Starting phenix.real_space_refine on Tue Mar 19 12:36:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpe_16150/03_2024/8bpe_16150.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpe_16150/03_2024/8bpe_16150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpe_16150/03_2024/8bpe_16150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpe_16150/03_2024/8bpe_16150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpe_16150/03_2024/8bpe_16150.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpe_16150/03_2024/8bpe_16150.pdb" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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 142 5.16 5 C 15196 2.51 5 N 4122 2.21 5 O 4735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 508": "OE1" <-> "OE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "H PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 525": "OE1" <-> "OE2" Residue "H GLU 541": "OE1" <-> "OE2" Residue "K GLU 532": "OE1" <-> "OE2" Residue "M ARG 45": "NH1" <-> "NH2" Residue "M ARG 75": "NH1" <-> "NH2" Residue "M ARG 83": "NH1" <-> "NH2" Residue "M ARG 112": "NH1" <-> "NH2" Residue "D ARG 346": "NH1" <-> "NH2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ARG 423": "NH1" <-> "NH2" Residue "D ARG 443": "NH1" <-> "NH2" Residue "D ARG 451": "NH1" <-> "NH2" Residue "D ARG 514": "NH1" <-> "NH2" Residue "D ARG 546": "NH1" <-> "NH2" Residue "D TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 45": "NH1" <-> "NH2" Residue "P ARG 75": "NH1" <-> "NH2" Residue "P ARG 83": "NH1" <-> "NH2" Residue "P ARG 112": "NH1" <-> "NH2" Residue "F ARG 346": "NH1" <-> "NH2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F ARG 423": "NH1" <-> "NH2" Residue "F ARG 443": "NH1" <-> "NH2" Residue "F ARG 451": "NH1" <-> "NH2" Residue "F ARG 461": "NH1" <-> "NH2" Residue "F ARG 467": "NH1" <-> "NH2" Residue "F ARG 491": "NH1" <-> "NH2" Residue "F TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 514": "NH1" <-> "NH2" Residue "F ARG 550": "NH1" <-> "NH2" Residue "G ARG 346": "NH1" <-> "NH2" Residue "G ARG 384": "NH1" <-> "NH2" Residue "G ARG 423": "NH1" <-> "NH2" Residue "G ARG 443": "NH1" <-> "NH2" Residue "G ARG 451": "NH1" <-> "NH2" Residue "G ARG 514": "NH1" <-> "NH2" Residue "G ARG 546": "NH1" <-> "NH2" Residue "G TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 346": "NH1" <-> "NH2" Residue "E ARG 384": "NH1" <-> "NH2" Residue "E ARG 423": "NH1" <-> "NH2" Residue "E ARG 443": "NH1" <-> "NH2" Residue "E ARG 461": "NH1" <-> "NH2" Residue "E ARG 467": "NH1" <-> "NH2" Residue "E ARG 491": "NH1" <-> "NH2" Residue "E TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 514": "NH1" <-> "NH2" Residue "E ARG 550": "NH1" <-> "NH2" Residue "O ARG 45": "NH1" <-> "NH2" Residue "O ARG 75": "NH1" <-> "NH2" Residue "O ARG 83": "NH1" <-> "NH2" Residue "O ARG 112": "NH1" <-> "NH2" Residue "R ARG 45": "NH1" <-> "NH2" Residue "R ARG 75": "NH1" <-> "NH2" Residue "R ARG 83": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N ARG 75": "NH1" <-> "NH2" Residue "N ARG 83": "NH1" <-> "NH2" Residue "N ARG 112": "NH1" <-> "NH2" Residue "Q ARG 45": "NH1" <-> "NH2" Residue "Q ARG 75": "NH1" <-> "NH2" Residue "Q ARG 83": "NH1" <-> "NH2" Residue "Q ARG 112": "NH1" <-> "NH2" Residue "S ARG 45": "NH1" <-> "NH2" Residue "S ARG 75": "NH1" <-> "NH2" Residue "S ARG 83": "NH1" <-> "NH2" Residue "S ARG 112": "NH1" <-> "NH2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "I GLU 22": "OE1" <-> "OE2" Residue "I GLU 51": "OE1" <-> "OE2" Residue "I TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 111": "OD1" <-> "OD2" Residue "J ASP 9": "OD1" <-> "OD2" Residue "J ASP 66": "OD1" <-> "OD2" Residue "L GLU 462": "OE1" <-> "OE2" Residue "L GLU 468": "OE1" <-> "OE2" Residue "L GLU 532": "OE1" <-> "OE2" Residue "L GLU 549": "OE1" <-> "OE2" Residue "L ARG 550": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24195 Number of models: 1 Model: "" Number of chains: 30 Chain: "C" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1740 Classifications: {'peptide': 224} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1757 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 207} Chain: "K" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1772 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 210} Chain: "M" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "P" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "G" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "O" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "R" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "N" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "Q" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "S" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "B" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1756 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 207} Chain: "A" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1790 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 212} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 805 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "J" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 827 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain breaks: 1 Chain: "L" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 115} Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 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: "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: "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: "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: "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: "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: 11.62, per 1000 atoms: 0.48 Number of scatterers: 24195 At special positions: 0 Unit cell: (191.16, 119.88, 170.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 142 16.00 O 4735 8.00 N 4122 7.00 C 15196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 414 " - pdb=" SG CYS B 414 " distance=2.06 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.04 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 414 " - pdb=" SG CYS K 414 " distance=1.69 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.04 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 M 37 " - pdb=" SG CYS M 104 " distance=2.03 Simple disulfide: pdb=" SG CYS M 49 " - pdb=" SG CYS M 58 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.03 Simple disulfide: pdb=" SG CYS D 414 " - pdb=" SG CYS E 414 " distance=2.21 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.03 Simple disulfide: pdb=" SG CYS P 37 " - pdb=" SG CYS P 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 49 " - pdb=" SG CYS P 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.05 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 E 367 " - pdb=" SG CYS E 426 " distance=2.05 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.04 Simple disulfide: pdb=" SG CYS O 37 " - pdb=" SG CYS O 104 " distance=2.03 Simple disulfide: pdb=" SG CYS O 49 " - pdb=" SG CYS O 58 " distance=2.03 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 N 37 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 49 " - pdb=" SG CYS N 58 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 37 " - pdb=" SG CYS Q 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 49 " - pdb=" SG CYS Q 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=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.04 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS J 68 " distance=2.16 Simple disulfide: pdb=" SG CYS I 37 " - pdb=" SG CYS I 104 " distance=2.03 Simple disulfide: pdb=" SG CYS I 49 " - pdb=" SG CYS I 58 " distance=1.58 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS L 575 " distance=2.03 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A 601 " - " ASN A 563 " " NAG B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 563 " " NAG G 601 " - " ASN G 563 " " NAG H 601 " - " ASN H 563 " " NAG K 601 " - " ASN K 563 " " NAG L 601 " - " ASN L 563 " " NAG T 1 " - " ASN F 563 " " NAG U 1 " - " ASN E 563 " " NAG V 1 " - " ASN J 48 " Time building additional restraints: 9.11 Conformation dependent library (CDL) restraints added in 4.2 seconds 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5850 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 72 sheets defined 10.2% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 496 through 498 No H-bonds generated for 'chain 'C' and resid 496 through 498' Processing helix chain 'C' and resid 524 through 529 Processing helix chain 'H' and resid 353 through 360 Processing helix chain 'H' and resid 414 through 419 Processing helix chain 'H' and resid 524 through 529 Processing helix chain 'K' and resid 353 through 360 removed outlier: 3.538A pdb=" N LEU K 359 " --> pdb=" O ALA K 355 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR K 360 " --> pdb=" O SER K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 421 removed outlier: 3.807A pdb=" N TRP K 418 " --> pdb=" O CYS K 414 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY K 421 " --> pdb=" O ASP K 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 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 524 through 531 Processing helix chain 'M' and resid 69 through 73 Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 414 through 420 removed outlier: 3.603A pdb=" N TRP D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 466 Processing helix chain 'D' and resid 525 through 530 Processing helix chain 'P' and resid 69 through 73 Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 462 through 466 removed outlier: 3.765A pdb=" N ASN F 465 " --> pdb=" O GLU F 462 " (cutoff:3.500A) removed outlier: 3.639A 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 496 through 498 No H-bonds generated for 'chain 'F' and resid 496 through 498' Processing helix chain 'F' and resid 524 through 530 Processing helix chain 'G' and resid 353 through 361 Processing helix chain 'G' and resid 414 through 420 removed outlier: 3.901A pdb=" N TRP G 418 " --> pdb=" O CYS G 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 466 removed outlier: 3.537A pdb=" N LEU G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 530 Processing helix chain 'E' and resid 353 through 361 Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.815A pdb=" N TRP E 418 " --> pdb=" O CYS E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 466 removed outlier: 3.765A pdb=" N ASN E 465 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 466 " --> pdb=" O GLN E 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 462 through 466' Processing helix chain 'E' and resid 496 through 498 No H-bonds generated for 'chain 'E' and resid 496 through 498' Processing helix chain 'E' and resid 524 through 530 Processing helix chain 'O' and resid 69 through 73 Processing helix chain 'R' and resid 69 through 73 Processing helix chain 'N' and resid 69 through 73 Processing helix chain 'Q' and resid 69 through 73 Processing helix chain 'S' and resid 69 through 73 Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.689A pdb=" N LEU B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 removed outlier: 3.855A pdb=" N TRP B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 525 through 531 removed outlier: 3.577A pdb=" N GLY B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.610A pdb=" N LEU A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 116 through 120 Processing helix chain 'L' and resid 526 through 530 removed outlier: 3.946A pdb=" N ASN L 529 " --> pdb=" O GLU L 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 347 through 350 removed outlier: 4.292A pdb=" N ASP C 371 " --> pdb=" O PHE C 405 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE C 405 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 379 through 383 removed outlier: 3.611A pdb=" N THR C 379 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 424 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 428 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU C 437 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N HIS C 430 " --> pdb=" O SER C 435 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER C 435 " --> pdb=" O HIS C 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 455 through 457 removed outlier: 3.680A pdb=" N THR C 473 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER C 519 " --> pdb=" O CYS C 474 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE C 520 " --> pdb=" O VAL C 501 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 455 through 457 removed outlier: 3.680A pdb=" N THR C 473 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 476 " --> pdb=" O ALA C 517 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 493 through 494 removed outlier: 3.566A pdb=" N MET C 489 " --> pdb=" O THR C 535 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 347 through 350 removed outlier: 3.533A pdb=" N THR H 366 " --> pdb=" O ILE H 350 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR H 370 " --> pdb=" O ALA H 407 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ALA H 407 " --> pdb=" O THR H 370 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU H 372 " --> pdb=" O PHE H 405 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 379 through 383 removed outlier: 4.352A pdb=" N THR H 379 " --> pdb=" O THR H 429 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR H 429 " --> pdb=" O THR H 379 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS H 426 " --> pdb=" O GLN H 439 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN H 439 " --> pdb=" O CYS H 426 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.653A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER H 519 " --> pdb=" O CYS H 474 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL H 501 " --> pdb=" O ILE H 520 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.653A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 493 through 494 Processing sheet with id=AB2, first strand: chain 'K' and resid 347 through 350 removed outlier: 4.376A pdb=" N THR K 366 " --> pdb=" O ILE K 350 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU K 365 " --> pdb=" O ALA K 411 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA K 411 " --> pdb=" O LEU K 365 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 379 through 383 removed outlier: 3.574A pdb=" N THR K 379 " --> pdb=" O THR K 429 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR K 425 " --> pdb=" O THR K 383 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.524A pdb=" N TYR K 455 " --> pdb=" O LEU K 475 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER K 519 " --> pdb=" O CYS K 474 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 493 through 494 Processing sheet with id=AB6, first strand: chain 'K' and resid 561 through 562 removed outlier: 7.185A pdb=" N LEU K 561 " --> pdb=" O TYR L 562 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL L 564 " --> pdb=" O LEU K 561 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL J 33 " --> pdb=" O LEU L 561 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASN L 563 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG J 35 " --> pdb=" O ASN L 563 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG J 20 " --> pdb=" O GLU J 34 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ALA J 15 " --> pdb=" O ASP J 9 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP J 9 " --> pdb=" O ALA J 15 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE J 17 " --> pdb=" O LEU J 7 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 32 through 38 removed outlier: 3.507A pdb=" N CYS M 37 " --> pdb=" O PHE M 87 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU M 86 " --> pdb=" O TYR M 81 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR M 81 " --> pdb=" O LEU M 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 46 through 48 Processing sheet with id=AB9, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.767A pdb=" N ARG D 346 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR D 366 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 379 through 383 removed outlier: 3.866A pdb=" N THR D 379 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE D 424 " --> pdb=" O ILE D 441 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE D 441 " --> pdb=" O PHE D 424 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 485 through 489 removed outlier: 3.744A pdb=" N THR D 535 " --> pdb=" O MET D 489 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 32 through 38 removed outlier: 3.507A pdb=" N CYS P 37 " --> pdb=" O PHE P 87 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU P 86 " --> pdb=" O TYR P 81 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR P 81 " --> pdb=" O LEU P 86 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 46 through 48 Processing sheet with id=AC7, first strand: chain 'F' and resid 346 through 350 removed outlier: 3.552A pdb=" N ARG F 346 " --> pdb=" O THR F 370 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR F 366 " --> pdb=" O ILE F 350 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 380 through 384 removed outlier: 3.529A pdb=" N CYS F 426 " --> pdb=" O GLN F 439 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN F 439 " --> pdb=" O CYS F 426 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL F 428 " --> pdb=" O LEU F 437 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 399 through 400 removed outlier: 3.755A pdb=" N THR F 404 " --> pdb=" O HIS F 400 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 453 through 457 removed outlier: 6.104A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 453 through 457 removed outlier: 6.104A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 493 through 494 Processing sheet with id=AD4, first strand: chain 'F' and resid 565 through 567 Processing sheet with id=AD5, first strand: chain 'G' and resid 346 through 350 removed outlier: 3.767A pdb=" N ARG G 346 " --> pdb=" O THR G 370 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR G 366 " --> pdb=" O ILE G 350 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 379 through 383 removed outlier: 3.866A pdb=" N THR G 379 " --> pdb=" O THR G 429 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE G 424 " --> pdb=" O ILE G 441 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE G 441 " --> pdb=" O PHE G 424 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 485 through 489 removed outlier: 3.604A pdb=" N THR G 535 " --> pdb=" O MET G 489 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 346 through 350 removed outlier: 3.552A pdb=" N ARG E 346 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR E 366 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 380 through 384 removed outlier: 3.529A pdb=" N CYS E 426 " --> pdb=" O GLN E 439 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN E 439 " --> pdb=" O CYS E 426 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL E 428 " --> pdb=" O LEU E 437 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 399 through 400 removed outlier: 3.755A pdb=" N THR E 404 " --> pdb=" O HIS E 400 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 453 through 457 removed outlier: 6.126A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 453 through 457 removed outlier: 6.126A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AE7, first strand: chain 'O' and resid 32 through 38 removed outlier: 3.507A pdb=" N CYS O 37 " --> pdb=" O PHE O 87 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU O 86 " --> pdb=" O TYR O 81 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR O 81 " --> pdb=" O LEU O 86 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 46 through 48 Processing sheet with id=AE9, first strand: chain 'O' and resid 50 through 51 Processing sheet with id=AF1, first strand: chain 'R' and resid 32 through 38 removed outlier: 3.508A pdb=" N CYS R 37 " --> pdb=" O PHE R 87 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU R 86 " --> pdb=" O TYR R 81 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR R 81 " --> pdb=" O LEU R 86 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 46 through 48 Processing sheet with id=AF3, first strand: chain 'N' and resid 32 through 38 removed outlier: 3.506A pdb=" N CYS N 37 " --> pdb=" O PHE N 87 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU N 86 " --> pdb=" O TYR N 81 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR N 81 " --> pdb=" O LEU N 86 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 46 through 48 Processing sheet with id=AF5, first strand: chain 'Q' and resid 32 through 38 removed outlier: 3.507A pdb=" N CYS Q 37 " --> pdb=" O PHE Q 87 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU Q 86 " --> pdb=" O TYR Q 81 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR Q 81 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 46 through 48 Processing sheet with id=AF7, first strand: chain 'S' and resid 32 through 38 removed outlier: 3.507A pdb=" N CYS S 37 " --> pdb=" O PHE S 87 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU S 86 " --> pdb=" O TYR S 81 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR S 81 " --> pdb=" O LEU S 86 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 46 through 48 Processing sheet with id=AF9, first strand: chain 'B' and resid 379 through 383 Processing sheet with id=AG1, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.503A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.503A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 493 through 494 removed outlier: 3.821A pdb=" N TYR B 534 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL B 552 " --> pdb=" O TYR B 534 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 561 through 563 Processing sheet with id=AG5, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AG6, first strand: chain 'A' and resid 380 through 384 Processing sheet with id=AG7, first strand: chain 'A' and resid 453 through 457 Processing sheet with id=AG8, first strand: chain 'A' and resid 453 through 457 removed outlier: 5.142A pdb=" N THR A 477 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA A 517 " --> pdb=" O THR A 477 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.687A pdb=" N MET A 489 " --> pdb=" O THR A 535 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.687A pdb=" N MET A 489 " --> pdb=" O THR A 535 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 534 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 565 through 569 removed outlier: 3.584A pdb=" N PHE J 60 " --> pdb=" O SER A 565 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 32 through 38 removed outlier: 3.681A pdb=" N CYS I 37 " --> pdb=" O PHE I 87 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 100 through 105 removed outlier: 3.589A pdb=" N CYS I 104 " --> pdb=" O GLN I 116 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN I 116 " --> pdb=" O CYS I 104 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 40 through 42 Processing sheet with id=AH6, first strand: chain 'J' and resid 110 through 115 Processing sheet with id=AH7, first strand: chain 'L' and resid 454 through 457 removed outlier: 3.923A pdb=" N ILE L 520 " --> pdb=" O VAL L 501 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 454 through 457 Processing sheet with id=AH9, first strand: chain 'L' and resid 489 through 490 712 hydrogen bonds defined for protein. 1824 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: 8.11 Time building geometry restraints manager: 9.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5680 1.33 - 1.45: 5084 1.45 - 1.58: 13767 1.58 - 1.70: 0 1.70 - 1.82: 197 Bond restraints: 24728 Sorted by residual: bond pdb=" N GLY K 557 " pdb=" CA GLY K 557 " ideal model delta sigma weight residual 1.443 1.477 -0.034 8.60e-03 1.35e+04 1.58e+01 bond pdb=" C MET B 568 " pdb=" N SER B 569 " ideal model delta sigma weight residual 1.331 1.380 -0.049 1.33e-02 5.65e+03 1.36e+01 bond pdb=" N VAL D 547 " pdb=" CA VAL D 547 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.14e-02 7.69e+03 1.31e+01 bond pdb=" N VAL G 547 " pdb=" CA VAL G 547 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.14e-02 7.69e+03 1.26e+01 bond pdb=" N VAL A 552 " pdb=" CA VAL A 552 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.25e+01 ... (remaining 24723 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.85: 1040 106.85 - 113.79: 14326 113.79 - 120.74: 9817 120.74 - 127.69: 8335 127.69 - 134.63: 206 Bond angle restraints: 33724 Sorted by residual: angle pdb=" CA GLY M 107 " pdb=" C GLY M 107 " pdb=" O GLY M 107 " ideal model delta sigma weight residual 122.29 118.20 4.09 8.10e-01 1.52e+00 2.55e+01 angle pdb=" CA GLY N 107 " pdb=" C GLY N 107 " pdb=" O GLY N 107 " ideal model delta sigma weight residual 122.29 118.20 4.09 8.10e-01 1.52e+00 2.54e+01 angle pdb=" CA GLY O 107 " pdb=" C GLY O 107 " pdb=" O GLY O 107 " ideal model delta sigma weight residual 122.29 118.24 4.05 8.10e-01 1.52e+00 2.50e+01 angle pdb=" CA GLY Q 107 " pdb=" C GLY Q 107 " pdb=" O GLY Q 107 " ideal model delta sigma weight residual 122.29 118.26 4.03 8.10e-01 1.52e+00 2.48e+01 angle pdb=" CA GLY P 107 " pdb=" C GLY P 107 " pdb=" O GLY P 107 " ideal model delta sigma weight residual 122.29 118.30 3.99 8.10e-01 1.52e+00 2.42e+01 ... (remaining 33719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 14004 17.97 - 35.93: 1023 35.93 - 53.90: 168 53.90 - 71.86: 71 71.86 - 89.83: 15 Dihedral angle restraints: 15281 sinusoidal: 6248 harmonic: 9033 Sorted by residual: dihedral pdb=" CB CYS A 367 " pdb=" SG CYS A 367 " pdb=" SG CYS A 426 " pdb=" CB CYS A 426 " ideal model delta sinusoidal sigma weight residual -86.00 -173.30 87.30 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS J 14 " pdb=" SG CYS J 14 " pdb=" SG CYS L 575 " pdb=" CB CYS L 575 " ideal model delta sinusoidal sigma weight residual -86.00 -160.89 74.89 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CB CYS J 12 " pdb=" SG CYS J 12 " pdb=" SG CYS J 100 " pdb=" CB CYS J 100 " ideal model delta sinusoidal sigma weight residual 93.00 155.46 -62.46 1 1.00e+01 1.00e-02 5.16e+01 ... (remaining 15278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.167: 3889 0.167 - 0.333: 114 0.333 - 0.500: 2 0.500 - 0.666: 0 0.666 - 0.833: 2 Chirality restraints: 4007 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN E 563 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN F 563 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.70e+01 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.23e+01 ... (remaining 4004 not shown) Planarity restraints: 4306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 563 " -0.039 2.00e-02 2.50e+03 4.17e-02 2.18e+01 pdb=" CG ASN K 563 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN K 563 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN K 563 " 0.066 2.00e-02 2.50e+03 pdb=" C1 NAG K 601 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 546 " -0.278 9.50e-02 1.11e+02 1.24e-01 9.51e+00 pdb=" NE ARG A 546 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 546 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 546 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 546 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 75 " -0.274 9.50e-02 1.11e+02 1.23e-01 9.31e+00 pdb=" NE ARG I 75 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG I 75 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG I 75 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG I 75 " -0.009 2.00e-02 2.50e+03 ... (remaining 4303 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5783 2.81 - 3.33: 21942 3.33 - 3.85: 37188 3.85 - 4.38: 42360 4.38 - 4.90: 73171 Nonbonded interactions: 180444 Sorted by model distance: nonbonded pdb=" O LEU H 372 " pdb=" OG1 THR H 404 " model vdw 2.283 2.440 nonbonded pdb=" OG SER L 469 " pdb=" O VAL L 523 " model vdw 2.287 2.440 nonbonded pdb=" OG1 THR K 379 " pdb=" OG1 THR K 429 " model vdw 2.305 2.440 nonbonded pdb=" O ILE J 5 " pdb=" OG1 THR J 18 " model vdw 2.308 2.440 nonbonded pdb=" O ASP K 417 " pdb=" OG SER K 420 " model vdw 2.319 2.440 ... (remaining 180439 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568)) selection = (chain 'B' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568)) selection = (chain 'C' and resid 346 through 568) selection = (chain 'D' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568)) selection = (chain 'E' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568)) selection = (chain 'F' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568)) selection = (chain 'G' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568)) selection = (chain 'H' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568)) selection = (chain 'K' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568)) } ncs_group { reference = (chain 'I' and resid 20 through 124) selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'T' 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.110 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 60.500 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.150 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 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 : 0.009 0.053 24728 Z= 0.598 Angle : 1.074 7.923 33724 Z= 0.772 Chirality : 0.076 0.833 4007 Planarity : 0.008 0.124 4295 Dihedral : 13.164 89.830 9302 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.15), residues: 3064 helix: -1.54 (0.29), residues: 250 sheet: 0.26 (0.16), residues: 1147 loop : -1.82 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 418 HIS 0.008 0.001 HIS A 450 PHE 0.019 0.002 PHE L 479 TYR 0.011 0.001 TYR E 500 ARG 0.006 0.001 ARG L 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 678 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: K 384 ARG cc_start: 0.6392 (mmm160) cc_final: 0.5639 (tpp-160) REVERT: G 432 ASP cc_start: 0.7823 (m-30) cc_final: 0.7505 (t70) REVERT: S 78 LEU cc_start: 0.4230 (tt) cc_final: 0.3482 (pp) REVERT: B 376 ASP cc_start: 0.7816 (p0) cc_final: 0.7435 (p0) REVERT: I 22 GLU cc_start: 0.8881 (mp0) cc_final: 0.8503 (mp0) REVERT: I 72 TYR cc_start: 0.7935 (m-80) cc_final: 0.7545 (m-80) REVERT: L 483 ASP cc_start: 0.7683 (m-30) cc_final: 0.7160 (m-30) outliers start: 0 outliers final: 0 residues processed: 678 average time/residue: 0.4587 time to fit residues: 438.9761 Evaluate side-chains 300 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 254 optimal weight: 6.9990 chunk 228 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 121 optimal weight: 0.4980 chunk 235 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 273 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 430 HIS ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 ASN D 419 ASN D 463 GLN D 493 GLN D 545 ASN P 43 HIS ** P 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 HIS F 465 ASN F 510 GLN F 529 ASN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 393 HIS E 465 ASN E 510 GLN ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 HIS ** N 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 HIS S 66 ASN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 529 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24728 Z= 0.272 Angle : 0.721 11.176 33724 Z= 0.371 Chirality : 0.048 0.223 4007 Planarity : 0.005 0.058 4295 Dihedral : 4.635 35.756 3633 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.15 % Allowed : 12.29 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.19 (0.15), residues: 3064 helix: -1.83 (0.26), residues: 301 sheet: 0.64 (0.15), residues: 1117 loop : -1.68 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 528 HIS 0.010 0.002 HIS B 400 PHE 0.030 0.002 PHE L 479 TYR 0.026 0.002 TYR K 515 ARG 0.008 0.001 ARG H 491 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 338 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 108 MET cc_start: 0.7994 (mmt) cc_final: 0.7457 (mmt) REVERT: D 506 MET cc_start: 0.7138 (mtt) cc_final: 0.6852 (mtt) REVERT: O 94 LEU cc_start: 0.6480 (tp) cc_final: 0.6208 (tt) REVERT: N 108 MET cc_start: 0.6634 (mmp) cc_final: 0.6300 (mmp) REVERT: Q 36 LYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6655 (tppt) REVERT: S 78 LEU cc_start: 0.4483 (tt) cc_final: 0.3574 (pp) REVERT: B 376 ASP cc_start: 0.7798 (p0) cc_final: 0.7452 (p0) REVERT: I 22 GLU cc_start: 0.8907 (mp0) cc_final: 0.8423 (mp0) REVERT: I 26 GLU cc_start: 0.6501 (mm-30) cc_final: 0.5952 (mm-30) REVERT: L 483 ASP cc_start: 0.7956 (m-30) cc_final: 0.7532 (m-30) REVERT: L 488 TRP cc_start: 0.6716 (m100) cc_final: 0.6463 (m100) outliers start: 59 outliers final: 34 residues processed: 384 average time/residue: 0.4221 time to fit residues: 238.3060 Evaluate side-chains 296 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 261 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain F residue 371 ASP Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain Q residue 36 LYS Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain L residue 457 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 227 optimal weight: 10.0000 chunk 186 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 273 optimal weight: 0.7980 chunk 295 optimal weight: 9.9990 chunk 243 optimal weight: 0.5980 chunk 271 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 545 ASN ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 HIS F 540 HIS G 463 GLN E 393 HIS O 43 HIS O 80 GLN ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 HIS ** Q 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN J 36 ASN L 518 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24728 Z= 0.247 Angle : 0.666 12.301 33724 Z= 0.341 Chirality : 0.046 0.216 4007 Planarity : 0.004 0.046 4295 Dihedral : 4.454 29.558 3633 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.76 % Favored : 93.21 % Rotamer: Outliers : 2.11 % Allowed : 15.24 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.15), residues: 3064 helix: -1.73 (0.25), residues: 296 sheet: 0.70 (0.15), residues: 1135 loop : -1.54 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 528 HIS 0.021 0.002 HIS F 393 PHE 0.034 0.002 PHE S 87 TYR 0.029 0.002 TYR L 534 ARG 0.005 0.001 ARG H 443 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 288 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: C 506 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7281 (mtm) REVERT: K 568 MET cc_start: 0.6747 (mtm) cc_final: 0.6266 (mtp) REVERT: D 506 MET cc_start: 0.7074 (mtt) cc_final: 0.6792 (mtt) REVERT: O 94 LEU cc_start: 0.6463 (tp) cc_final: 0.6252 (tt) REVERT: Q 36 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6910 (tppt) REVERT: B 376 ASP cc_start: 0.7997 (p0) cc_final: 0.7633 (p0) REVERT: B 570 ASP cc_start: 0.7046 (t0) cc_final: 0.6843 (t0) REVERT: I 22 GLU cc_start: 0.8926 (mp0) cc_final: 0.8480 (mp0) REVERT: I 72 TYR cc_start: 0.7644 (m-80) cc_final: 0.7291 (m-80) REVERT: I 79 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7785 (mmtm) REVERT: L 483 ASP cc_start: 0.7990 (m-30) cc_final: 0.7613 (m-30) outliers start: 58 outliers final: 31 residues processed: 329 average time/residue: 0.4037 time to fit residues: 197.3515 Evaluate side-chains 277 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 243 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain K residue 376 ASP Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 506 MET Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain Q residue 36 LYS Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain L residue 457 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 270 optimal weight: 20.0000 chunk 205 optimal weight: 0.0870 chunk 142 optimal weight: 0.8980 chunk 30 optimal weight: 20.0000 chunk 130 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 274 optimal weight: 9.9990 chunk 290 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 260 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 GLN ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 123 HIS ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24728 Z= 0.253 Angle : 0.661 11.755 33724 Z= 0.335 Chirality : 0.046 0.206 4007 Planarity : 0.004 0.040 4295 Dihedral : 4.414 25.210 3633 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.76 % Favored : 93.21 % Rotamer: Outliers : 3.24 % Allowed : 15.90 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 3064 helix: -1.71 (0.25), residues: 294 sheet: 0.66 (0.15), residues: 1140 loop : -1.52 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 528 HIS 0.009 0.001 HIS A 400 PHE 0.020 0.002 PHE D 405 TYR 0.028 0.002 TYR K 515 ARG 0.005 0.000 ARG R 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 285 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 506 MET cc_start: 0.7119 (mtt) cc_final: 0.6795 (mtt) REVERT: O 94 LEU cc_start: 0.6811 (tp) cc_final: 0.6567 (tt) REVERT: Q 36 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6786 (tppt) REVERT: Q 88 LEU cc_start: 0.4748 (mt) cc_final: 0.4314 (mp) REVERT: B 376 ASP cc_start: 0.8021 (p0) cc_final: 0.7663 (p0) REVERT: A 489 MET cc_start: 0.7309 (pmm) cc_final: 0.6873 (ptp) REVERT: I 22 GLU cc_start: 0.8928 (mp0) cc_final: 0.8456 (mp0) REVERT: I 72 TYR cc_start: 0.7746 (m-80) cc_final: 0.7440 (m-80) REVERT: L 483 ASP cc_start: 0.8064 (m-30) cc_final: 0.7696 (m-30) REVERT: L 488 TRP cc_start: 0.6796 (m100) cc_final: 0.6375 (m100) REVERT: L 515 TYR cc_start: 0.7613 (m-80) cc_final: 0.7045 (m-80) outliers start: 89 outliers final: 48 residues processed: 350 average time/residue: 0.3775 time to fit residues: 198.2180 Evaluate side-chains 285 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 236 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain K residue 376 ASP Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 506 MET Chi-restraints excluded: chain M residue 43 HIS Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain Q residue 36 LYS Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 502 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 242 optimal weight: 3.9990 chunk 165 optimal weight: 0.4980 chunk 4 optimal weight: 8.9990 chunk 216 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 201 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 439 GLN ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 ASN ** P 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS O 85 ASN ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 510 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 24728 Z= 0.335 Angle : 0.710 14.757 33724 Z= 0.362 Chirality : 0.048 0.227 4007 Planarity : 0.005 0.042 4295 Dihedral : 4.718 25.398 3633 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.93 % Favored : 92.00 % Rotamer: Outliers : 3.61 % Allowed : 17.03 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.15), residues: 3064 helix: -1.70 (0.26), residues: 294 sheet: 0.30 (0.15), residues: 1156 loop : -1.57 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 488 HIS 0.011 0.002 HIS A 400 PHE 0.027 0.002 PHE E 405 TYR 0.032 0.002 TYR K 515 ARG 0.006 0.001 ARG P 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 261 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 506 MET cc_start: 0.7008 (mtt) cc_final: 0.6735 (mtt) REVERT: Q 36 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6941 (tppt) REVERT: Q 88 LEU cc_start: 0.4776 (mt) cc_final: 0.4516 (mp) REVERT: B 376 ASP cc_start: 0.8131 (p0) cc_final: 0.7743 (p0) REVERT: A 361 LYS cc_start: 0.8354 (tppt) cc_final: 0.8147 (tppt) REVERT: I 22 GLU cc_start: 0.8901 (mp0) cc_final: 0.8423 (mp0) REVERT: I 72 TYR cc_start: 0.7795 (m-80) cc_final: 0.7558 (m-80) REVERT: J 22 ILE cc_start: 0.8286 (pt) cc_final: 0.8065 (pt) REVERT: L 483 ASP cc_start: 0.8165 (m-30) cc_final: 0.7755 (m-30) REVERT: L 488 TRP cc_start: 0.6919 (m100) cc_final: 0.6488 (m100) REVERT: L 515 TYR cc_start: 0.7634 (m-80) cc_final: 0.7079 (m-80) outliers start: 99 outliers final: 69 residues processed: 340 average time/residue: 0.3767 time to fit residues: 194.6324 Evaluate side-chains 296 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 226 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain K residue 376 ASP Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 506 MET Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain N residue 24 LYS Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain Q residue 36 LYS Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 524 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 97 optimal weight: 5.9990 chunk 262 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 291 optimal weight: 0.8980 chunk 241 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 152 optimal weight: 0.0050 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24728 Z= 0.209 Angle : 0.665 14.453 33724 Z= 0.333 Chirality : 0.045 0.201 4007 Planarity : 0.004 0.063 4295 Dihedral : 4.473 23.496 3633 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.63 % Favored : 93.31 % Rotamer: Outliers : 3.06 % Allowed : 18.52 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.15), residues: 3064 helix: -1.61 (0.26), residues: 296 sheet: 0.33 (0.15), residues: 1158 loop : -1.47 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 528 HIS 0.009 0.001 HIS A 400 PHE 0.021 0.002 PHE L 479 TYR 0.031 0.002 TYR R 81 ARG 0.007 0.000 ARG L 546 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 257 time to evaluate : 2.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 506 MET cc_start: 0.6945 (mtt) cc_final: 0.6670 (mtt) REVERT: P 108 MET cc_start: 0.8098 (mmt) cc_final: 0.7746 (mmt) REVERT: Q 36 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6857 (tppt) REVERT: B 376 ASP cc_start: 0.8098 (p0) cc_final: 0.7664 (p0) REVERT: A 575 CYS cc_start: 0.2710 (m) cc_final: 0.2387 (m) REVERT: I 22 GLU cc_start: 0.8901 (mp0) cc_final: 0.8385 (mp0) REVERT: L 483 ASP cc_start: 0.8061 (m-30) cc_final: 0.7702 (m-30) REVERT: L 488 TRP cc_start: 0.6808 (m100) cc_final: 0.6466 (m100) REVERT: L 549 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7997 (tp30) outliers start: 84 outliers final: 62 residues processed: 324 average time/residue: 0.4004 time to fit residues: 197.8856 Evaluate side-chains 294 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 231 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain K residue 376 ASP Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 506 MET Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain N residue 24 LYS Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain Q residue 36 LYS Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 502 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 280 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 chunk 164 optimal weight: 0.8980 chunk 245 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 290 optimal weight: 0.8980 chunk 181 optimal weight: 9.9990 chunk 176 optimal weight: 0.2980 chunk 133 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 ASN ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24728 Z= 0.210 Angle : 0.660 15.049 33724 Z= 0.330 Chirality : 0.045 0.201 4007 Planarity : 0.004 0.050 4295 Dihedral : 4.352 21.488 3633 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.21 % Favored : 92.72 % Rotamer: Outliers : 3.28 % Allowed : 19.14 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 3064 helix: -1.54 (0.26), residues: 296 sheet: 0.33 (0.15), residues: 1152 loop : -1.45 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 528 HIS 0.006 0.001 HIS A 400 PHE 0.022 0.001 PHE L 479 TYR 0.025 0.001 TYR K 515 ARG 0.008 0.000 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 257 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 428 VAL cc_start: 0.5414 (OUTLIER) cc_final: 0.5199 (p) REVERT: D 506 MET cc_start: 0.6933 (mtt) cc_final: 0.6670 (mtt) REVERT: P 24 LYS cc_start: 0.6307 (tptp) cc_final: 0.5865 (tptt) REVERT: P 90 GLU cc_start: 0.4902 (tp30) cc_final: 0.4398 (tp30) REVERT: P 108 MET cc_start: 0.8048 (mmt) cc_final: 0.7754 (mmt) REVERT: B 376 ASP cc_start: 0.8141 (p0) cc_final: 0.7710 (p0) REVERT: A 575 CYS cc_start: 0.2804 (m) cc_final: 0.2498 (m) REVERT: I 22 GLU cc_start: 0.8885 (mp0) cc_final: 0.8398 (mp0) REVERT: I 41 GLU cc_start: 0.7207 (tp30) cc_final: 0.7003 (tp30) REVERT: L 483 ASP cc_start: 0.8113 (m-30) cc_final: 0.7748 (m-30) REVERT: L 488 TRP cc_start: 0.6744 (m100) cc_final: 0.6218 (m100) REVERT: L 549 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8015 (tp30) outliers start: 90 outliers final: 72 residues processed: 329 average time/residue: 0.3535 time to fit residues: 178.5361 Evaluate side-chains 311 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 238 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 506 MET Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 519 SER Chi-restraints excluded: chain K residue 549 GLU Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain N residue 24 LYS Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 524 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 179 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 385 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24728 Z= 0.195 Angle : 0.654 15.374 33724 Z= 0.325 Chirality : 0.045 0.198 4007 Planarity : 0.004 0.046 4295 Dihedral : 4.272 25.907 3633 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.02 % Favored : 92.92 % Rotamer: Outliers : 2.81 % Allowed : 19.94 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 3064 helix: -1.48 (0.27), residues: 297 sheet: 0.44 (0.15), residues: 1154 loop : -1.41 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 528 HIS 0.006 0.001 HIS A 400 PHE 0.024 0.001 PHE D 405 TYR 0.024 0.001 TYR R 81 ARG 0.007 0.000 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 256 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 428 VAL cc_start: 0.5414 (OUTLIER) cc_final: 0.5206 (p) REVERT: M 42 MET cc_start: -0.0475 (tpp) cc_final: -0.1064 (tpt) REVERT: D 506 MET cc_start: 0.6945 (mtt) cc_final: 0.6664 (mtt) REVERT: P 90 GLU cc_start: 0.4835 (tp30) cc_final: 0.4373 (tp30) REVERT: N 121 ASN cc_start: 0.2714 (OUTLIER) cc_final: 0.2286 (m110) REVERT: B 376 ASP cc_start: 0.8084 (p0) cc_final: 0.7638 (p0) REVERT: A 575 CYS cc_start: 0.2888 (m) cc_final: 0.2583 (m) REVERT: I 22 GLU cc_start: 0.8856 (mp0) cc_final: 0.8337 (mp0) REVERT: L 483 ASP cc_start: 0.8066 (m-30) cc_final: 0.7686 (m-30) REVERT: L 488 TRP cc_start: 0.6758 (m100) cc_final: 0.6453 (m100) REVERT: L 549 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8100 (tp30) outliers start: 77 outliers final: 67 residues processed: 318 average time/residue: 0.3567 time to fit residues: 174.6303 Evaluate side-chains 301 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 232 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 506 MET Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 519 SER Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 483 ASP Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 121 ASN Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 524 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 263 optimal weight: 0.9980 chunk 277 optimal weight: 9.9990 chunk 253 optimal weight: 0.6980 chunk 270 optimal weight: 7.9990 chunk 162 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 212 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 269 optimal weight: 8.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24728 Z= 0.290 Angle : 0.699 16.125 33724 Z= 0.349 Chirality : 0.046 0.250 4007 Planarity : 0.004 0.050 4295 Dihedral : 4.461 23.227 3633 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.03 % Favored : 91.91 % Rotamer: Outliers : 3.24 % Allowed : 20.27 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 3064 helix: -1.49 (0.27), residues: 297 sheet: 0.17 (0.15), residues: 1212 loop : -1.46 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 488 HIS 0.005 0.001 HIS A 400 PHE 0.020 0.002 PHE G 479 TYR 0.029 0.002 TYR R 81 ARG 0.007 0.001 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 243 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 428 VAL cc_start: 0.5448 (OUTLIER) cc_final: 0.5246 (p) REVERT: D 506 MET cc_start: 0.6994 (mtt) cc_final: 0.6743 (mtt) REVERT: P 90 GLU cc_start: 0.4902 (tp30) cc_final: 0.4484 (tp30) REVERT: A 575 CYS cc_start: 0.2990 (m) cc_final: 0.2681 (m) REVERT: I 22 GLU cc_start: 0.8838 (mp0) cc_final: 0.8339 (mp0) REVERT: L 483 ASP cc_start: 0.8066 (m-30) cc_final: 0.7685 (m-30) REVERT: L 488 TRP cc_start: 0.6828 (m100) cc_final: 0.6489 (m100) REVERT: L 549 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8123 (tp30) outliers start: 89 outliers final: 77 residues processed: 314 average time/residue: 0.3846 time to fit residues: 188.0294 Evaluate side-chains 303 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 225 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 519 SER Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 483 ASP Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 524 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 177 optimal weight: 7.9990 chunk 285 optimal weight: 0.6980 chunk 174 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 299 optimal weight: 2.9990 chunk 275 optimal weight: 3.9990 chunk 238 optimal weight: 0.6980 chunk 24 optimal weight: 20.0000 chunk 184 optimal weight: 0.5980 chunk 146 optimal weight: 0.0670 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 123 HIS S 43 HIS ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24728 Z= 0.218 Angle : 0.693 16.480 33724 Z= 0.343 Chirality : 0.046 0.238 4007 Planarity : 0.004 0.044 4295 Dihedral : 4.378 24.537 3633 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.85 % Favored : 93.08 % Rotamer: Outliers : 2.88 % Allowed : 20.74 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 3064 helix: -1.41 (0.27), residues: 290 sheet: 0.19 (0.15), residues: 1220 loop : -1.41 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 528 HIS 0.007 0.001 HIS H 400 PHE 0.036 0.002 PHE F 405 TYR 0.031 0.001 TYR R 81 ARG 0.007 0.000 ARG J 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 244 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 372 LEU cc_start: 0.7522 (mt) cc_final: 0.7134 (mt) REVERT: P 90 GLU cc_start: 0.4911 (tp30) cc_final: 0.4575 (tp30) REVERT: R 80 GLN cc_start: 0.6548 (mm110) cc_final: 0.6007 (mt0) REVERT: Q 42 MET cc_start: 0.3544 (tpp) cc_final: 0.2845 (tpt) REVERT: A 575 CYS cc_start: 0.2958 (m) cc_final: 0.2654 (m) REVERT: I 22 GLU cc_start: 0.8833 (mp0) cc_final: 0.8298 (mp0) REVERT: L 483 ASP cc_start: 0.8023 (m-30) cc_final: 0.7649 (m-30) REVERT: L 488 TRP cc_start: 0.6904 (m100) cc_final: 0.6532 (m100) REVERT: L 489 MET cc_start: 0.6270 (pmm) cc_final: 0.5712 (pmm) REVERT: L 549 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8100 (mm-30) outliers start: 79 outliers final: 74 residues processed: 309 average time/residue: 0.3559 time to fit residues: 169.3675 Evaluate side-chains 300 residues out of total 2743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 226 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 519 SER Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 483 ASP Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain N residue 24 LYS Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 524 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 189 optimal weight: 0.8980 chunk 254 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 220 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 239 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.107134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.077130 restraints weight = 88955.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.078067 restraints weight = 62117.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.078138 restraints weight = 46260.850| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.6345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 24728 Z= 0.336 Angle : 0.733 16.622 33724 Z= 0.368 Chirality : 0.047 0.199 4007 Planarity : 0.005 0.083 4295 Dihedral : 4.692 23.256 3633 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.91 % Favored : 91.02 % Rotamer: Outliers : 2.95 % Allowed : 20.89 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.15), residues: 3064 helix: -1.56 (0.27), residues: 290 sheet: 0.06 (0.15), residues: 1192 loop : -1.51 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 488 HIS 0.008 0.001 HIS I 43 PHE 0.029 0.002 PHE F 405 TYR 0.025 0.002 TYR R 81 ARG 0.008 0.001 ARG Q 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4965.55 seconds wall clock time: 91 minutes 22.46 seconds (5482.46 seconds total)