Starting phenix.real_space_refine on Fri Feb 16 06:44:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyt_27781/02_2024/8dyt_27781.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyt_27781/02_2024/8dyt_27781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyt_27781/02_2024/8dyt_27781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyt_27781/02_2024/8dyt_27781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyt_27781/02_2024/8dyt_27781.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyt_27781/02_2024/8dyt_27781.pdb" } resolution = 3.3 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= 0.005 sd= 0.203 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 56 5.16 5 C 9152 2.51 5 N 2544 2.21 5 O 2826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L GLU 81": "OE1" <-> "OE2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 82": "OD1" <-> "OD2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "F TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 61": "OD1" <-> "OD2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 83": "OE1" <-> "OE2" Residue "N ASP 85": "OD1" <-> "OD2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 81": "OE1" <-> "OE2" Residue "P GLU 83": "OE1" <-> "OE2" Residue "O ASP 53": "OD1" <-> "OD2" Residue "O ASP 72": "OD1" <-> "OD2" Residue "O GLU 85": "OE1" <-> "OE2" Residue "O ASP 86": "OD1" <-> "OD2" Residue "O GLU 99": "OE1" <-> "OE2" Residue "O TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 60": "OD1" <-> "OD2" Residue "R GLU 81": "OE1" <-> "OE2" Residue "R GLU 83": "OE1" <-> "OE2" Residue "Q TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 85": "OE1" <-> "OE2" Residue "Q GLU 99": "OE1" <-> "OE2" Residue "Q TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 82": "OD1" <-> "OD2" Residue "T GLU 83": "OE1" <-> "OE2" Residue "S ASP 53": "OD1" <-> "OD2" Residue "S TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14578 Number of models: 1 Model: "" Number of chains: 18 Chain: "I" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 225 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 23} Chain: "J" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 225 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 23} Chain: "L" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "B" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "A" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "D" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "C" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "F" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "E" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "N" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "M" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "P" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "O" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "R" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "Q" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "T" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "S" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Time building chain proxies: 7.70, per 1000 atoms: 0.53 Number of scatterers: 14578 At special positions: 0 Unit cell: (109.25, 125.35, 92, 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 56 16.00 O 2826 8.00 N 2544 7.00 C 9152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " 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: 5.64 Conformation dependent library (CDL) restraints added in 2.7 seconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 48 sheets defined 5.6% alpha, 41.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 73 through 75 No H-bonds generated for 'chain 'O' and resid 73 through 75' Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'Q' and resid 28 through 32 Processing helix chain 'Q' and resid 61 through 64 Processing helix chain 'Q' and resid 73 through 75 No H-bonds generated for 'chain 'Q' and resid 73 through 75' Processing helix chain 'T' and resid 79 through 83 Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 11 removed outlier: 5.871A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA3, first strand: chain 'L' and resid 89 through 92 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.544A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.871A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.267A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 11 removed outlier: 6.515A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 19 through 24 Processing sheet with id=AA9, first strand: chain 'B' and resid 89 through 92 Processing sheet with id=AB1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.631A pdb=" N THR A 77 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.451A pdb=" N GLY A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET A 34 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.451A pdb=" N GLY A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 9 through 11 removed outlier: 6.598A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 92 Processing sheet with id=AB7, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.570A pdb=" N THR C 77 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.877A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.200A pdb=" N CYS C 92 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TRP C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 9 through 11 removed outlier: 6.718A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 9 through 11 Processing sheet with id=AC3, first strand: chain 'F' and resid 19 through 24 removed outlier: 3.503A pdb=" N SER F 65 " --> pdb=" O SER F 72 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.696A pdb=" N THR E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.762A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.132A pdb=" N TYR E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 9 through 11 removed outlier: 6.715A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 9 through 11 Processing sheet with id=AC9, first strand: chain 'N' and resid 19 through 24 removed outlier: 3.504A pdb=" N SER N 65 " --> pdb=" O SER N 72 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.691A pdb=" N THR M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.763A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 10 through 12 removed outlier: 4.129A pdb=" N TYR M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 9 through 11 removed outlier: 6.597A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AD6, first strand: chain 'P' and resid 89 through 92 Processing sheet with id=AD7, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.575A pdb=" N THR O 77 " --> pdb=" O ASP O 72 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.876A pdb=" N MET O 34 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.193A pdb=" N CYS O 92 " --> pdb=" O TRP O 103 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TRP O 103 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG O 94 " --> pdb=" O ASP O 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 9 through 11 removed outlier: 5.866A pdb=" N GLN R 37 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LEU R 46 " --> pdb=" O GLN R 37 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'R' and resid 19 through 24 Processing sheet with id=AE3, first strand: chain 'R' and resid 89 through 92 Processing sheet with id=AE4, first strand: chain 'Q' and resid 3 through 7 removed outlier: 3.513A pdb=" N THR Q 77 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.869A pdb=" N MET Q 34 " --> pdb=" O VAL Q 50 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.268A pdb=" N CYS Q 92 " --> pdb=" O TRP Q 103 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TRP Q 103 " --> pdb=" O CYS Q 92 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG Q 94 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 9 through 11 removed outlier: 6.513A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'T' and resid 19 through 24 Processing sheet with id=AE9, first strand: chain 'T' and resid 89 through 92 Processing sheet with id=AF1, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.630A pdb=" N THR S 77 " --> pdb=" O ASP S 72 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.483A pdb=" N GLY S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N MET S 34 " --> pdb=" O VAL S 50 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.483A pdb=" N GLY S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR S 102 " --> pdb=" O ARG S 94 " (cutoff:3.500A) 586 hydrogen bonds defined for protein. 1314 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: 5.25 Time building geometry restraints manager: 6.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3569 1.33 - 1.45: 3330 1.45 - 1.56: 7964 1.56 - 1.68: 1 1.68 - 1.80: 72 Bond restraints: 14936 Sorted by residual: bond pdb=" CB CYS P 88 " pdb=" SG CYS P 88 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.76e+00 bond pdb=" CG1 ILE T 27C" pdb=" CD1 ILE T 27C" ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.73e+00 bond pdb=" CB CYS D 88 " pdb=" SG CYS D 88 " ideal model delta sigma weight residual 1.808 1.765 0.043 3.30e-02 9.18e+02 1.70e+00 bond pdb=" CG1 ILE B 27C" pdb=" CD1 ILE B 27C" ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.60e+00 bond pdb=" CB THR C 77 " pdb=" CG2 THR C 77 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 ... (remaining 14931 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.58: 444 106.58 - 113.47: 7928 113.47 - 120.36: 5185 120.36 - 127.24: 6577 127.24 - 134.13: 192 Bond angle restraints: 20326 Sorted by residual: angle pdb=" N ILE D 27C" pdb=" CA ILE D 27C" pdb=" C ILE D 27C" ideal model delta sigma weight residual 113.53 110.66 2.87 9.80e-01 1.04e+00 8.59e+00 angle pdb=" CA PRO I 2 " pdb=" N PRO I 2 " pdb=" CD PRO I 2 " ideal model delta sigma weight residual 112.00 108.29 3.71 1.40e+00 5.10e-01 7.02e+00 angle pdb=" N THR D 42 " pdb=" CA THR D 42 " pdb=" C THR D 42 " ideal model delta sigma weight residual 111.02 114.08 -3.06 1.25e+00 6.40e-01 5.99e+00 angle pdb=" C PRO L 59 " pdb=" N ASP L 60 " pdb=" CA ASP L 60 " ideal model delta sigma weight residual 120.60 124.46 -3.86 1.60e+00 3.91e-01 5.82e+00 angle pdb=" N THR P 42 " pdb=" CA THR P 42 " pdb=" C THR P 42 " ideal model delta sigma weight residual 111.02 114.01 -2.99 1.25e+00 6.40e-01 5.71e+00 ... (remaining 20321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7839 17.95 - 35.90: 639 35.90 - 53.84: 168 53.84 - 71.79: 36 71.79 - 89.74: 22 Dihedral angle restraints: 8704 sinusoidal: 3274 harmonic: 5430 Sorted by residual: dihedral pdb=" CB CYS T 23 " pdb=" SG CYS T 23 " pdb=" SG CYS T 88 " pdb=" CB CYS T 88 " ideal model delta sinusoidal sigma weight residual 93.00 136.26 -43.26 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual 93.00 136.23 -43.23 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 134.44 -41.44 1 1.00e+01 1.00e-02 2.40e+01 ... (remaining 8701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1242 0.033 - 0.065: 596 0.065 - 0.098: 213 0.098 - 0.131: 118 0.131 - 0.163: 15 Chirality restraints: 2184 Sorted by residual: chirality pdb=" CA PRO I 10 " pdb=" N PRO I 10 " pdb=" C PRO I 10 " pdb=" CB PRO I 10 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CB THR E 87 " pdb=" CA THR E 87 " pdb=" OG1 THR E 87 " pdb=" CG2 THR E 87 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA VAL S 89 " pdb=" N VAL S 89 " pdb=" C VAL S 89 " pdb=" CB VAL S 89 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 2181 not shown) Planarity restraints: 2648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 7 " 0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO F 8 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO F 8 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 8 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO N 7 " -0.052 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO N 8 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO N 8 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO N 8 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN I 1 " 0.046 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO I 2 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO I 2 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO I 2 " 0.038 5.00e-02 4.00e+02 ... (remaining 2645 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 994 2.72 - 3.27: 13717 3.27 - 3.81: 23874 3.81 - 4.36: 30383 4.36 - 4.90: 54389 Nonbonded interactions: 123357 Sorted by model distance: nonbonded pdb=" ND2 ASN I 3 " pdb=" O TYR A 100C" model vdw 2.181 2.520 nonbonded pdb=" ND2 ASN J 15 " pdb=" OD1 ASN Q 97 " model vdw 2.217 2.520 nonbonded pdb=" ND2 ASN J 31 " pdb=" OD1 ASN M 97 " model vdw 2.235 2.520 nonbonded pdb=" NH2 ARG N 61 " pdb=" OD1 ASP N 82 " model vdw 2.244 2.520 nonbonded pdb=" NH2 ARG F 61 " pdb=" OD1 ASP F 82 " model vdw 2.260 2.520 ... (remaining 123352 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' } 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' } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 0.720 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: 3.310 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 41.190 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 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 : 0.007 0.061 14936 Z= 0.459 Angle : 0.672 4.289 20326 Z= 0.387 Chirality : 0.047 0.163 2184 Planarity : 0.006 0.080 2648 Dihedral : 15.304 89.740 5248 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.45 % Allowed : 17.22 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.16 (0.19), residues: 824 loop : -0.57 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 47 HIS 0.006 0.002 HIS M 82A PHE 0.023 0.002 PHE B 96 TYR 0.026 0.002 TYR E 52A ARG 0.006 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 229 time to evaluate : 1.734 Fit side-chains REVERT: A 68 THR cc_start: 0.9310 (t) cc_final: 0.9084 (p) outliers start: 7 outliers final: 4 residues processed: 230 average time/residue: 0.3189 time to fit residues: 101.5746 Evaluate side-chains 232 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 228 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain R residue 105 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.5980 chunk 137 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 55 optimal weight: 0.0870 chunk 86 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 165 optimal weight: 9.9990 overall best weight: 0.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN M 105 GLN S 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14936 Z= 0.161 Angle : 0.521 4.451 20326 Z= 0.281 Chirality : 0.043 0.168 2184 Planarity : 0.004 0.058 2648 Dihedral : 5.012 50.336 2126 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.61 % Allowed : 15.24 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.19 (0.18), residues: 800 loop : -0.57 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 47 HIS 0.004 0.001 HIS O 35 PHE 0.011 0.001 PHE B 96 TYR 0.018 0.001 TYR M 52A ARG 0.003 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 248 time to evaluate : 1.796 Fit side-chains REVERT: B 69 THR cc_start: 0.8462 (p) cc_final: 0.8111 (t) REVERT: B 79 GLN cc_start: 0.8318 (mp10) cc_final: 0.8023 (mp10) REVERT: B 106 VAL cc_start: 0.4972 (m) cc_final: 0.4720 (m) REVERT: A 68 THR cc_start: 0.9306 (t) cc_final: 0.9054 (p) REVERT: A 73 ASN cc_start: 0.9253 (OUTLIER) cc_final: 0.8951 (t0) REVERT: C 3 GLN cc_start: 0.8488 (mt0) cc_final: 0.8135 (mm-40) REVERT: O 3 GLN cc_start: 0.8483 (mt0) cc_final: 0.8138 (mm-40) REVERT: O 73 ASN cc_start: 0.9171 (t0) cc_final: 0.8899 (m-40) REVERT: T 69 THR cc_start: 0.8362 (p) cc_final: 0.8053 (t) REVERT: T 79 GLN cc_start: 0.8329 (mp10) cc_final: 0.8007 (mp10) REVERT: S 73 ASN cc_start: 0.9242 (OUTLIER) cc_final: 0.8957 (t0) outliers start: 41 outliers final: 19 residues processed: 274 average time/residue: 0.3182 time to fit residues: 124.1952 Evaluate side-chains 257 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 236 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 165 optimal weight: 0.3980 chunk 178 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 14936 Z= 0.320 Angle : 0.539 4.399 20326 Z= 0.290 Chirality : 0.044 0.135 2184 Planarity : 0.005 0.049 2648 Dihedral : 4.923 46.000 2122 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.57 % Allowed : 15.62 % Favored : 80.80 % 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: -0.28 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.20 (0.18), residues: 848 loop : -0.44 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.004 0.002 HIS O 35 PHE 0.013 0.002 PHE B 96 TYR 0.017 0.002 TYR H 79 ARG 0.004 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 239 time to evaluate : 1.819 Fit side-chains REVERT: B 69 THR cc_start: 0.8401 (p) cc_final: 0.8039 (t) REVERT: B 79 GLN cc_start: 0.8393 (mp10) cc_final: 0.8086 (mp10) REVERT: B 106 VAL cc_start: 0.5050 (OUTLIER) cc_final: 0.4778 (m) REVERT: A 68 THR cc_start: 0.9271 (t) cc_final: 0.9022 (p) REVERT: A 73 ASN cc_start: 0.9306 (OUTLIER) cc_final: 0.8994 (t0) REVERT: C 3 GLN cc_start: 0.8541 (mt0) cc_final: 0.8150 (mm-40) REVERT: C 73 ASN cc_start: 0.9201 (t0) cc_final: 0.8971 (m-40) REVERT: O 3 GLN cc_start: 0.8551 (mt0) cc_final: 0.8171 (mm-40) REVERT: O 19 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8308 (ttt-90) REVERT: O 73 ASN cc_start: 0.9207 (m-40) cc_final: 0.8996 (m-40) REVERT: T 69 THR cc_start: 0.8340 (p) cc_final: 0.8028 (t) REVERT: T 79 GLN cc_start: 0.8351 (mp10) cc_final: 0.7976 (mp10) REVERT: S 73 ASN cc_start: 0.9289 (OUTLIER) cc_final: 0.8991 (t0) outliers start: 56 outliers final: 39 residues processed: 266 average time/residue: 0.3159 time to fit residues: 117.0812 Evaluate side-chains 278 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 235 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain O residue 19 ARG Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 166 optimal weight: 20.0000 chunk 175 optimal weight: 0.0470 chunk 86 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 14936 Z= 0.299 Angle : 0.528 4.430 20326 Z= 0.283 Chirality : 0.044 0.136 2184 Planarity : 0.004 0.043 2648 Dihedral : 4.937 40.384 2122 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.27 % Allowed : 15.31 % Favored : 80.42 % 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: -0.26 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.23 (0.18), residues: 848 loop : -0.46 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 47 HIS 0.004 0.001 HIS O 35 PHE 0.011 0.002 PHE B 98 TYR 0.020 0.002 TYR E 52A ARG 0.003 0.001 ARG F 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 239 time to evaluate : 1.706 Fit side-chains REVERT: B 69 THR cc_start: 0.8453 (p) cc_final: 0.8060 (t) REVERT: B 79 GLN cc_start: 0.8390 (mp10) cc_final: 0.8017 (mp10) REVERT: B 106 VAL cc_start: 0.5095 (OUTLIER) cc_final: 0.4838 (m) REVERT: A 68 THR cc_start: 0.9255 (t) cc_final: 0.9020 (p) REVERT: A 73 ASN cc_start: 0.9312 (OUTLIER) cc_final: 0.8988 (t0) REVERT: C 3 GLN cc_start: 0.8547 (mt0) cc_final: 0.8197 (mm-40) REVERT: C 61 ASP cc_start: 0.8564 (t70) cc_final: 0.8204 (t0) REVERT: O 3 GLN cc_start: 0.8540 (mt0) cc_final: 0.8189 (mm-40) REVERT: O 19 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8299 (ttt-90) REVERT: O 61 ASP cc_start: 0.8554 (t70) cc_final: 0.8191 (t0) REVERT: T 69 THR cc_start: 0.8351 (p) cc_final: 0.8023 (t) REVERT: S 73 ASN cc_start: 0.9291 (OUTLIER) cc_final: 0.8972 (t0) outliers start: 67 outliers final: 52 residues processed: 276 average time/residue: 0.3151 time to fit residues: 121.9415 Evaluate side-chains 285 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 229 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain O residue 19 ARG Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 107 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 chunk 150 optimal weight: 1.9990 chunk 121 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 6 GLN S 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14936 Z= 0.207 Angle : 0.499 5.138 20326 Z= 0.266 Chirality : 0.043 0.134 2184 Planarity : 0.004 0.040 2648 Dihedral : 4.754 42.415 2122 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.70 % Allowed : 16.58 % Favored : 79.72 % 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: -0.20 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.36 (0.18), residues: 800 loop : -0.48 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 47 HIS 0.004 0.001 HIS C 35 PHE 0.010 0.001 PHE A 29 TYR 0.020 0.001 TYR E 52A ARG 0.009 0.000 ARG F 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 231 time to evaluate : 1.787 Fit side-chains REVERT: B 69 THR cc_start: 0.8460 (p) cc_final: 0.8069 (t) REVERT: B 79 GLN cc_start: 0.8402 (mp10) cc_final: 0.8020 (mp10) REVERT: B 106 VAL cc_start: 0.5037 (OUTLIER) cc_final: 0.4766 (m) REVERT: A 68 THR cc_start: 0.9268 (t) cc_final: 0.9029 (p) REVERT: A 73 ASN cc_start: 0.9308 (OUTLIER) cc_final: 0.9007 (t0) REVERT: C 3 GLN cc_start: 0.8534 (mt0) cc_final: 0.8226 (mm-40) REVERT: C 19 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8752 (ttp-170) REVERT: C 61 ASP cc_start: 0.8517 (t70) cc_final: 0.8151 (t0) REVERT: C 85 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8216 (mt-10) REVERT: O 3 GLN cc_start: 0.8483 (mt0) cc_final: 0.8187 (mm-40) REVERT: O 19 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8321 (ttt-90) REVERT: O 61 ASP cc_start: 0.8502 (t70) cc_final: 0.8131 (t0) REVERT: O 85 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8233 (mt-10) REVERT: Q 101 ASP cc_start: 0.8337 (p0) cc_final: 0.8121 (p0) REVERT: T 69 THR cc_start: 0.8383 (p) cc_final: 0.8046 (t) REVERT: S 73 ASN cc_start: 0.9282 (OUTLIER) cc_final: 0.8996 (t0) outliers start: 58 outliers final: 41 residues processed: 268 average time/residue: 0.3203 time to fit residues: 118.6952 Evaluate side-chains 270 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 224 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain O residue 19 ARG Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 107 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 105 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14936 Z= 0.227 Angle : 0.501 4.475 20326 Z= 0.266 Chirality : 0.043 0.152 2184 Planarity : 0.004 0.042 2648 Dihedral : 4.708 43.205 2122 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.27 % Allowed : 16.07 % Favored : 79.66 % 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: -0.19 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.22 (0.18), residues: 848 loop : -0.35 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 47 HIS 0.004 0.001 HIS O 35 PHE 0.010 0.001 PHE A 29 TYR 0.016 0.001 TYR E 52A ARG 0.009 0.000 ARG N 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 235 time to evaluate : 1.592 Fit side-chains REVERT: B 69 THR cc_start: 0.8485 (p) cc_final: 0.8097 (t) REVERT: B 79 GLN cc_start: 0.8434 (mp10) cc_final: 0.8026 (mp10) REVERT: B 106 VAL cc_start: 0.5195 (OUTLIER) cc_final: 0.4951 (m) REVERT: A 68 THR cc_start: 0.9245 (t) cc_final: 0.9022 (p) REVERT: A 73 ASN cc_start: 0.9302 (OUTLIER) cc_final: 0.8995 (t0) REVERT: D 38 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: C 3 GLN cc_start: 0.8460 (mt0) cc_final: 0.8128 (mm-40) REVERT: C 61 ASP cc_start: 0.8506 (t70) cc_final: 0.8142 (t0) REVERT: C 85 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8198 (mt-10) REVERT: P 38 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: O 3 GLN cc_start: 0.8504 (mt0) cc_final: 0.8217 (mm-40) REVERT: O 19 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8296 (ttt-90) REVERT: O 61 ASP cc_start: 0.8494 (t70) cc_final: 0.8127 (t0) REVERT: O 85 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8213 (mt-10) REVERT: Q 101 ASP cc_start: 0.8326 (p0) cc_final: 0.8121 (p0) REVERT: T 69 THR cc_start: 0.8407 (p) cc_final: 0.8083 (t) REVERT: S 73 ASN cc_start: 0.9278 (OUTLIER) cc_final: 0.8985 (t0) outliers start: 67 outliers final: 55 residues processed: 281 average time/residue: 0.3113 time to fit residues: 121.8329 Evaluate side-chains 283 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 222 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain O residue 19 ARG Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 107 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 99 optimal weight: 0.0670 chunk 148 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 overall best weight: 2.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN M 105 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 14936 Z= 0.297 Angle : 0.523 4.749 20326 Z= 0.279 Chirality : 0.044 0.159 2184 Planarity : 0.004 0.038 2648 Dihedral : 4.785 45.520 2122 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.78 % Allowed : 16.33 % Favored : 78.89 % 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: -0.20 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.19 (0.18), residues: 848 loop : -0.34 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.004 0.001 HIS C 35 PHE 0.011 0.002 PHE A 29 TYR 0.015 0.001 TYR E 52A ARG 0.010 0.001 ARG N 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 226 time to evaluate : 1.801 Fit side-chains REVERT: L 38 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: B 69 THR cc_start: 0.8508 (p) cc_final: 0.8111 (t) REVERT: B 79 GLN cc_start: 0.8408 (mp10) cc_final: 0.7998 (mp10) REVERT: B 106 VAL cc_start: 0.5270 (OUTLIER) cc_final: 0.5025 (m) REVERT: A 68 THR cc_start: 0.9248 (t) cc_final: 0.9039 (p) REVERT: A 73 ASN cc_start: 0.9310 (OUTLIER) cc_final: 0.8999 (t0) REVERT: D 38 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: C 3 GLN cc_start: 0.8468 (mt0) cc_final: 0.8120 (mm-40) REVERT: C 19 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8236 (ttt-90) REVERT: C 61 ASP cc_start: 0.8555 (t70) cc_final: 0.8196 (t0) REVERT: P 38 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: O 3 GLN cc_start: 0.8490 (mt0) cc_final: 0.8118 (mm-40) REVERT: O 19 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8388 (ttt-90) REVERT: O 61 ASP cc_start: 0.8544 (t70) cc_final: 0.8178 (t0) REVERT: R 38 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8392 (tt0) REVERT: T 69 THR cc_start: 0.8451 (p) cc_final: 0.8115 (t) REVERT: S 73 ASN cc_start: 0.9290 (OUTLIER) cc_final: 0.8984 (t0) outliers start: 75 outliers final: 60 residues processed: 278 average time/residue: 0.3216 time to fit residues: 124.4350 Evaluate side-chains 292 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 223 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain O residue 19 ARG Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 38 GLN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 107 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 11 ASN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN M 105 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 14936 Z= 0.440 Angle : 0.586 5.130 20326 Z= 0.314 Chirality : 0.046 0.169 2184 Planarity : 0.005 0.043 2648 Dihedral : 5.093 49.858 2122 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.91 % Allowed : 16.39 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.13 (0.18), residues: 848 loop : -0.44 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Q 47 HIS 0.005 0.001 HIS S 82A PHE 0.014 0.002 PHE B 98 TYR 0.020 0.002 TYR M 52A ARG 0.004 0.001 ARG Q 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 229 time to evaluate : 1.585 Fit side-chains REVERT: L 38 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8540 (tt0) REVERT: H 13 GLN cc_start: 0.7821 (mp10) cc_final: 0.7605 (mp10) REVERT: B 69 THR cc_start: 0.8543 (p) cc_final: 0.8118 (t) REVERT: B 106 VAL cc_start: 0.5233 (OUTLIER) cc_final: 0.5018 (m) REVERT: A 68 THR cc_start: 0.9258 (t) cc_final: 0.9031 (p) REVERT: A 73 ASN cc_start: 0.9342 (OUTLIER) cc_final: 0.9028 (t0) REVERT: D 38 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: C 3 GLN cc_start: 0.8522 (mt0) cc_final: 0.8095 (mm-40) REVERT: C 19 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8164 (ttt-90) REVERT: C 61 ASP cc_start: 0.8628 (t70) cc_final: 0.8263 (t0) REVERT: C 85 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8234 (mt-10) REVERT: M 87 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8603 (t) REVERT: P 38 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: O 3 GLN cc_start: 0.8563 (mt0) cc_final: 0.8121 (mm-40) REVERT: O 19 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8410 (ttt-90) REVERT: O 61 ASP cc_start: 0.8617 (t70) cc_final: 0.8250 (t0) REVERT: O 85 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8245 (mt-10) REVERT: R 38 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8594 (tt0) REVERT: T 69 THR cc_start: 0.8491 (p) cc_final: 0.8133 (t) REVERT: S 73 ASN cc_start: 0.9320 (OUTLIER) cc_final: 0.9018 (t0) outliers start: 77 outliers final: 65 residues processed: 281 average time/residue: 0.3106 time to fit residues: 122.4390 Evaluate side-chains 298 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 223 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 11 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain O residue 19 ARG Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 38 GLN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 107 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 147 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14936 Z= 0.162 Angle : 0.497 5.011 20326 Z= 0.265 Chirality : 0.042 0.161 2184 Planarity : 0.004 0.046 2648 Dihedral : 4.761 53.710 2122 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.83 % Allowed : 17.86 % Favored : 78.32 % 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: -0.25 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.29 (0.18), residues: 800 loop : -0.48 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q 47 HIS 0.004 0.001 HIS C 35 PHE 0.010 0.001 PHE S 29 TYR 0.016 0.001 TYR L 91 ARG 0.004 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 232 time to evaluate : 1.659 Fit side-chains REVERT: L 38 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8388 (tt0) REVERT: B 69 THR cc_start: 0.8511 (p) cc_final: 0.8097 (t) REVERT: B 106 VAL cc_start: 0.5214 (OUTLIER) cc_final: 0.4974 (m) REVERT: A 73 ASN cc_start: 0.9312 (OUTLIER) cc_final: 0.8977 (t0) REVERT: D 38 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: C 3 GLN cc_start: 0.8412 (mt0) cc_final: 0.8099 (mm-40) REVERT: C 19 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8715 (ttp-170) REVERT: C 61 ASP cc_start: 0.8511 (t70) cc_final: 0.8149 (t0) REVERT: C 85 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8222 (mt-10) REVERT: N 69 THR cc_start: 0.8846 (p) cc_final: 0.8508 (t) REVERT: M 87 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8388 (t) REVERT: P 38 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: O 3 GLN cc_start: 0.8463 (mt0) cc_final: 0.8095 (mm-40) REVERT: O 19 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8621 (ttp-170) REVERT: O 61 ASP cc_start: 0.8502 (t70) cc_final: 0.8133 (t0) REVERT: O 85 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8242 (mt-10) REVERT: R 38 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: T 69 THR cc_start: 0.8485 (p) cc_final: 0.8127 (t) REVERT: S 73 ASN cc_start: 0.9296 (OUTLIER) cc_final: 0.8966 (t0) outliers start: 60 outliers final: 40 residues processed: 275 average time/residue: 0.3151 time to fit residues: 120.4008 Evaluate side-chains 274 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 224 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain O residue 19 ARG Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 38 GLN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.5980 chunk 172 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 166 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN M 105 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 : 0.003 0.030 14936 Z= 0.188 Angle : 0.500 4.954 20326 Z= 0.266 Chirality : 0.043 0.173 2184 Planarity : 0.004 0.035 2648 Dihedral : 4.648 53.189 2122 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.51 % Allowed : 18.24 % Favored : 78.25 % 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: -0.06 (0.20), residues: 1884 helix: None (None), residues: 0 sheet: 0.29 (0.19), residues: 768 loop : -0.21 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 47 HIS 0.003 0.001 HIS O 35 PHE 0.010 0.001 PHE A 29 TYR 0.016 0.001 TYR O 52A ARG 0.004 0.000 ARG N 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 231 time to evaluate : 1.628 Fit side-chains REVERT: L 38 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8251 (tt0) REVERT: B 69 THR cc_start: 0.8533 (p) cc_final: 0.8125 (t) REVERT: B 106 VAL cc_start: 0.5136 (OUTLIER) cc_final: 0.4891 (m) REVERT: A 73 ASN cc_start: 0.9307 (OUTLIER) cc_final: 0.8965 (t0) REVERT: D 38 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: C 3 GLN cc_start: 0.8400 (mt0) cc_final: 0.8108 (mm-40) REVERT: C 19 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8739 (ttp-170) REVERT: C 61 ASP cc_start: 0.8523 (t70) cc_final: 0.8166 (t0) REVERT: C 85 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8232 (mt-10) REVERT: N 69 THR cc_start: 0.8852 (p) cc_final: 0.8517 (t) REVERT: M 87 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8393 (t) REVERT: P 38 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: O 3 GLN cc_start: 0.8446 (mt0) cc_final: 0.8142 (mm-40) REVERT: O 19 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8660 (ttp-170) REVERT: O 61 ASP cc_start: 0.8512 (t70) cc_final: 0.8138 (t0) REVERT: O 85 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8249 (mt-10) REVERT: R 38 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: T 69 THR cc_start: 0.8496 (p) cc_final: 0.8149 (t) REVERT: S 73 ASN cc_start: 0.9279 (OUTLIER) cc_final: 0.8946 (t0) outliers start: 55 outliers final: 43 residues processed: 270 average time/residue: 0.3204 time to fit residues: 120.1431 Evaluate side-chains 282 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 229 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain O residue 19 ARG Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 38 GLN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 133 optimal weight: 0.0870 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 overall best weight: 1.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN M 105 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.111829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.091838 restraints weight = 20181.429| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.59 r_work: 0.2955 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14936 Z= 0.229 Angle : 0.505 5.250 20326 Z= 0.268 Chirality : 0.043 0.176 2184 Planarity : 0.004 0.038 2648 Dihedral : 4.672 54.452 2122 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.64 % Allowed : 17.92 % Favored : 78.44 % 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: -0.07 (0.20), residues: 1884 helix: None (None), residues: 0 sheet: 0.28 (0.19), residues: 768 loop : -0.20 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 47 HIS 0.004 0.001 HIS C 35 PHE 0.010 0.001 PHE A 29 TYR 0.016 0.001 TYR A 58 ARG 0.005 0.000 ARG N 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3289.18 seconds wall clock time: 60 minutes 51.12 seconds (3651.12 seconds total)