Starting phenix.real_space_refine on Sat Feb 17 23:21:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyx_27785/02_2024/8dyx_27785.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyx_27785/02_2024/8dyx_27785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyx_27785/02_2024/8dyx_27785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyx_27785/02_2024/8dyx_27785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyx_27785/02_2024/8dyx_27785.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyx_27785/02_2024/8dyx_27785.pdb" } resolution = 3.0 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= 0.000 sd= 0.004 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 66 5.16 5 C 12566 2.51 5 N 3464 2.21 5 O 3934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I ASP 111": "OD1" <-> "OD2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H ASP 99": "OD1" <-> "OD2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 85": "OD1" <-> "OD2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 92": "OD1" <-> "OD2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ASP 53": "OD1" <-> "OD2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 32": "OD1" <-> "OD2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 82": "OD1" <-> "OD2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 92": "OD1" <-> "OD2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 86": "OD1" <-> "OD2" Residue "M TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 32": "OD1" <-> "OD2" Residue "N TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 64": "OE1" <-> "OE2" Residue "P PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 85": "OD1" <-> "OD2" Residue "P ASP 92": "OD1" <-> "OD2" Residue "Q GLU 46": "OE1" <-> "OE2" Residue "Q GLU 64": "OE1" <-> "OE2" Residue "Q GLU 85": "OE1" <-> "OE2" Residue "Q ASP 86": "OD1" <-> "OD2" Residue "Q ASP 99": "OD1" <-> "OD2" Residue "Q TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 32": "OD1" <-> "OD2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 82": "OD1" <-> "OD2" Residue "R ASP 85": "OD1" <-> "OD2" Residue "R ASP 92": "OD1" <-> "OD2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "T TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 60": "OD1" <-> "OD2" Residue "T GLU 81": "OE1" <-> "OE2" Residue "T ASP 82": "OD1" <-> "OD2" Residue "T TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 92": "OD1" <-> "OD2" Residue "U GLU 46": "OE1" <-> "OE2" Residue "U TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 64": "OE1" <-> "OE2" Residue "U TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 85": "OD1" <-> "OD2" Residue "V TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 53": "OD1" <-> "OD2" Residue "X TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 92": "OD1" <-> "OD2" Residue "Y TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20030 Number of models: 1 Model: "" Number of chains: 23 Chain: "I" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 637 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 23, 'TRANS': 66} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "A" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "B" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "C" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "E" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "M" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "N" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "O" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "P" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "Q" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "R" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "S" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "T" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "U" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "V" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "W" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "X" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "Y" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "Z" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Time building chain proxies: 10.36, per 1000 atoms: 0.52 Number of scatterers: 20030 At special positions: 0 Unit cell: (131.84, 121.54, 159.65, 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 66 16.00 O 3934 8.00 N 3464 7.00 C 12566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 92 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " 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 Time building additional restraints: 7.21 Conformation dependent library (CDL) restraints added in 4.3 seconds 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 66 sheets defined 6.2% alpha, 47.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.696A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.536A pdb=" N ASN A 31 " --> pdb=" O THR A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.872A pdb=" N GLU B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.784A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.987A pdb=" N GLU F 83 " --> pdb=" O ALA F 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.543A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.602A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 removed outlier: 4.121A pdb=" N GLU P 83 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 removed outlier: 3.539A pdb=" N ASN Q 31 " --> pdb=" O THR Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.686A pdb=" N ASP R 82 " --> pdb=" O GLN R 79 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU R 83 " --> pdb=" O ALA R 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 79 through 83' Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 83 through 87 Processing helix chain 'T' and resid 79 through 83 removed outlier: 4.118A pdb=" N GLU T 83 " --> pdb=" O ALA T 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 32 Processing helix chain 'U' and resid 83 through 87 Processing helix chain 'V' and resid 79 through 83 removed outlier: 3.865A pdb=" N GLU V 83 " --> pdb=" O ALA V 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 32 Processing helix chain 'W' and resid 83 through 87 Processing helix chain 'X' and resid 79 through 83 removed outlier: 3.681A pdb=" N GLU X 83 " --> pdb=" O ALA X 80 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 32 Processing helix chain 'Y' and resid 83 through 87 removed outlier: 3.502A pdb=" N THR Y 87 " --> pdb=" O VAL Y 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 83 removed outlier: 3.782A pdb=" N GLU Z 83 " --> pdb=" O ALA Z 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.203A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.203A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA H 96 " --> pdb=" O GLY H 100D" (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLY H 100D" --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.435A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AA7, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.599A pdb=" N THR A 77 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.091A pdb=" N GLY A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N MET A 34 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.091A pdb=" N GLY A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N CYS A 92 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TRP A 103 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ARG A 94 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 9 through 13 removed outlier: 6.494A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 9 through 13 Processing sheet with id=AB3, first strand: chain 'B' and resid 19 through 24 Processing sheet with id=AB4, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.548A pdb=" N THR C 77 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.913A pdb=" N MET C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.939A pdb=" N CYS C 92 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TRP C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.596A pdb=" N THR D 105 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D 13 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.596A pdb=" N THR D 105 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D 13 " --> pdb=" O THR D 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AC1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.585A pdb=" N THR E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.277A pdb=" N GLY E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET E 34 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.277A pdb=" N GLY E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA E 96 " --> pdb=" O GLY E 100D" (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLY E 100D" --> pdb=" O ALA E 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 9 through 13 removed outlier: 6.719A pdb=" N VAL F 11 " --> pdb=" O THR F 105 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 9 through 13 removed outlier: 6.719A pdb=" N VAL F 11 " --> pdb=" O THR F 105 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 19 through 24 Processing sheet with id=AC7, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.503A pdb=" N SER M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.764A pdb=" N MET M 34 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.769A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 9 through 13 removed outlier: 3.747A pdb=" N ALA N 84 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 9 through 13 removed outlier: 3.747A pdb=" N ALA N 84 " --> pdb=" O LEU N 104 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AD4, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.437A pdb=" N GLY O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET O 34 " --> pdb=" O ILE O 50 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.437A pdb=" N GLY O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N CYS O 92 " --> pdb=" O TRP O 103 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N TRP O 103 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG O 94 " --> pdb=" O ASP O 101 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP O 101 " --> pdb=" O ARG O 94 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 9 through 13 removed outlier: 5.854A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 9 through 13 Processing sheet with id=AD9, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AE1, first strand: chain 'Q' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.234A pdb=" N GLY Q 10 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET Q 34 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.234A pdb=" N GLY Q 10 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR Q 102 " --> pdb=" O ARG Q 94 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA Q 96 " --> pdb=" O GLY Q 100D" (cutoff:3.500A) removed outlier: 5.482A pdb=" N GLY Q 100D" --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 9 through 13 removed outlier: 5.715A pdb=" N GLN R 37 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU R 46 " --> pdb=" O GLN R 37 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 9 through 13 Processing sheet with id=AE6, first strand: chain 'R' and resid 18 through 24 Processing sheet with id=AE7, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.562A pdb=" N GLY S 10 " --> pdb=" O LEU S 108 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET S 34 " --> pdb=" O ILE S 50 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.562A pdb=" N GLY S 10 " --> pdb=" O LEU S 108 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR S 102 " --> pdb=" O ARG S 94 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA S 96 " --> pdb=" O GLY S 100D" (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLY S 100D" --> pdb=" O ALA S 96 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 9 through 13 removed outlier: 6.436A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 9 through 13 Processing sheet with id=AF3, first strand: chain 'T' and resid 19 through 24 Processing sheet with id=AF4, first strand: chain 'U' and resid 3 through 7 removed outlier: 3.540A pdb=" N SER U 70 " --> pdb=" O TYR U 79 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 10 through 12 removed outlier: 3.546A pdb=" N GLY U 10 " --> pdb=" O LEU U 108 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA U 93 " --> pdb=" O HIS U 35 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET U 34 " --> pdb=" O ILE U 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 10 through 12 removed outlier: 3.546A pdb=" N GLY U 10 " --> pdb=" O LEU U 108 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR U 102 " --> pdb=" O ARG U 94 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA U 96 " --> pdb=" O GLY U 100D" (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLY U 100D" --> pdb=" O ALA U 96 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 9 through 13 removed outlier: 5.836A pdb=" N GLN V 37 " --> pdb=" O LEU V 46 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU V 46 " --> pdb=" O GLN V 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 9 through 13 Processing sheet with id=AF9, first strand: chain 'V' and resid 18 through 24 Processing sheet with id=AG1, first strand: chain 'W' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'W' and resid 10 through 12 removed outlier: 3.755A pdb=" N GLY W 10 " --> pdb=" O LEU W 108 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N MET W 34 " --> pdb=" O ILE W 50 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE W 50 " --> pdb=" O MET W 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP W 36 " --> pdb=" O VAL W 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 10 through 12 removed outlier: 3.755A pdb=" N GLY W 10 " --> pdb=" O LEU W 108 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS W 92 " --> pdb=" O TRP W 103 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TRP W 103 " --> pdb=" O CYS W 92 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG W 94 " --> pdb=" O ASP W 101 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 9 through 13 removed outlier: 6.644A pdb=" N TRP X 35 " --> pdb=" O LEU X 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 9 through 13 Processing sheet with id=AG6, first strand: chain 'X' and resid 19 through 24 Processing sheet with id=AG7, first strand: chain 'Y' and resid 3 through 7 removed outlier: 3.632A pdb=" N THR Y 77 " --> pdb=" O ASP Y 72 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 10 through 12 removed outlier: 6.101A pdb=" N GLY Y 10 " --> pdb=" O THR Y 110 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA Y 93 " --> pdb=" O HIS Y 35 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N MET Y 34 " --> pdb=" O ILE Y 50 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE Y 50 " --> pdb=" O MET Y 34 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 96 through 97 Processing sheet with id=AH1, first strand: chain 'Z' and resid 9 through 13 removed outlier: 6.623A pdb=" N VAL Z 11 " --> pdb=" O THR Z 105 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP Z 35 " --> pdb=" O LEU Z 47 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 9 through 13 removed outlier: 6.623A pdb=" N VAL Z 11 " --> pdb=" O THR Z 105 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 19 through 24 832 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.76 Time building geometry restraints manager: 7.92 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: 6582 1.34 - 1.46: 5469 1.46 - 1.58: 8397 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 20536 Sorted by residual: bond pdb=" CA ASP H 101 " pdb=" C ASP H 101 " ideal model delta sigma weight residual 1.521 1.534 -0.013 1.36e-02 5.41e+03 9.17e-01 bond pdb=" N TYR U 98 " pdb=" CA TYR U 98 " ideal model delta sigma weight residual 1.468 1.456 0.012 1.24e-02 6.50e+03 9.04e-01 bond pdb=" CA ASN I 177 " pdb=" C ASN I 177 " ideal model delta sigma weight residual 1.530 1.521 0.009 1.08e-02 8.57e+03 7.48e-01 bond pdb=" N ASN I 183 " pdb=" CA ASN I 183 " ideal model delta sigma weight residual 1.465 1.456 0.009 1.05e-02 9.07e+03 7.06e-01 bond pdb=" CB GLN C 3 " pdb=" CG GLN C 3 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.84e-01 ... (remaining 20531 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.89: 632 106.89 - 113.69: 10761 113.69 - 120.49: 7564 120.49 - 127.30: 8757 127.30 - 134.10: 266 Bond angle restraints: 27980 Sorted by residual: angle pdb=" C ASP H 101 " pdb=" CA ASP H 101 " pdb=" CB ASP H 101 " ideal model delta sigma weight residual 109.24 114.21 -4.97 1.75e+00 3.27e-01 8.08e+00 angle pdb=" C GLY P 50 " pdb=" N ASN P 51 " pdb=" CA ASN P 51 " ideal model delta sigma weight residual 121.54 126.87 -5.33 1.91e+00 2.74e-01 7.78e+00 angle pdb=" C GLY V 50 " pdb=" N ASN V 51 " pdb=" CA ASN V 51 " ideal model delta sigma weight residual 121.54 126.83 -5.29 1.91e+00 2.74e-01 7.66e+00 angle pdb=" C GLY L 50 " pdb=" N ASN L 51 " pdb=" CA ASN L 51 " ideal model delta sigma weight residual 121.54 126.74 -5.20 1.91e+00 2.74e-01 7.42e+00 angle pdb=" C GLY N 50 " pdb=" N ASN N 51 " pdb=" CA ASN N 51 " ideal model delta sigma weight residual 121.54 126.74 -5.20 1.91e+00 2.74e-01 7.42e+00 ... (remaining 27975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 10854 17.86 - 35.72: 725 35.72 - 53.59: 201 53.59 - 71.45: 25 71.45 - 89.31: 33 Dihedral angle restraints: 11838 sinusoidal: 4408 harmonic: 7430 Sorted by residual: dihedral pdb=" CB CYS Z 23 " pdb=" SG CYS Z 23 " pdb=" SG CYS Z 88 " pdb=" CB CYS Z 88 " ideal model delta sinusoidal sigma weight residual 93.00 55.97 37.03 1 1.00e+01 1.00e-02 1.94e+01 dihedral pdb=" CB CYS Y 22 " pdb=" SG CYS Y 22 " pdb=" SG CYS Y 92 " pdb=" CB CYS Y 92 " ideal model delta sinusoidal sigma weight residual 93.00 59.65 33.35 1 1.00e+01 1.00e-02 1.58e+01 dihedral pdb=" CB CYS X 23 " pdb=" SG CYS X 23 " pdb=" SG CYS X 88 " pdb=" CB CYS X 88 " ideal model delta sinusoidal sigma weight residual 93.00 59.70 33.30 1 1.00e+01 1.00e-02 1.58e+01 ... (remaining 11835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1791 0.028 - 0.056: 836 0.056 - 0.084: 128 0.084 - 0.112: 152 0.112 - 0.140: 68 Chirality restraints: 2975 Sorted by residual: chirality pdb=" CA ASP H 101 " pdb=" N ASP H 101 " pdb=" C ASP H 101 " pdb=" CB ASP H 101 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE E 50 " pdb=" N ILE E 50 " pdb=" C ILE E 50 " pdb=" CB ILE E 50 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE Y 50 " pdb=" N ILE Y 50 " pdb=" C ILE Y 50 " pdb=" CB ILE Y 50 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 2972 not shown) Planarity restraints: 3655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 7 " -0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO R 8 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO R 8 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 8 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP I 111 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.14e+00 pdb=" CG ASP I 111 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP I 111 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP I 111 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG N 54 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO N 55 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO N 55 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO N 55 " -0.023 5.00e-02 4.00e+02 ... (remaining 3652 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 635 2.71 - 3.25: 17730 3.25 - 3.80: 31494 3.80 - 4.35: 42344 4.35 - 4.90: 73408 Nonbonded interactions: 165611 Sorted by model distance: nonbonded pdb=" NH2 ARG M 16 " pdb=" O THR T 18 " model vdw 2.157 2.520 nonbonded pdb=" OG1 THR S 24 " pdb=" O ASN S 76 " model vdw 2.197 2.440 nonbonded pdb=" N GLU E 85 " pdb=" OE1 GLU E 85 " model vdw 2.201 2.520 nonbonded pdb=" O PRO P 7 " pdb=" OG1 THR P 102 " model vdw 2.223 2.440 nonbonded pdb=" OG SER V 27A" pdb=" OD1 ASP V 92 " model vdw 2.236 2.440 ... (remaining 165606 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' selection = chain 'H' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.220 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 54.600 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.180 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 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 : 0.003 0.032 20536 Z= 0.175 Angle : 0.568 8.545 27980 Z= 0.323 Chirality : 0.040 0.140 2975 Planarity : 0.004 0.055 3655 Dihedral : 13.780 89.309 7148 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.24 % Allowed : 12.05 % Favored : 87.72 % 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: -0.08 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.69 (0.15), residues: 1100 loop : -0.61 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 103 HIS 0.003 0.001 HIS S 35 PHE 0.009 0.001 PHE B 98 TYR 0.014 0.001 TYR U 52A ARG 0.005 0.000 ARG T 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 332 time to evaluate : 2.124 Fit side-chains revert: symmetry clash REVERT: A 50 ILE cc_start: 0.8695 (tt) cc_final: 0.8415 (tp) REVERT: C 56 ARG cc_start: 0.8011 (mmt90) cc_final: 0.7580 (mpp80) REVERT: M 3 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7649 (mm110) REVERT: M 108 LEU cc_start: 0.8969 (tt) cc_final: 0.8720 (tp) REVERT: N 45 LYS cc_start: 0.9014 (ttpt) cc_final: 0.8738 (tttp) REVERT: T 24 THR cc_start: 0.8366 (m) cc_final: 0.8102 (p) REVERT: U 56 ARG cc_start: 0.8402 (mmt-90) cc_final: 0.8128 (ttm-80) REVERT: V 79 GLN cc_start: 0.7866 (tt0) cc_final: 0.7534 (mm-40) outliers start: 5 outliers final: 2 residues processed: 333 average time/residue: 1.2152 time to fit residues: 459.3788 Evaluate side-chains 313 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 311 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain V residue 65 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 205 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 237 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN N 79 GLN Q 105 GLN R 79 GLN V 89 GLN W 76 ASN X 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20536 Z= 0.240 Angle : 0.578 8.508 27980 Z= 0.309 Chirality : 0.042 0.133 2975 Planarity : 0.005 0.040 3655 Dihedral : 4.238 22.107 2940 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.12 % Allowed : 12.85 % Favored : 84.03 % 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: -0.22 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.56 (0.15), residues: 1133 loop : -0.70 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 103 HIS 0.004 0.001 HIS H 35 PHE 0.011 0.001 PHE Q 29 TYR 0.018 0.001 TYR S 90 ARG 0.005 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 332 time to evaluate : 2.232 Fit side-chains revert: symmetry clash REVERT: L 85 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: A 50 ILE cc_start: 0.8748 (tt) cc_final: 0.8396 (tp) REVERT: C 6 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: C 81 GLN cc_start: 0.8413 (tp40) cc_final: 0.8185 (tp40) REVERT: M 108 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8726 (tp) REVERT: N 45 LYS cc_start: 0.9013 (ttpt) cc_final: 0.8756 (tttp) REVERT: N 51 ASN cc_start: 0.8777 (m-40) cc_final: 0.8511 (m110) REVERT: O 3 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7566 (mp10) REVERT: P 17 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7413 (pt0) REVERT: P 81 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: Q 43 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.7818 (mppt) REVERT: T 24 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8104 (p) REVERT: U 56 ARG cc_start: 0.8377 (mmt-90) cc_final: 0.8082 (ttm-80) REVERT: V 66 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7200 (ptpt) REVERT: V 79 GLN cc_start: 0.7470 (tt0) cc_final: 0.7226 (mm-40) REVERT: W 94 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7158 (ttm170) REVERT: Y 82 MET cc_start: 0.5691 (mpm) cc_final: 0.2712 (ptp) outliers start: 66 outliers final: 37 residues processed: 358 average time/residue: 1.1945 time to fit residues: 487.5865 Evaluate side-chains 359 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 312 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 43 LYS Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 72 SER Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain X residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 198 optimal weight: 0.7980 chunk 162 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 238 optimal weight: 9.9990 chunk 257 optimal weight: 20.0000 chunk 212 optimal weight: 8.9990 chunk 236 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 185 ASN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN M 1 GLN M 3 GLN Q 39 GLN Q 105 GLN V 53 ASN W 76 ASN X 37 GLN X 89 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 20536 Z= 0.518 Angle : 0.701 6.790 27980 Z= 0.376 Chirality : 0.047 0.152 2975 Planarity : 0.006 0.056 3655 Dihedral : 4.812 20.726 2938 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.49 % Allowed : 14.31 % Favored : 81.20 % 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: -0.73 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.20 (0.14), residues: 1177 loop : -1.08 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP U 103 HIS 0.009 0.002 HIS S 35 PHE 0.017 0.003 PHE U 29 TYR 0.020 0.002 TYR S 90 ARG 0.005 0.001 ARG T 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 303 time to evaluate : 2.250 Fit side-chains revert: symmetry clash REVERT: L 85 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8115 (m-30) REVERT: A 50 ILE cc_start: 0.8733 (tt) cc_final: 0.8352 (OUTLIER) REVERT: C 6 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: F 45 LYS cc_start: 0.9151 (ttpt) cc_final: 0.8900 (pttp) REVERT: M 57 ASN cc_start: 0.9194 (OUTLIER) cc_final: 0.8964 (m-40) REVERT: O 3 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7508 (mp10) REVERT: P 17 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7479 (pt0) REVERT: P 81 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: Q 43 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.7854 (mppt) REVERT: T 24 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8140 (p) REVERT: T 45 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8491 (mmtm) REVERT: U 56 ARG cc_start: 0.8385 (mmt-90) cc_final: 0.7997 (ttm-80) REVERT: U 105 GLN cc_start: 0.8112 (pt0) cc_final: 0.7821 (mm110) REVERT: V 66 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7386 (ptpp) REVERT: V 79 GLN cc_start: 0.7367 (tt0) cc_final: 0.7065 (mm-40) REVERT: W 94 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7187 (ttm170) REVERT: Y 82 MET cc_start: 0.5581 (mpm) cc_final: 0.2792 (ptt) outliers start: 95 outliers final: 64 residues processed: 346 average time/residue: 1.1836 time to fit residues: 466.7648 Evaluate side-chains 363 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 289 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain M residue 1 GLN Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain M residue 57 ASN Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 82 SER Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 43 LYS Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain T residue 72 SER Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain X residue 27 ILE Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 50 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 30.0000 chunk 179 optimal weight: 1.9990 chunk 123 optimal weight: 0.0270 chunk 26 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 239 optimal weight: 20.0000 chunk 253 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 226 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 185 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN Q 105 GLN R 79 GLN X 37 GLN X 53 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20536 Z= 0.145 Angle : 0.528 7.183 27980 Z= 0.281 Chirality : 0.041 0.136 2975 Planarity : 0.004 0.042 3655 Dihedral : 4.306 19.969 2938 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.69 % Allowed : 16.30 % Favored : 81.01 % 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: -0.44 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.44 (0.14), residues: 1188 loop : -0.93 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 103 HIS 0.003 0.001 HIS H 35 PHE 0.007 0.001 PHE H 29 TYR 0.015 0.001 TYR U 79 ARG 0.002 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 319 time to evaluate : 2.368 Fit side-chains revert: symmetry clash REVERT: H 1 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6512 (pp30) REVERT: A 50 ILE cc_start: 0.8720 (tt) cc_final: 0.8351 (tp) REVERT: C 6 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7109 (mt-10) REVERT: C 38 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8221 (ptt180) REVERT: C 70 SER cc_start: 0.8279 (p) cc_final: 0.8006 (m) REVERT: F 45 LYS cc_start: 0.9097 (ttpt) cc_final: 0.8867 (pttp) REVERT: O 3 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7404 (mp10) REVERT: O 46 GLU cc_start: 0.8493 (tt0) cc_final: 0.8223 (tt0) REVERT: O 105 GLN cc_start: 0.7776 (pt0) cc_final: 0.7480 (pm20) REVERT: P 17 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: T 24 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.8004 (p) REVERT: U 56 ARG cc_start: 0.8362 (mmt-90) cc_final: 0.8062 (ttm-80) REVERT: U 105 GLN cc_start: 0.8046 (pt0) cc_final: 0.7828 (mm-40) REVERT: V 66 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7356 (ptpp) REVERT: V 79 GLN cc_start: 0.7415 (tt0) cc_final: 0.7121 (mm-40) REVERT: W 64 GLU cc_start: 0.7726 (tt0) cc_final: 0.7476 (tt0) REVERT: W 94 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7197 (ttm170) REVERT: Y 82 MET cc_start: 0.5450 (mpm) cc_final: 0.2765 (ptt) outliers start: 57 outliers final: 34 residues processed: 347 average time/residue: 1.1751 time to fit residues: 464.8141 Evaluate side-chains 341 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 299 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 72 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain X residue 45 LYS Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 50 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 3 optimal weight: 0.0270 chunk 188 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 227 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 113 ASN I 185 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN E 81 GLN M 3 GLN P 79 GLN Q 105 GLN R 53 ASN X 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 20536 Z= 0.372 Angle : 0.615 8.451 27980 Z= 0.326 Chirality : 0.044 0.142 2975 Planarity : 0.005 0.038 3655 Dihedral : 4.504 20.482 2938 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.87 % Allowed : 15.92 % Favored : 80.21 % 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: -0.82 (0.15), residues: 2607 helix: None (None), residues: 0 sheet: 0.15 (0.14), residues: 1111 loop : -1.11 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP U 103 HIS 0.007 0.002 HIS H 35 PHE 0.012 0.002 PHE U 29 TYR 0.019 0.002 TYR S 90 ARG 0.005 0.000 ARG E 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 298 time to evaluate : 2.328 Fit side-chains revert: symmetry clash REVERT: H 1 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.6645 (pp30) REVERT: H 82 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8602 (mtp) REVERT: L 85 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.8074 (m-30) REVERT: A 50 ILE cc_start: 0.8732 (tt) cc_final: 0.8338 (OUTLIER) REVERT: C 6 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: C 70 SER cc_start: 0.8389 (p) cc_final: 0.8133 (m) REVERT: F 45 LYS cc_start: 0.9122 (ttpt) cc_final: 0.8899 (pttp) REVERT: O 3 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7464 (mp10) REVERT: P 17 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7466 (pt0) REVERT: P 27 ASN cc_start: 0.9367 (OUTLIER) cc_final: 0.9035 (p0) REVERT: P 81 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: Q 16 ARG cc_start: 0.7869 (ptp-110) cc_final: 0.7599 (ptp-110) REVERT: Q 43 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.7789 (mppt) REVERT: T 24 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8155 (p) REVERT: U 56 ARG cc_start: 0.8378 (mmt-90) cc_final: 0.7992 (ttm-80) REVERT: U 105 GLN cc_start: 0.8115 (pt0) cc_final: 0.7828 (mm-40) REVERT: V 66 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7439 (ptpp) REVERT: V 79 GLN cc_start: 0.7388 (tt0) cc_final: 0.7129 (mm-40) REVERT: W 94 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7309 (ttm170) REVERT: Y 34 MET cc_start: 0.6221 (ppp) cc_final: 0.5928 (ptt) REVERT: Y 82 MET cc_start: 0.5458 (mpm) cc_final: 0.2838 (ptt) outliers start: 82 outliers final: 54 residues processed: 335 average time/residue: 1.2037 time to fit residues: 462.3990 Evaluate side-chains 355 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 290 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain Q residue 43 LYS Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain T residue 72 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 50 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 1.9990 chunk 228 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 253 optimal weight: 40.0000 chunk 210 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN M 3 GLN P 79 GLN Q 105 GLN R 53 ASN S 81 GLN X 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20536 Z= 0.231 Angle : 0.559 7.880 27980 Z= 0.295 Chirality : 0.042 0.145 2975 Planarity : 0.004 0.041 3655 Dihedral : 4.346 20.102 2938 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.59 % Allowed : 16.39 % Favored : 80.02 % 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: -0.59 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.34 (0.14), residues: 1199 loop : -1.05 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 103 HIS 0.005 0.001 HIS H 35 PHE 0.009 0.001 PHE C 29 TYR 0.016 0.001 TYR U 79 ARG 0.009 0.000 ARG S 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 311 time to evaluate : 2.369 Fit side-chains revert: symmetry clash REVERT: H 1 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6502 (pp30) REVERT: L 85 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: A 50 ILE cc_start: 0.8728 (tt) cc_final: 0.8338 (OUTLIER) REVERT: C 6 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7057 (mt-10) REVERT: O 3 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7437 (mp10) REVERT: P 17 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7473 (pt0) REVERT: Q 16 ARG cc_start: 0.7822 (ptp-110) cc_final: 0.7501 (ptp-110) REVERT: T 24 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8077 (p) REVERT: V 51 ASN cc_start: 0.6496 (OUTLIER) cc_final: 0.5677 (t160) REVERT: V 66 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.6925 (pttm) REVERT: V 79 GLN cc_start: 0.7524 (tt0) cc_final: 0.7261 (mm-40) REVERT: W 94 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7300 (ttm170) REVERT: Y 82 MET cc_start: 0.5252 (mpm) cc_final: 0.2773 (ptt) outliers start: 76 outliers final: 51 residues processed: 348 average time/residue: 1.1657 time to fit residues: 463.4860 Evaluate side-chains 359 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 300 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 72 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 51 ASN Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain X residue 45 LYS Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 50 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 141 optimal weight: 0.0670 chunk 252 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 113 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN M 3 GLN P 79 GLN Q 105 GLN R 53 ASN W 81 GLN X 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20536 Z= 0.206 Angle : 0.547 7.864 27980 Z= 0.288 Chirality : 0.042 0.144 2975 Planarity : 0.004 0.039 3655 Dihedral : 4.242 19.658 2938 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.40 % Allowed : 16.82 % Favored : 79.78 % 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: -0.66 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.33 (0.14), residues: 1133 loop : -1.08 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 47 HIS 0.004 0.001 HIS H 35 PHE 0.008 0.001 PHE C 29 TYR 0.017 0.001 TYR S 90 ARG 0.010 0.000 ARG S 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 314 time to evaluate : 2.104 Fit side-chains revert: symmetry clash REVERT: H 82 MET cc_start: 0.8942 (mtp) cc_final: 0.8601 (mtp) REVERT: L 85 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.8038 (m-30) REVERT: A 20 LEU cc_start: 0.5988 (OUTLIER) cc_final: 0.5533 (mp) REVERT: A 50 ILE cc_start: 0.8728 (tt) cc_final: 0.8348 (tp) REVERT: C 6 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7064 (mt-10) REVERT: C 38 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8240 (ptt180) REVERT: C 76 ASN cc_start: 0.8829 (m-40) cc_final: 0.8531 (m-40) REVERT: P 17 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7507 (pt0) REVERT: Q 16 ARG cc_start: 0.7795 (ptp-110) cc_final: 0.7460 (ptp-110) REVERT: T 24 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8106 (p) REVERT: T 72 SER cc_start: 0.8147 (OUTLIER) cc_final: 0.7918 (p) REVERT: V 51 ASN cc_start: 0.6446 (OUTLIER) cc_final: 0.5624 (t160) REVERT: V 66 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.6908 (pttm) REVERT: V 79 GLN cc_start: 0.7513 (tt0) cc_final: 0.7258 (mm-40) REVERT: W 94 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7236 (ttm170) REVERT: Y 82 MET cc_start: 0.5274 (mpm) cc_final: 0.2829 (ptt) outliers start: 72 outliers final: 49 residues processed: 346 average time/residue: 1.2003 time to fit residues: 473.0431 Evaluate side-chains 360 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 301 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain T residue 72 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 51 ASN Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 50 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 160 optimal weight: 0.0870 chunk 172 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 185 ASN ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 GLN R 53 ASN X 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20536 Z= 0.275 Angle : 0.580 7.861 27980 Z= 0.306 Chirality : 0.043 0.149 2975 Planarity : 0.004 0.039 3655 Dihedral : 4.356 19.969 2938 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.83 % Allowed : 17.15 % Favored : 79.03 % 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: -0.75 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.28 (0.14), residues: 1133 loop : -1.14 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 47 HIS 0.005 0.002 HIS H 35 PHE 0.010 0.001 PHE W 29 TYR 0.018 0.002 TYR S 90 ARG 0.009 0.000 ARG S 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 309 time to evaluate : 2.272 Fit side-chains revert: symmetry clash REVERT: H 82 MET cc_start: 0.8981 (mtp) cc_final: 0.8558 (mtp) REVERT: L 85 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.8061 (m-30) REVERT: A 50 ILE cc_start: 0.8726 (tt) cc_final: 0.8337 (OUTLIER) REVERT: C 6 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7071 (mt-10) REVERT: C 76 ASN cc_start: 0.8842 (m-40) cc_final: 0.8565 (m-40) REVERT: Q 16 ARG cc_start: 0.7844 (ptp-110) cc_final: 0.7527 (ptp-110) REVERT: Q 43 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.7778 (mppt) REVERT: T 24 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8152 (p) REVERT: T 72 SER cc_start: 0.8133 (OUTLIER) cc_final: 0.7928 (p) REVERT: V 66 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7392 (ptpp) REVERT: V 79 GLN cc_start: 0.7515 (tt0) cc_final: 0.7266 (mm-40) REVERT: W 17 SER cc_start: 0.6899 (p) cc_final: 0.6368 (t) REVERT: W 94 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7316 (ttm170) REVERT: Y 82 MET cc_start: 0.5165 (mpm) cc_final: 0.2776 (ptt) outliers start: 81 outliers final: 56 residues processed: 347 average time/residue: 1.1783 time to fit residues: 465.9123 Evaluate side-chains 366 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 304 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain Q residue 43 LYS Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain T residue 72 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 50 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 8.9990 chunk 241 optimal weight: 6.9990 chunk 220 optimal weight: 0.7980 chunk 235 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 184 optimal weight: 0.0970 chunk 72 optimal weight: 5.9990 chunk 212 optimal weight: 9.9990 chunk 222 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 185 ASN ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN E 57 ASN M 3 GLN P 79 GLN R 53 ASN X 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20536 Z= 0.328 Angle : 0.610 7.619 27980 Z= 0.323 Chirality : 0.044 0.166 2975 Planarity : 0.005 0.039 3655 Dihedral : 4.535 21.114 2938 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.54 % Allowed : 17.67 % Favored : 78.79 % 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: -0.91 (0.15), residues: 2607 helix: None (None), residues: 0 sheet: 0.12 (0.14), residues: 1111 loop : -1.20 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 47 HIS 0.006 0.002 HIS H 35 PHE 0.012 0.002 PHE C 29 TYR 0.020 0.002 TYR S 90 ARG 0.009 0.000 ARG X 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 308 time to evaluate : 2.548 Fit side-chains revert: symmetry clash REVERT: H 82 MET cc_start: 0.8953 (mtp) cc_final: 0.8578 (mtp) REVERT: L 85 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: A 50 ILE cc_start: 0.8715 (tt) cc_final: 0.8321 (OUTLIER) REVERT: C 6 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7080 (mt-10) REVERT: C 76 ASN cc_start: 0.8840 (m-40) cc_final: 0.8639 (m-40) REVERT: P 27 ASN cc_start: 0.9364 (OUTLIER) cc_final: 0.9029 (p0) REVERT: Q 16 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7555 (ptp-110) REVERT: Q 43 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.7782 (mppt) REVERT: T 24 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8138 (p) REVERT: V 79 GLN cc_start: 0.7512 (tt0) cc_final: 0.7255 (mm-40) REVERT: W 17 SER cc_start: 0.6839 (p) cc_final: 0.6258 (t) REVERT: W 94 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7251 (ttm170) REVERT: X 37 GLN cc_start: 0.6615 (OUTLIER) cc_final: 0.6360 (tm-30) REVERT: Y 34 MET cc_start: 0.6021 (ppp) cc_final: 0.5647 (ptt) REVERT: Y 82 MET cc_start: 0.5131 (mpm) cc_final: 0.2818 (ptt) outliers start: 75 outliers final: 57 residues processed: 344 average time/residue: 1.2246 time to fit residues: 483.5717 Evaluate side-chains 367 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 303 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain Q residue 16 ARG Chi-restraints excluded: chain Q residue 43 LYS Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 51 ASN Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain X residue 37 GLN Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 240 optimal weight: 0.0070 chunk 207 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN E 57 ASN M 3 GLN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 GLN R 53 ASN X 37 GLN ** Y 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20536 Z= 0.228 Angle : 0.575 7.805 27980 Z= 0.304 Chirality : 0.042 0.197 2975 Planarity : 0.004 0.040 3655 Dihedral : 4.411 21.097 2938 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.07 % Allowed : 18.28 % Favored : 78.65 % 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: -0.85 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.15 (0.14), residues: 1111 loop : -1.14 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 47 HIS 0.005 0.001 HIS H 35 PHE 0.008 0.001 PHE H 29 TYR 0.018 0.001 TYR U 79 ARG 0.009 0.000 ARG X 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 313 time to evaluate : 2.474 Fit side-chains revert: symmetry clash REVERT: H 82 MET cc_start: 0.8967 (mtp) cc_final: 0.8618 (mtp) REVERT: L 85 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.8053 (m-30) REVERT: A 50 ILE cc_start: 0.8717 (tt) cc_final: 0.8324 (OUTLIER) REVERT: C 6 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: C 76 ASN cc_start: 0.8793 (m-40) cc_final: 0.8586 (m-40) REVERT: Q 16 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7447 (ptp-110) REVERT: Q 43 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.7761 (mppt) REVERT: Q 105 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.7157 (mm-40) REVERT: T 24 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8112 (p) REVERT: W 17 SER cc_start: 0.6819 (p) cc_final: 0.6300 (t) REVERT: W 94 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7251 (ttm170) REVERT: Y 34 MET cc_start: 0.5980 (OUTLIER) cc_final: 0.5666 (ptt) REVERT: Y 82 MET cc_start: 0.5119 (mpm) cc_final: 0.2802 (ptt) outliers start: 65 outliers final: 54 residues processed: 343 average time/residue: 1.1716 time to fit residues: 458.9154 Evaluate side-chains 369 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 308 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain Q residue 16 ARG Chi-restraints excluded: chain Q residue 43 LYS Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 51 ASN Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 34 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 0.0980 chunk 221 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 208 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN M 3 GLN P 79 GLN R 53 ASN X 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.171836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116787 restraints weight = 25019.509| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.47 r_work: 0.3080 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20536 Z= 0.193 Angle : 0.550 7.797 27980 Z= 0.290 Chirality : 0.042 0.209 2975 Planarity : 0.004 0.041 3655 Dihedral : 4.250 19.882 2938 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.88 % Allowed : 18.66 % Favored : 78.46 % 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: -0.75 (0.16), residues: 2607 helix: None (None), residues: 0 sheet: 0.22 (0.15), residues: 1111 loop : -1.07 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 47 HIS 0.004 0.001 HIS H 35 PHE 0.007 0.001 PHE C 29 TYR 0.017 0.001 TYR U 52A ARG 0.009 0.000 ARG X 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7498.87 seconds wall clock time: 133 minutes 57.39 seconds (8037.39 seconds total)