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.00 % Allowed : 21.56 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.56 (0.16), residues: 2737 helix: -0.46 (0.34), residues: 226 sheet: -0.77 (0.16), residues: 1023 loop : -1.28 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 528 HIS 0.006 0.001 HIS D 540 PHE 0.031 0.002 PHE A 354 TYR 0.035 0.002 TYR H 375 ARG 0.004 0.000 ARG S 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 258 time to evaluate : 2.571 Fit side-chains 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: A 376 ASP cc_start: 0.6561 (t0) cc_final: 0.6046 (p0) REVERT: A 550 ARG cc_start: 0.8378 (mmm160) cc_final: 0.7803 (mmm160) REVERT: B 415 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: B 515 TYR cc_start: 0.7834 (m-80) cc_final: 0.7504 (t80) REVERT: C 395 ASN cc_start: 0.5098 (t0) cc_final: 0.4600 (m-40) REVERT: D 510 GLN cc_start: 0.8547 (pp30) cc_final: 0.8231 (pp30) REVERT: D 534 TYR cc_start: 0.8825 (m-80) cc_final: 0.8301 (m-80) REVERT: E 483 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7901 (t0) REVERT: G 483 ASP cc_start: 0.7847 (t0) cc_final: 0.7590 (t0) REVERT: J 19 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8288 (p) REVERT: J 46 ARG cc_start: 0.7957 (mmt180) cc_final: 0.7196 (mmm160) REVERT: J 67 LEU cc_start: 0.7063 (mp) cc_final: 0.6777 (mp) REVERT: K 347 VAL cc_start: 0.0111 (OUTLIER) cc_final: -0.0280 (m) REVERT: K 453 ASP cc_start: 0.8388 (m-30) cc_final: 0.7605 (p0) REVERT: K 483 ASP cc_start: 0.8240 (t0) cc_final: 0.7958 (t0) REVERT: K 506 MET cc_start: 0.7699 (mpp) cc_final: 0.7433 (mpp) REVERT: L 489 MET cc_start: 0.7515 (ttm) cc_final: 0.7249 (tpp) REVERT: R 36 LYS cc_start: 0.7299 (tptt) cc_final: 0.6892 (tppt) REVERT: S 51 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6201 (mp0) REVERT: S 69 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.8017 (tptp) REVERT: S 87 PHE cc_start: 0.7991 (m-10) cc_final: 0.7663 (m-80) REVERT: U 22 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7738 (tp30) REVERT: V 87 PHE cc_start: 0.7816 (t80) cc_final: 0.7471 (t80) outliers start: 99 outliers final: 85 residues processed: 336 average time/residue: 0.3185 time to fit residues: 169.2514 Evaluate side-chains 343 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 251 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 553 ASP Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 545 ASN Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 375 TYR Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 475 LEU Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 562 TYR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 69 LYS Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 27 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 419 ASN ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 386 ASN ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.114586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.075458 restraints weight = 78459.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.077159 restraints weight = 48092.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.077593 restraints weight = 31637.147| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 22196 Z= 0.401 Angle : 0.780 14.023 30314 Z= 0.390 Chirality : 0.049 0.540 3600 Planarity : 0.005 0.083 3863 Dihedral : 6.772 57.782 3215 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 4.17 % Allowed : 22.09 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.73 (0.16), residues: 2737 helix: -0.53 (0.34), residues: 220 sheet: -0.97 (0.16), residues: 1019 loop : -1.34 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 528 HIS 0.006 0.001 HIS L 450 PHE 0.031 0.002 PHE A 354 TYR 0.031 0.002 TYR H 375 ARG 0.005 0.001 ARG D 461 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4944.75 seconds wall clock time: 90 minutes 54.40 seconds (5454.40 seconds total)