Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 02:57:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mb3_9065/04_2023/6mb3_9065.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mb3_9065/04_2023/6mb3_9065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mb3_9065/04_2023/6mb3_9065.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mb3_9065/04_2023/6mb3_9065.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mb3_9065/04_2023/6mb3_9065.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mb3_9065/04_2023/6mb3_9065.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.010 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 54 5.16 5 C 10303 2.51 5 N 2840 2.21 5 O 3226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16423 Number of models: 1 Model: "" Number of chains: 19 Chain: "E" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 637 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 23, 'TRANS': 66} Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "A" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "K" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "B" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "M" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "N" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "D" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "O" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "F" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "P" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "G" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "Q" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "I" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "R" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "J" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "S" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Time building chain proxies: 8.22, per 1000 atoms: 0.50 Number of scatterers: 16423 At special positions: 0 Unit cell: (122.57, 116.39, 161.71, 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 54 16.00 O 3226 8.00 N 2840 7.00 C 10303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.07 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.08 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.13 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.09 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.07 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=1.84 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.02 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.05 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.08 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.41 Conformation dependent library (CDL) restraints added in 2.5 seconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3798 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 54 sheets defined 7.4% alpha, 48.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'O' and resid 79 through 83 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'S' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.741A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.894A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.549A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.549A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA7, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.182A pdb=" N GLY A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET A 34 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.182A pdb=" N GLY A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA A 96 " --> pdb=" O GLY A 100D" (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLY A 100D" --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.523A pdb=" N VAL K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.523A pdb=" N VAL K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AB4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.370A pdb=" N GLY B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET B 34 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.370A pdb=" N GLY B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR B 102 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA B 96 " --> pdb=" O GLY B 100D" (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLY B 100D" --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.506A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.506A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AC1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.292A pdb=" N GLY C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N MET C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.292A pdb=" N GLY C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA C 96 " --> pdb=" O GLY C 100D" (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLY C 100D" --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.532A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.532A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AC7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.191A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N MET D 34 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.191A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ALA D 96 " --> pdb=" O GLY D 100D" (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLY D 100D" --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 9 through 13 removed outlier: 6.445A pdb=" N VAL O 11 " --> pdb=" O THR O 105 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 9 through 13 removed outlier: 6.445A pdb=" N VAL O 11 " --> pdb=" O THR O 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 19 through 24 Processing sheet with id=AD4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.212A pdb=" N GLY F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET F 34 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.212A pdb=" N GLY F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA F 96 " --> pdb=" O GLY F 100D" (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLY F 100D" --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 9 through 13 removed outlier: 6.583A pdb=" N VAL P 11 " --> pdb=" O THR P 105 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 9 through 13 removed outlier: 6.583A pdb=" N VAL P 11 " --> pdb=" O THR P 105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AE1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.379A pdb=" N GLY G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.379A pdb=" N GLY G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA G 96 " --> pdb=" O GLY G 100D" (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLY G 100D" --> pdb=" O ALA G 96 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 9 through 13 removed outlier: 6.578A pdb=" N VAL Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 9 through 13 removed outlier: 6.578A pdb=" N VAL Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.007A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 10 through 12 removed outlier: 4.433A pdb=" N TYR I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA I 96 " --> pdb=" O GLY I 100D" (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLY I 100D" --> pdb=" O ALA I 96 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'R' and resid 9 through 13 removed outlier: 6.528A pdb=" N VAL R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 9 through 13 removed outlier: 6.528A pdb=" N VAL R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 19 through 24 Processing sheet with id=AF4, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.808A pdb=" N MET J 34 " --> pdb=" O ILE J 50 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 10 through 12 removed outlier: 7.118A pdb=" N CYS J 92 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TRP J 103 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG J 94 " --> pdb=" O ASP J 101 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 9 through 13 removed outlier: 6.544A pdb=" N VAL S 11 " --> pdb=" O THR S 105 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 9 through 13 removed outlier: 6.544A pdb=" N VAL S 11 " --> pdb=" O THR S 105 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 19 through 24 699 hydrogen bonds defined for protein. 1464 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: 5.14 Time building geometry restraints manager: 6.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3587 1.32 - 1.45: 4936 1.45 - 1.58: 8234 1.58 - 1.70: 12 1.70 - 1.83: 72 Bond restraints: 16841 Sorted by residual: bond pdb=" CB HIS D 35 " pdb=" CG HIS D 35 " ideal model delta sigma weight residual 1.497 1.393 0.104 1.40e-02 5.10e+03 5.47e+01 bond pdb=" CG GLU A 6 " pdb=" CD GLU A 6 " ideal model delta sigma weight residual 1.516 1.348 0.168 2.50e-02 1.60e+03 4.54e+01 bond pdb=" CB HIS J 35 " pdb=" CG HIS J 35 " ideal model delta sigma weight residual 1.497 1.404 0.093 1.40e-02 5.10e+03 4.37e+01 bond pdb=" CG GLU C 6 " pdb=" CD GLU C 6 " ideal model delta sigma weight residual 1.516 1.353 0.163 2.50e-02 1.60e+03 4.27e+01 bond pdb=" CB HIS G 35 " pdb=" CG HIS G 35 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.16e+01 ... (remaining 16836 not shown) Histogram of bond angle deviations from ideal: 97.86 - 105.12: 459 105.12 - 112.37: 7480 112.37 - 119.63: 6367 119.63 - 126.88: 8452 126.88 - 134.14: 196 Bond angle restraints: 22954 Sorted by residual: angle pdb=" N ARG M 61 " pdb=" CA ARG M 61 " pdb=" C ARG M 61 " ideal model delta sigma weight residual 114.75 102.24 12.51 1.26e+00 6.30e-01 9.86e+01 angle pdb=" N ARG O 61 " pdb=" CA ARG O 61 " pdb=" C ARG O 61 " ideal model delta sigma weight residual 114.75 102.66 12.09 1.26e+00 6.30e-01 9.20e+01 angle pdb=" N ARG K 61 " pdb=" CA ARG K 61 " pdb=" C ARG K 61 " ideal model delta sigma weight residual 114.75 102.93 11.82 1.26e+00 6.30e-01 8.79e+01 angle pdb=" C VAL G 12 " pdb=" N PRO G 13 " pdb=" CA PRO G 13 " ideal model delta sigma weight residual 119.66 126.18 -6.52 7.30e-01 1.88e+00 7.97e+01 angle pdb=" C VAL C 12 " pdb=" N PRO C 13 " pdb=" CA PRO C 13 " ideal model delta sigma weight residual 119.66 126.16 -6.50 7.30e-01 1.88e+00 7.93e+01 ... (remaining 22949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.65: 9349 15.65 - 31.30: 214 31.30 - 46.95: 77 46.95 - 62.60: 60 62.60 - 78.25: 10 Dihedral angle restraints: 9710 sinusoidal: 3609 harmonic: 6101 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 47.04 45.96 1 1.00e+01 1.00e-02 2.93e+01 dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 92 " pdb=" CB CYS F 92 " ideal model delta sinusoidal sigma weight residual 93.00 48.13 44.87 1 1.00e+01 1.00e-02 2.80e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 50.61 42.39 1 1.00e+01 1.00e-02 2.51e+01 ... (remaining 9707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1395 0.064 - 0.128: 710 0.128 - 0.192: 266 0.192 - 0.255: 65 0.255 - 0.319: 6 Chirality restraints: 2442 Sorted by residual: chirality pdb=" CA ASN N 27B" pdb=" N ASN N 27B" pdb=" C ASN N 27B" pdb=" CB ASN N 27B" both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA ASN S 27B" pdb=" N ASN S 27B" pdb=" C ASN S 27B" pdb=" CB ASN S 27B" both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA ASN O 27B" pdb=" N ASN O 27B" pdb=" C ASN O 27B" pdb=" CB ASN O 27B" both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 2439 not shown) Planarity restraints: 3001 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 31 " -0.069 2.00e-02 2.50e+03 3.68e-02 2.71e+01 pdb=" CG TYR R 31 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR R 31 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR R 31 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR R 31 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR R 31 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR R 31 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR R 31 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 36 " -0.053 2.00e-02 2.50e+03 3.14e-02 1.97e+01 pdb=" CG TYR P 36 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR P 36 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR P 36 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR P 36 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR P 36 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR P 36 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR P 36 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 36 " -0.052 2.00e-02 2.50e+03 3.10e-02 1.92e+01 pdb=" CG TYR Q 36 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 36 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 36 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 36 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 36 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR Q 36 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR Q 36 " -0.055 2.00e-02 2.50e+03 ... (remaining 2998 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4429 2.80 - 3.32: 13705 3.32 - 3.85: 28288 3.85 - 4.37: 35127 4.37 - 4.90: 57173 Nonbonded interactions: 138722 Sorted by model distance: nonbonded pdb=" N PRO E 144 " pdb=" O PRO E 144 " model vdw 2.273 2.496 nonbonded pdb=" OD2 ASP D 72 " pdb=" NZ LYS D 75 " model vdw 2.351 2.520 nonbonded pdb=" OD2 ASP C 72 " pdb=" NZ LYS C 75 " model vdw 2.379 2.520 nonbonded pdb=" N ARG O 61 " pdb=" N PHE O 62 " model vdw 2.394 2.560 nonbonded pdb=" N ARG M 61 " pdb=" N PHE M 62 " model vdw 2.408 2.560 ... (remaining 138717 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.720 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 42.410 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 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 : 0.020 0.168 16841 Z= 1.310 Angle : 1.748 13.266 22954 Z= 1.173 Chirality : 0.085 0.319 2442 Planarity : 0.009 0.044 3001 Dihedral : 9.448 78.247 5858 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.74 % Favored : 96.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 0.64 (0.17), residues: 873 loop : 0.00 (0.17), residues: 1267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 505 average time/residue: 0.3156 time to fit residues: 228.5500 Evaluate side-chains 314 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 1.773 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 0.4980 chunk 126 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 89 GLN B 105 GLN O 53 ASN P 34 HIS P 51 ASN P 89 GLN ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 GLN R 34 HIS R 37 GLN R 38 GLN R 53 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 16841 Z= 0.209 Angle : 0.665 10.207 22954 Z= 0.362 Chirality : 0.045 0.152 2442 Planarity : 0.004 0.044 3001 Dihedral : 4.814 20.792 2411 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.64 % Favored : 96.26 % Rotamer Outliers : 2.59 % 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: 0.55 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 0.85 (0.16), residues: 900 loop : 0.07 (0.18), residues: 1240 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 379 time to evaluate : 1.842 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 32 residues processed: 400 average time/residue: 0.2890 time to fit residues: 171.9358 Evaluate side-chains 331 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 299 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1475 time to fit residues: 11.3704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 212 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 HIS K 34 HIS B 105 GLN M 34 HIS N 34 HIS ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 HIS P 53 ASN Q 34 HIS ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN S 34 HIS S 38 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.072 16841 Z= 0.379 Angle : 0.711 11.418 22954 Z= 0.378 Chirality : 0.045 0.154 2442 Planarity : 0.005 0.044 3001 Dihedral : 4.890 20.956 2411 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.72 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 0.84 (0.16), residues: 900 loop : -0.37 (0.18), residues: 1240 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 303 time to evaluate : 1.893 Fit side-chains outliers start: 35 outliers final: 23 residues processed: 321 average time/residue: 0.2843 time to fit residues: 136.0883 Evaluate side-chains 283 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 260 time to evaluate : 2.347 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1525 time to fit residues: 9.1650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 GLN ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 16841 Z= 0.255 Angle : 0.621 12.277 22954 Z= 0.322 Chirality : 0.043 0.150 2442 Planarity : 0.004 0.043 3001 Dihedral : 4.621 20.292 2411 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.44 % Favored : 95.47 % Rotamer Outliers : 1.90 % 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 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 0.98 (0.16), residues: 882 loop : -0.49 (0.18), residues: 1258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 286 time to evaluate : 2.049 Fit side-chains outliers start: 33 outliers final: 24 residues processed: 298 average time/residue: 0.2849 time to fit residues: 128.2128 Evaluate side-chains 290 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 266 time to evaluate : 1.983 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1573 time to fit residues: 9.4472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 ASN ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.074 16841 Z= 0.498 Angle : 0.723 12.125 22954 Z= 0.381 Chirality : 0.046 0.155 2442 Planarity : 0.005 0.044 3001 Dihedral : 4.962 21.066 2411 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.40 % Favored : 93.50 % Rotamer Outliers : 2.19 % 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 (0.17), residues: 2140 helix: None (None), residues: 0 sheet: 0.84 (0.16), residues: 882 loop : -0.87 (0.17), residues: 1258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 269 time to evaluate : 1.880 Fit side-chains outliers start: 38 outliers final: 25 residues processed: 288 average time/residue: 0.2802 time to fit residues: 122.9357 Evaluate side-chains 276 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 251 time to evaluate : 1.873 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1523 time to fit residues: 9.7183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 6.9990 chunk 188 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 208 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 16841 Z= 0.220 Angle : 0.603 11.831 22954 Z= 0.313 Chirality : 0.042 0.141 2442 Planarity : 0.004 0.040 3001 Dihedral : 4.597 20.721 2411 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.37 % Favored : 94.53 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.17), residues: 2140 helix: None (None), residues: 0 sheet: 1.02 (0.16), residues: 873 loop : -0.86 (0.17), residues: 1267 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 274 time to evaluate : 1.937 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 282 average time/residue: 0.2870 time to fit residues: 121.5212 Evaluate side-chains 274 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 262 time to evaluate : 1.813 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1814 time to fit residues: 6.2616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 96 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 16841 Z= 0.373 Angle : 0.656 12.741 22954 Z= 0.343 Chirality : 0.044 0.151 2442 Planarity : 0.005 0.044 3001 Dihedral : 4.738 21.416 2411 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.96 % Favored : 92.99 % Rotamer Outliers : 0.98 % 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 (0.17), residues: 2140 helix: None (None), residues: 0 sheet: 0.93 (0.16), residues: 873 loop : -1.03 (0.17), residues: 1267 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 268 time to evaluate : 1.826 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 274 average time/residue: 0.2942 time to fit residues: 120.3763 Evaluate side-chains 271 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 257 time to evaluate : 1.787 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1454 time to fit residues: 6.2590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 132 optimal weight: 0.4980 chunk 141 optimal weight: 4.9990 chunk 102 optimal weight: 0.0770 chunk 19 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 ASN Q 51 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 16841 Z= 0.163 Angle : 0.573 11.950 22954 Z= 0.296 Chirality : 0.041 0.151 2442 Planarity : 0.004 0.044 3001 Dihedral : 4.409 20.122 2411 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.67 % Rotamer Outliers : 0.40 % 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: -0.10 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.07 (0.16), residues: 873 loop : -0.93 (0.17), residues: 1267 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 284 time to evaluate : 1.945 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 287 average time/residue: 0.3275 time to fit residues: 139.7635 Evaluate side-chains 273 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 269 time to evaluate : 1.861 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1453 time to fit residues: 3.6142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 81 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 16841 Z= 0.262 Angle : 0.601 12.395 22954 Z= 0.311 Chirality : 0.042 0.152 2442 Planarity : 0.004 0.045 3001 Dihedral : 4.440 20.525 2411 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.07 % Favored : 93.88 % Rotamer Outliers : 0.29 % 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: -0.12 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.08 (0.17), residues: 873 loop : -0.98 (0.17), residues: 1267 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 268 time to evaluate : 1.791 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 270 average time/residue: 0.2985 time to fit residues: 120.1356 Evaluate side-chains 268 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 264 time to evaluate : 1.708 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1544 time to fit residues: 3.5829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.8980 chunk 125 optimal weight: 0.2980 chunk 97 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 132 optimal weight: 0.0170 chunk 105 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN B 105 GLN Q 53 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 16841 Z= 0.152 Angle : 0.563 11.707 22954 Z= 0.289 Chirality : 0.041 0.142 2442 Planarity : 0.004 0.051 3001 Dihedral : 4.264 19.229 2411 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.14 % Favored : 94.81 % Rotamer Outliers : 0.12 % 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: -0.05 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.14 (0.17), residues: 873 loop : -0.94 (0.17), residues: 1267 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 277 time to evaluate : 1.883 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 277 average time/residue: 0.2903 time to fit residues: 120.3710 Evaluate side-chains 265 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.915 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.0010 chunk 52 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.127387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.097892 restraints weight = 26277.384| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.19 r_work: 0.3044 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 16841 Z= 0.147 Angle : 0.560 10.975 22954 Z= 0.286 Chirality : 0.041 0.141 2442 Planarity : 0.004 0.045 3001 Dihedral : 4.134 18.613 2411 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.51 % Favored : 94.44 % Rotamer Outliers : 0.17 % 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: 0.04 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.22 (0.17), residues: 873 loop : -0.90 (0.17), residues: 1267 =============================================================================== Job complete usr+sys time: 3703.72 seconds wall clock time: 67 minutes 56.50 seconds (4076.50 seconds total)