Starting phenix.real_space_refine on Thu Feb 15 12:59:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8d_10118/02_2024/6s8d_10118.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8d_10118/02_2024/6s8d_10118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8d_10118/02_2024/6s8d_10118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8d_10118/02_2024/6s8d_10118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8d_10118/02_2024/6s8d_10118.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8d_10118/02_2024/6s8d_10118.pdb" } resolution = 3.49 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= 0.008 sd= 0.104 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 51 5.16 5 C 7782 2.51 5 N 2091 2.21 5 O 2343 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 35": "OD1" <-> "OD2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 63": "OD1" <-> "OD2" Residue "L ASP 85": "OD1" <-> "OD2" Residue "L ASP 95": "OD1" <-> "OD2" Residue "L PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A ASP 49": "OD1" <-> "OD2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ASP 55": "OD1" <-> "OD2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "B ARG 559": "NH1" <-> "NH2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B ASP 607": "OD1" <-> "OD2" Residue "B GLU 611": "OE1" <-> "OE2" Residue "D ARG 559": "NH1" <-> "NH2" Residue "D GLU 578": "OE1" <-> "OE2" Residue "D ASP 607": "OD1" <-> "OD2" Residue "D GLU 611": "OE1" <-> "OE2" Residue "F ARG 559": "NH1" <-> "NH2" Residue "F GLU 578": "OE1" <-> "OE2" Residue "F ASP 607": "OD1" <-> "OD2" Residue "F GLU 611": "OE1" <-> "OE2" Residue "O TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 35": "OD1" <-> "OD2" Residue "O TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 63": "OD1" <-> "OD2" Residue "O ASP 85": "OD1" <-> "OD2" Residue "O ASP 95": "OD1" <-> "OD2" Residue "O PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 35": "OD1" <-> "OD2" Residue "U TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 63": "OD1" <-> "OD2" Residue "U ASP 85": "OD1" <-> "OD2" Residue "U ASP 95": "OD1" <-> "OD2" Residue "U PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C ASP 49": "OD1" <-> "OD2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ASP 55": "OD1" <-> "OD2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ASP 150": "OD1" <-> "OD2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "C ASP 192": "OD1" <-> "OD2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E ASP 49": "OD1" <-> "OD2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ASP 55": "OD1" <-> "OD2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E ASP 192": "OD1" <-> "OD2" Residue "E PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 219": "NH1" <-> "NH2" Residue "E PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 229": "OE1" <-> "OE2" Residue "E GLU 231": "OE1" <-> "OE2" Residue "E PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 235": "OE1" <-> "OE2" Residue "P PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12267 Number of models: 1 Model: "" Number of chains: 15 Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 817 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 8, 'TRANS': 101} Chain: "H" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "A" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "D" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "F" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "O" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 817 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 8, 'TRANS': 101} Chain: "U" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 817 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 8, 'TRANS': 101} Chain: "C" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "P" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "Y" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "G" 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: "I" 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.86, per 1000 atoms: 0.56 Number of scatterers: 12267 At special positions: 0 Unit cell: (100.182, 101.031, 123.105, 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 51 16.00 O 2343 8.00 N 2091 7.00 C 7782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 609 " distance=2.05 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.04 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.03 Simple disulfide: pdb=" SG CYS D 609 " - pdb=" SG CYS C 53 " distance=2.11 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.03 Simple disulfide: pdb=" SG CYS F 609 " - pdb=" SG CYS E 53 " distance=1.93 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 91 " distance=2.04 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 91 " distance=2.04 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 98 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 98 " distance=2.03 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 G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG G 1 " - " ASN B 563 " " NAG I 1 " - " ASN D 563 " " NAG J 1 " - " ASN F 563 " Time building additional restraints: 4.82 Conformation dependent library (CDL) restraints added in 2.4 seconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2844 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 33 sheets defined 12.7% alpha, 38.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.871A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.779A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 4.019A pdb=" N ILE B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 576 removed outlier: 3.680A pdb=" N GLY B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 598 removed outlier: 3.705A pdb=" N ARG B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 4.018A pdb=" N ILE D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 553 through 576 removed outlier: 3.680A pdb=" N GLY D 557 " --> pdb=" O GLY D 553 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.705A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 4.019A pdb=" N ILE F 542 " --> pdb=" O ALA F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 576 removed outlier: 3.679A pdb=" N GLY F 557 " --> pdb=" O GLY F 553 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA F 575 " --> pdb=" O LEU F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 3.704A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 86 removed outlier: 3.871A pdb=" N GLU O 86 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 86 removed outlier: 3.872A pdb=" N GLU U 86 " --> pdb=" O ALA U 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.779A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 78 through 84 removed outlier: 3.779A pdb=" N LYS E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.480A pdb=" N TRP L 38 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS L 48 " --> pdb=" O GLN L 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA3, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 61 through 62 removed outlier: 4.688A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR H 100 " --> pdb=" O TYR H 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 61 through 62 removed outlier: 4.688A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 42 through 45 removed outlier: 7.133A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 42 through 45 removed outlier: 7.133A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AB1, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AB2, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.453A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG A 136 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 544 through 548 Processing sheet with id=AB4, first strand: chain 'D' and resid 580 through 581 removed outlier: 7.132A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 580 through 581 Processing sheet with id=AB6, first strand: chain 'F' and resid 544 through 548 Processing sheet with id=AB7, first strand: chain 'F' and resid 580 through 581 removed outlier: 7.133A pdb=" N GLY E 36 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 580 through 581 Processing sheet with id=AB9, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.480A pdb=" N TRP O 38 " --> pdb=" O ILE O 50 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS O 48 " --> pdb=" O GLN O 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 10 through 12 Processing sheet with id=AC2, first strand: chain 'O' and resid 18 through 24 Processing sheet with id=AC3, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.479A pdb=" N TRP U 38 " --> pdb=" O ILE U 50 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS U 48 " --> pdb=" O GLN U 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'U' and resid 10 through 12 Processing sheet with id=AC5, first strand: chain 'U' and resid 18 through 24 Processing sheet with id=AC6, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AC7, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.452A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG C 136 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AC9, first strand: chain 'E' and resid 105 through 114 removed outlier: 6.452A pdb=" N GLU E 106 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N HIS E 139 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N CYS E 108 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL E 141 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN E 110 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLY E 143 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU E 112 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG E 136 " --> pdb=" O THR E 216 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE E 218 " --> pdb=" O ARG E 136 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL E 138 " --> pdb=" O ILE E 218 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR E 220 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS E 140 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ALA E 222 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER E 142 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'P' and resid 61 through 62 removed outlier: 4.688A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR P 100 " --> pdb=" O TYR P 113 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 61 through 62 removed outlier: 4.688A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'Y' and resid 61 through 62 removed outlier: 4.688A pdb=" N TRP Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ARG Y 38 " --> pdb=" O TRP Y 47 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR Y 100 " --> pdb=" O TYR Y 113 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 61 through 62 removed outlier: 4.688A pdb=" N TRP Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ARG Y 38 " --> pdb=" O TRP Y 47 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 5.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3976 1.34 - 1.46: 2859 1.46 - 1.58: 5675 1.58 - 1.69: 3 1.69 - 1.81: 60 Bond restraints: 12573 Sorted by residual: bond pdb=" CB ILE D 527 " pdb=" CG2 ILE D 527 " ideal model delta sigma weight residual 1.521 1.584 -0.063 3.30e-02 9.18e+02 3.61e+00 bond pdb=" CB ILE F 527 " pdb=" CG2 ILE F 527 " ideal model delta sigma weight residual 1.521 1.583 -0.062 3.30e-02 9.18e+02 3.57e+00 bond pdb=" CB ILE B 527 " pdb=" CG2 ILE B 527 " ideal model delta sigma weight residual 1.521 1.583 -0.062 3.30e-02 9.18e+02 3.51e+00 bond pdb=" CB ILE D 527 " pdb=" CG1 ILE D 527 " ideal model delta sigma weight residual 1.530 1.559 -0.029 2.00e-02 2.50e+03 2.12e+00 bond pdb=" CB ILE F 527 " pdb=" CG1 ILE F 527 " ideal model delta sigma weight residual 1.530 1.559 -0.029 2.00e-02 2.50e+03 2.06e+00 ... (remaining 12568 not shown) Histogram of bond angle deviations from ideal: 100.26 - 107.03: 420 107.03 - 113.80: 6743 113.80 - 120.58: 4971 120.58 - 127.35: 4825 127.35 - 134.13: 153 Bond angle restraints: 17112 Sorted by residual: angle pdb=" N ILE F 527 " pdb=" CA ILE F 527 " pdb=" C ILE F 527 " ideal model delta sigma weight residual 106.53 113.33 -6.80 1.41e+00 5.03e-01 2.32e+01 angle pdb=" N ILE B 527 " pdb=" CA ILE B 527 " pdb=" C ILE B 527 " ideal model delta sigma weight residual 106.53 113.30 -6.77 1.41e+00 5.03e-01 2.30e+01 angle pdb=" N ILE D 527 " pdb=" CA ILE D 527 " pdb=" C ILE D 527 " ideal model delta sigma weight residual 106.53 113.29 -6.76 1.41e+00 5.03e-01 2.30e+01 angle pdb=" C ASP Y 92 " pdb=" N THR Y 93 " pdb=" CA THR Y 93 " ideal model delta sigma weight residual 122.85 127.48 -4.63 1.39e+00 5.18e-01 1.11e+01 angle pdb=" CG1 ILE B 527 " pdb=" CB ILE B 527 " pdb=" CG2 ILE B 527 " ideal model delta sigma weight residual 110.70 120.67 -9.97 3.00e+00 1.11e-01 1.10e+01 ... (remaining 17107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 6742 17.85 - 35.70: 563 35.70 - 53.56: 117 53.56 - 71.41: 21 71.41 - 89.26: 15 Dihedral angle restraints: 7458 sinusoidal: 2961 harmonic: 4497 Sorted by residual: dihedral pdb=" CB CYS E 121 " pdb=" SG CYS E 121 " pdb=" SG CYS E 147 " pdb=" CB CYS E 147 " ideal model delta sinusoidal sigma weight residual -86.00 3.26 -89.26 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 147 " pdb=" CB CYS C 147 " ideal model delta sinusoidal sigma weight residual -86.00 3.25 -89.25 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS A 121 " pdb=" SG CYS A 121 " pdb=" SG CYS A 147 " pdb=" CB CYS A 147 " ideal model delta sinusoidal sigma weight residual -86.00 3.23 -89.23 1 1.00e+01 1.00e-02 9.47e+01 ... (remaining 7455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.327: 1866 0.327 - 0.655: 3 0.655 - 0.982: 0 0.982 - 1.309: 0 1.309 - 1.636: 3 Chirality restraints: 1872 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-02 2.50e+03 6.69e+03 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-02 2.50e+03 6.69e+03 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-02 2.50e+03 6.69e+03 ... (remaining 1869 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA H 94 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C ALA H 94 " 0.046 2.00e-02 2.50e+03 pdb=" O ALA H 94 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL H 95 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA P 94 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" C ALA P 94 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA P 94 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL P 95 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 94 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C ALA Y 94 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA Y 94 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL Y 95 " -0.015 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2768 2.78 - 3.31: 10659 3.31 - 3.84: 18665 3.84 - 4.37: 21850 4.37 - 4.90: 39083 Nonbonded interactions: 93025 Sorted by model distance: nonbonded pdb=" O GLY O 80 " pdb=" NE2 GLN O 82 " model vdw 2.255 2.520 nonbonded pdb=" O GLY U 80 " pdb=" NE2 GLN U 82 " model vdw 2.255 2.520 nonbonded pdb=" O GLY L 80 " pdb=" NE2 GLN L 82 " model vdw 2.256 2.520 nonbonded pdb=" OD2 ASP L 100 " pdb=" OG1 THR A 144 " model vdw 2.287 2.440 nonbonded pdb=" O SER U 3 " pdb=" OG SER U 3 " model vdw 2.324 2.440 ... (remaining 93020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 6.010 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 35.960 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12573 Z= 0.385 Angle : 0.851 9.968 17112 Z= 0.468 Chirality : 0.085 1.636 1872 Planarity : 0.005 0.043 2217 Dihedral : 13.950 88.998 4551 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.25 % Favored : 95.56 % Rotamer: Outliers : 2.56 % Allowed : 4.74 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1554 helix: 0.45 (0.43), residues: 126 sheet: -0.17 (0.20), residues: 624 loop : -1.03 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 597 HIS 0.004 0.001 HIS F 516 PHE 0.014 0.002 PHE C 132 TYR 0.021 0.002 TYR P 97 ARG 0.004 0.000 ARG D 559 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 258 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 100 ASP cc_start: 0.8253 (m-30) cc_final: 0.8006 (m-30) REVERT: P 3 GLN cc_start: 0.7395 (tm-30) cc_final: 0.6999 (tm-30) outliers start: 33 outliers final: 12 residues processed: 282 average time/residue: 0.2735 time to fit residues: 107.2333 Evaluate side-chains 202 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain E residue 229 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 0.4980 chunk 141 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 HIS A 61 ASN B 516 HIS D 516 HIS ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 56 ASN U 41 GLN ** U 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 56 ASN C 39 HIS C 61 ASN C 188 GLN E 39 HIS E 61 ASN P 35 ASN Y 39 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12573 Z= 0.199 Angle : 0.612 6.529 17112 Z= 0.321 Chirality : 0.044 0.168 1872 Planarity : 0.004 0.043 2217 Dihedral : 7.549 86.146 1881 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.80 % Allowed : 12.20 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1554 helix: 1.55 (0.47), residues: 126 sheet: 0.11 (0.20), residues: 642 loop : -0.73 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 104 HIS 0.004 0.001 HIS Y 101 PHE 0.014 0.001 PHE D 592 TYR 0.016 0.001 TYR Y 62 ARG 0.008 0.001 ARG Y 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 197 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 ASP cc_start: 0.7500 (m-30) cc_final: 0.7274 (m-30) REVERT: L 100 ASP cc_start: 0.7885 (m-30) cc_final: 0.7679 (m-30) REVERT: H 19 ARG cc_start: 0.7025 (ttm170) cc_final: 0.6134 (ttm170) REVERT: B 596 ARG cc_start: 0.7807 (mtt90) cc_final: 0.7570 (mtt90) REVERT: P 3 GLN cc_start: 0.7343 (tm-30) cc_final: 0.6939 (tm-30) REVERT: Y 19 ARG cc_start: 0.7407 (ttt-90) cc_final: 0.6846 (ttt90) outliers start: 36 outliers final: 22 residues processed: 213 average time/residue: 0.2647 time to fit residues: 78.9746 Evaluate side-chains 205 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 183 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 86 ASN Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 86 ASN Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 96 optimal weight: 0.4980 chunk 39 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN E 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12573 Z= 0.340 Angle : 0.634 6.616 17112 Z= 0.331 Chirality : 0.045 0.152 1872 Planarity : 0.005 0.065 2217 Dihedral : 6.588 43.502 1870 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.34 % Allowed : 14.53 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.21), residues: 1554 helix: 1.22 (0.49), residues: 126 sheet: 0.07 (0.20), residues: 645 loop : -0.75 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 38 HIS 0.003 0.001 HIS E 139 PHE 0.019 0.002 PHE H 29 TYR 0.017 0.002 TYR H 97 ARG 0.012 0.001 ARG P 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 206 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7114 (ttm170) cc_final: 0.6159 (ttm170) REVERT: P 3 GLN cc_start: 0.7428 (tm-30) cc_final: 0.7153 (tm-30) outliers start: 43 outliers final: 34 residues processed: 225 average time/residue: 0.2559 time to fit residues: 81.4962 Evaluate side-chains 225 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain P residue 19 ARG Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 86 ASN Chi-restraints excluded: chain Y residue 91 GLU Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 99 THR Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.0770 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 150 optimal weight: 0.0970 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 GLN ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN E 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12573 Z= 0.191 Angle : 0.562 6.817 17112 Z= 0.295 Chirality : 0.043 0.160 1872 Planarity : 0.004 0.050 2217 Dihedral : 5.958 40.464 1867 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.57 % Allowed : 15.15 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.21), residues: 1554 helix: 1.53 (0.49), residues: 126 sheet: 0.19 (0.22), residues: 585 loop : -0.68 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 36 HIS 0.002 0.000 HIS F 516 PHE 0.015 0.001 PHE D 592 TYR 0.012 0.001 TYR H 97 ARG 0.008 0.000 ARG E 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 195 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 61 ASP cc_start: 0.6318 (OUTLIER) cc_final: 0.6069 (m-30) outliers start: 46 outliers final: 32 residues processed: 220 average time/residue: 0.2542 time to fit residues: 82.0809 Evaluate side-chains 218 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 GLN ** U 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN E 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 12573 Z= 0.502 Angle : 0.700 6.362 17112 Z= 0.366 Chirality : 0.048 0.157 1872 Planarity : 0.005 0.060 2217 Dihedral : 6.266 39.288 1867 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.51 % Allowed : 15.54 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.21), residues: 1554 helix: 0.81 (0.48), residues: 126 sheet: 0.22 (0.22), residues: 540 loop : -0.96 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 36 HIS 0.004 0.001 HIS C 139 PHE 0.022 0.003 PHE F 592 TYR 0.022 0.002 TYR P 97 ARG 0.004 0.001 ARG Y 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 195 time to evaluate : 1.413 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7141 (tp30) REVERT: F 545 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6530 (mt-10) REVERT: O 54 ASN cc_start: 0.7727 (p0) cc_final: 0.7481 (p0) REVERT: E 106 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7622 (mm-30) REVERT: P 82 TYR cc_start: 0.7159 (m-80) cc_final: 0.6906 (m-10) REVERT: P 93 THR cc_start: 0.8177 (p) cc_final: 0.7914 (p) outliers start: 58 outliers final: 46 residues processed: 228 average time/residue: 0.2543 time to fit residues: 82.0201 Evaluate side-chains 231 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 185 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 92 GLN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 86 ASN Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 80 THR Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 99 THR Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.1980 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 150 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 29 ASN U 29 ASN C 188 GLN E 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12573 Z= 0.182 Angle : 0.567 8.115 17112 Z= 0.297 Chirality : 0.042 0.172 1872 Planarity : 0.004 0.045 2217 Dihedral : 5.755 38.932 1867 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.03 % Allowed : 18.03 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.21), residues: 1554 helix: 1.40 (0.49), residues: 126 sheet: -0.01 (0.22), residues: 588 loop : -0.69 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.002 0.000 HIS F 516 PHE 0.015 0.001 PHE Y 29 TYR 0.012 0.001 TYR H 97 ARG 0.007 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 197 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 61 ASP cc_start: 0.6241 (OUTLIER) cc_final: 0.5979 (m-30) REVERT: A 120 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6978 (tp30) REVERT: E 188 GLN cc_start: 0.6007 (tp40) cc_final: 0.5684 (mm-40) REVERT: P 18 LEU cc_start: 0.7698 (mp) cc_final: 0.7402 (mp) REVERT: P 19 ARG cc_start: 0.7138 (mmm160) cc_final: 0.6781 (mmm160) REVERT: P 93 THR cc_start: 0.8045 (p) cc_final: 0.7712 (p) REVERT: Y 84 GLN cc_start: 0.7860 (tp40) cc_final: 0.7515 (mp10) outliers start: 39 outliers final: 29 residues processed: 220 average time/residue: 0.2377 time to fit residues: 76.1031 Evaluate side-chains 214 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 184 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 92 GLN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 6.9990 chunk 17 optimal weight: 0.2980 chunk 85 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 127 optimal weight: 0.1980 chunk 84 optimal weight: 4.9990 chunk 150 optimal weight: 0.0980 chunk 94 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 GLN C 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12573 Z= 0.165 Angle : 0.551 6.731 17112 Z= 0.287 Chirality : 0.042 0.162 1872 Planarity : 0.004 0.050 2217 Dihedral : 5.288 39.167 1867 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.72 % Allowed : 18.26 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1554 helix: 1.64 (0.48), residues: 126 sheet: 0.06 (0.22), residues: 585 loop : -0.61 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 36 HIS 0.001 0.000 HIS F 516 PHE 0.014 0.001 PHE P 29 TYR 0.013 0.001 TYR H 62 ARG 0.006 0.000 ARG L 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 194 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: C 120 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6700 (mt-10) REVERT: C 188 GLN cc_start: 0.5673 (tp40) cc_final: 0.5451 (mm-40) REVERT: E 188 GLN cc_start: 0.5930 (tp40) cc_final: 0.5716 (mm-40) REVERT: P 93 THR cc_start: 0.7946 (p) cc_final: 0.7690 (p) outliers start: 35 outliers final: 27 residues processed: 215 average time/residue: 0.2343 time to fit residues: 73.3685 Evaluate side-chains 212 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 92 GLN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 1.9990 chunk 89 optimal weight: 0.0050 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 144 optimal weight: 0.0770 overall best weight: 0.9756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12573 Z= 0.209 Angle : 0.568 7.479 17112 Z= 0.296 Chirality : 0.043 0.140 1872 Planarity : 0.004 0.052 2217 Dihedral : 4.964 39.474 1859 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.87 % Allowed : 18.41 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1554 helix: 1.58 (0.48), residues: 126 sheet: 0.05 (0.22), residues: 579 loop : -0.63 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Y 36 HIS 0.002 0.001 HIS F 516 PHE 0.018 0.001 PHE Y 29 TYR 0.013 0.001 TYR H 97 ARG 0.007 0.000 ARG U 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 196 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8452 (mmt) cc_final: 0.8064 (mmp) REVERT: C 120 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6844 (mt-10) REVERT: C 188 GLN cc_start: 0.5696 (tp40) cc_final: 0.5494 (mm-40) REVERT: E 188 GLN cc_start: 0.5960 (tp40) cc_final: 0.5749 (mm-40) REVERT: P 61 ASP cc_start: 0.6032 (OUTLIER) cc_final: 0.5673 (m-30) REVERT: P 93 THR cc_start: 0.7980 (p) cc_final: 0.7718 (p) REVERT: Y 93 THR cc_start: 0.8089 (p) cc_final: 0.7836 (p) outliers start: 37 outliers final: 29 residues processed: 216 average time/residue: 0.2278 time to fit residues: 72.3242 Evaluate side-chains 219 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 92 GLN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 80 THR Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12573 Z= 0.338 Angle : 0.635 7.573 17112 Z= 0.331 Chirality : 0.045 0.148 1872 Planarity : 0.005 0.048 2217 Dihedral : 5.105 27.194 1857 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.03 % Allowed : 19.04 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.21), residues: 1554 helix: 1.26 (0.48), residues: 126 sheet: 0.39 (0.23), residues: 516 loop : -0.91 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 36 HIS 0.003 0.001 HIS C 139 PHE 0.018 0.002 PHE B 592 TYR 0.018 0.002 TYR H 97 ARG 0.008 0.001 ARG P 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 1.287 Fit side-chains revert: symmetry clash REVERT: C 120 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6919 (mt-10) REVERT: C 188 GLN cc_start: 0.5653 (tp40) cc_final: 0.5438 (mm-40) REVERT: E 188 GLN cc_start: 0.5969 (tp40) cc_final: 0.5736 (mm-40) REVERT: P 61 ASP cc_start: 0.6122 (OUTLIER) cc_final: 0.5722 (m-30) REVERT: P 93 THR cc_start: 0.8034 (p) cc_final: 0.7726 (p) REVERT: Y 93 THR cc_start: 0.8099 (p) cc_final: 0.7764 (p) outliers start: 39 outliers final: 33 residues processed: 218 average time/residue: 0.2253 time to fit residues: 72.0168 Evaluate side-chains 222 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 188 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain O residue 92 GLN Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 86 ASN Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 80 THR Chi-restraints excluded: chain Y residue 86 ASN Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 3.9990 chunk 90 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 0.1980 chunk 155 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12573 Z= 0.218 Angle : 0.599 7.987 17112 Z= 0.313 Chirality : 0.044 0.200 1872 Planarity : 0.004 0.046 2217 Dihedral : 4.945 26.276 1857 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.72 % Allowed : 19.35 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1554 helix: 1.46 (0.48), residues: 126 sheet: 0.42 (0.23), residues: 516 loop : -0.89 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 36 HIS 0.003 0.001 HIS H 101 PHE 0.014 0.001 PHE B 592 TYR 0.019 0.001 TYR P 62 ARG 0.009 0.000 ARG P 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 596 ARG cc_start: 0.8323 (mtm-85) cc_final: 0.7982 (mtt90) REVERT: U 52 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7731 (t80) REVERT: U 109 LYS cc_start: 0.6076 (mmmt) cc_final: 0.5797 (mmmt) REVERT: C 120 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6833 (mt-10) REVERT: C 188 GLN cc_start: 0.5739 (tp40) cc_final: 0.5537 (mm-40) REVERT: E 188 GLN cc_start: 0.5934 (tp40) cc_final: 0.5716 (mm-40) REVERT: P 93 THR cc_start: 0.7953 (p) cc_final: 0.7681 (p) REVERT: Y 19 ARG cc_start: 0.7645 (ttt-90) cc_final: 0.6842 (ttm-80) REVERT: Y 93 THR cc_start: 0.8094 (p) cc_final: 0.7729 (p) outliers start: 35 outliers final: 31 residues processed: 203 average time/residue: 0.2165 time to fit residues: 65.2377 Evaluate side-chains 221 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 189 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain O residue 92 GLN Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 86 ASN Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 109 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 51 optimal weight: 30.0000 chunk 127 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 516 HIS ** Y 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.187615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.150785 restraints weight = 15129.634| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.81 r_work: 0.3380 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12573 Z= 0.272 Angle : 0.616 7.852 17112 Z= 0.322 Chirality : 0.044 0.184 1872 Planarity : 0.005 0.044 2217 Dihedral : 4.971 26.254 1857 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.95 % Allowed : 19.27 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.21), residues: 1554 helix: 1.40 (0.48), residues: 126 sheet: 0.39 (0.23), residues: 516 loop : -0.94 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 36 HIS 0.002 0.001 HIS F 516 PHE 0.016 0.002 PHE B 592 TYR 0.015 0.001 TYR P 97 ARG 0.009 0.001 ARG P 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2626.46 seconds wall clock time: 48 minutes 44.69 seconds (2924.69 seconds total)