Starting phenix.real_space_refine on Tue Apr 9 13:40:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mb3_9065/04_2024/6mb3_9065.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mb3_9065/04_2024/6mb3_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_2024/6mb3_9065.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mb3_9065/04_2024/6mb3_9065.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mb3_9065/04_2024/6mb3_9065.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mb3_9065/04_2024/6mb3_9065.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.010 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 9.28, per 1000 atoms: 0.57 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: 6.38 Conformation dependent library (CDL) restraints added in 3.0 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: 2.27 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: 5.78 Time building geometry restraints manager: 6.86 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.010 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 47.470 Find NCS groups from input model: 1.120 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: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.360 ------------------------------------------------------------------------------- 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 % Allowed : 0.58 % Favored : 99.42 % 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: 0.34 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 0.64 (0.17), residues: 873 loop : 0.00 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.007 TRP B 36 HIS 0.027 0.008 HIS O 34 PHE 0.029 0.007 PHE D 29 TYR 0.069 0.010 TYR R 31 ARG 0.006 0.001 ARG F 66 *********************** 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 : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 85 ASP cc_start: 0.7756 (m-30) cc_final: 0.7061 (m-30) REVERT: N 5 THR cc_start: 0.8696 (m) cc_final: 0.8449 (p) REVERT: N 70 SER cc_start: 0.8412 (t) cc_final: 0.8201 (p) REVERT: Q 104 LEU cc_start: 0.8650 (tp) cc_final: 0.8297 (tt) REVERT: I 28 THR cc_start: 0.8960 (m) cc_final: 0.8499 (p) REVERT: I 34 MET cc_start: 0.8501 (mmm) cc_final: 0.8282 (mmm) REVERT: I 98 TYR cc_start: 0.8288 (t80) cc_final: 0.8084 (t80) REVERT: R 54 ARG cc_start: 0.8011 (pmm-80) cc_final: 0.7744 (ptt90) REVERT: R 91 TYR cc_start: 0.7810 (t80) cc_final: 0.7569 (t80) REVERT: J 12 VAL cc_start: 0.6641 (t) cc_final: 0.6422 (m) REVERT: J 68 THR cc_start: 0.8385 (m) cc_final: 0.8046 (p) REVERT: J 82 LEU cc_start: 0.8301 (mt) cc_final: 0.8057 (mp) outliers start: 0 outliers final: 0 residues processed: 505 average time/residue: 0.3216 time to fit residues: 233.1064 Evaluate side-chains 319 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 2.047 ------------------------------------------------------------------------------- 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: 8.9990 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 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: 0.7982 ------------------------------------------------------------------------------- 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 6 GLN 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16841 Z= 0.191 Angle : 0.670 10.601 22954 Z= 0.363 Chirality : 0.045 0.151 2442 Planarity : 0.004 0.043 3001 Dihedral : 4.850 20.666 2411 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.55 % Favored : 96.36 % Rotamer: Outliers : 2.59 % Allowed : 8.87 % Favored : 88.54 % 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: 0.87 (0.16), residues: 900 loop : 0.06 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 103 HIS 0.004 0.002 HIS B 35 PHE 0.019 0.002 PHE I 29 TYR 0.022 0.001 TYR G 79 ARG 0.006 0.001 ARG H 16 *********************** 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 430 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 385 time to evaluate : 1.900 Fit side-chains revert: symmetry clash REVERT: H 105 GLN cc_start: 0.8480 (pm20) cc_final: 0.8230 (pm20) REVERT: A 56 ARG cc_start: 0.8159 (mtt-85) cc_final: 0.7785 (mtt-85) REVERT: K 104 LEU cc_start: 0.7011 (tp) cc_final: 0.6718 (tp) REVERT: N 5 THR cc_start: 0.8750 (m) cc_final: 0.8433 (p) REVERT: N 47 LEU cc_start: 0.9211 (tp) cc_final: 0.8903 (tt) REVERT: N 103 LYS cc_start: 0.8469 (mtpt) cc_final: 0.8150 (tttp) REVERT: P 32 ASP cc_start: 0.8799 (m-30) cc_final: 0.8547 (m-30) REVERT: I 82 MET cc_start: 0.7487 (mtm) cc_final: 0.7071 (mtm) REVERT: R 54 ARG cc_start: 0.8070 (pmm-80) cc_final: 0.7754 (ptt90) REVERT: R 82 ASP cc_start: 0.7105 (m-30) cc_final: 0.6841 (p0) REVERT: J 4 LEU cc_start: 0.6793 (mt) cc_final: 0.6382 (mt) REVERT: J 110 THR cc_start: 0.5772 (m) cc_final: 0.5339 (p) REVERT: S 38 GLN cc_start: 0.6433 (tt0) cc_final: 0.5744 (tt0) outliers start: 45 outliers final: 31 residues processed: 405 average time/residue: 0.2922 time to fit residues: 175.2946 Evaluate side-chains 338 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 307 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain S residue 37 GLN 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: 1.9990 chunk 163 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 chunk 212 optimal weight: 10.0000 chunk 175 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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** P 51 ASN Q 34 HIS ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 GLN S 34 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 16841 Z= 0.312 Angle : 0.659 11.684 22954 Z= 0.351 Chirality : 0.044 0.148 2442 Planarity : 0.005 0.034 3001 Dihedral : 4.713 20.151 2411 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 3.17 % Allowed : 11.58 % Favored : 85.25 % 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: 0.36 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 0.89 (0.16), residues: 900 loop : -0.22 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 103 HIS 0.005 0.001 HIS B 35 PHE 0.018 0.002 PHE L 98 TYR 0.025 0.002 TYR J 52A ARG 0.010 0.001 ARG A 16 *********************** 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 376 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 321 time to evaluate : 1.894 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7669 (mpp80) REVERT: A 105 GLN cc_start: 0.8625 (pp30) cc_final: 0.8171 (pp30) REVERT: N 5 THR cc_start: 0.8714 (m) cc_final: 0.8448 (p) REVERT: N 45 LYS cc_start: 0.9127 (tttt) cc_final: 0.8905 (ptmm) REVERT: D 18 LEU cc_start: 0.7416 (tp) cc_final: 0.7215 (tp) REVERT: I 79 TYR cc_start: 0.8264 (m-80) cc_final: 0.8011 (m-80) REVERT: I 80 LEU cc_start: 0.8174 (tp) cc_final: 0.7970 (tp) REVERT: R 93 ARG cc_start: 0.7242 (ttp-110) cc_final: 0.6853 (mtp-110) REVERT: J 82 LEU cc_start: 0.8394 (mt) cc_final: 0.8166 (mp) REVERT: J 87 THR cc_start: 0.8104 (m) cc_final: 0.7856 (m) REVERT: S 31 TYR cc_start: 0.8564 (m-80) cc_final: 0.8328 (m-80) REVERT: S 38 GLN cc_start: 0.6650 (tt0) cc_final: 0.5907 (tt0) outliers start: 55 outliers final: 43 residues processed: 348 average time/residue: 0.2932 time to fit residues: 152.3347 Evaluate side-chains 325 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 281 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 62 PHE Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 37 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 186 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 GLN P 51 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16841 Z= 0.198 Angle : 0.592 13.059 22954 Z= 0.307 Chirality : 0.042 0.139 2442 Planarity : 0.004 0.040 3001 Dihedral : 4.500 19.954 2411 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.65 % Rotamer: Outliers : 2.88 % Allowed : 13.71 % Favored : 83.41 % 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: 0.37 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.03 (0.16), residues: 882 loop : -0.32 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 47 HIS 0.003 0.001 HIS B 35 PHE 0.029 0.002 PHE I 67 TYR 0.022 0.001 TYR L 49 ARG 0.008 0.000 ARG H 16 *********************** 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 350 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 300 time to evaluate : 1.890 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8675 (pp30) cc_final: 0.8248 (pp30) REVERT: N 5 THR cc_start: 0.8684 (m) cc_final: 0.8452 (p) REVERT: N 47 LEU cc_start: 0.9242 (tp) cc_final: 0.9022 (tt) REVERT: N 103 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8335 (tttp) REVERT: P 67 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.8419 (p) REVERT: R 93 ARG cc_start: 0.7285 (ttp-110) cc_final: 0.6839 (mtp-110) REVERT: J 82 LEU cc_start: 0.8183 (mt) cc_final: 0.7877 (mp) REVERT: J 87 THR cc_start: 0.7925 (m) cc_final: 0.7672 (m) REVERT: S 31 TYR cc_start: 0.8655 (m-80) cc_final: 0.8316 (m-80) REVERT: S 93 ARG cc_start: 0.8281 (ttp-170) cc_final: 0.7994 (ttp-170) outliers start: 50 outliers final: 37 residues processed: 326 average time/residue: 0.2885 time to fit residues: 140.4754 Evaluate side-chains 313 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 274 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 62 PHE Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain S residue 37 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 O 34 HIS P 53 ASN Q 89 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 16841 Z= 0.405 Angle : 0.683 11.282 22954 Z= 0.360 Chirality : 0.045 0.154 2442 Planarity : 0.005 0.042 3001 Dihedral : 4.807 21.223 2411 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.56 % Favored : 94.35 % Rotamer: Outliers : 4.21 % Allowed : 14.29 % Favored : 81.51 % 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: 0.03 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 0.95 (0.16), residues: 882 loop : -0.68 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 47 HIS 0.007 0.002 HIS B 35 PHE 0.021 0.002 PHE L 98 TYR 0.022 0.002 TYR L 49 ARG 0.007 0.001 ARG R 54 *********************** 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 345 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 272 time to evaluate : 1.993 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8766 (pp30) cc_final: 0.8308 (pp30) REVERT: K 106 LEU cc_start: 0.5041 (OUTLIER) cc_final: 0.3797 (tp) REVERT: N 103 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8396 (tttp) REVERT: O 5 THR cc_start: 0.8816 (m) cc_final: 0.8589 (p) REVERT: R 93 ARG cc_start: 0.7293 (ttp-110) cc_final: 0.6859 (mtp-110) REVERT: J 82 LEU cc_start: 0.8362 (mt) cc_final: 0.7986 (mp) REVERT: J 87 THR cc_start: 0.8006 (m) cc_final: 0.7783 (m) REVERT: S 93 ARG cc_start: 0.8365 (ttp-170) cc_final: 0.8084 (ttp-170) outliers start: 73 outliers final: 56 residues processed: 316 average time/residue: 0.2753 time to fit residues: 132.2723 Evaluate side-chains 315 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 257 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain S residue 37 GLN Chi-restraints excluded: chain S residue 72 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 9.9990 chunk 188 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 208 optimal weight: 0.0970 chunk 173 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 17 GLN B 105 GLN ** 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: 0.8510 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16841 Z= 0.223 Angle : 0.590 11.449 22954 Z= 0.307 Chirality : 0.042 0.138 2442 Planarity : 0.004 0.038 3001 Dihedral : 4.541 20.370 2411 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 3.11 % Allowed : 15.44 % Favored : 81.45 % 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 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.02 (0.16), residues: 882 loop : -0.68 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 47 HIS 0.003 0.001 HIS B 35 PHE 0.011 0.001 PHE I 67 TYR 0.022 0.001 TYR L 49 ARG 0.007 0.000 ARG B 16 *********************** 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 342 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 288 time to evaluate : 1.933 Fit side-chains revert: symmetry clash REVERT: H 16 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.7427 (mtm-85) REVERT: L 66 LYS cc_start: 0.7691 (tttt) cc_final: 0.7428 (ttpt) REVERT: L 78 LEU cc_start: 0.7786 (tt) cc_final: 0.7431 (mt) REVERT: A 105 GLN cc_start: 0.8688 (pp30) cc_final: 0.8319 (pp30) REVERT: K 106 LEU cc_start: 0.4863 (OUTLIER) cc_final: 0.3706 (tp) REVERT: N 103 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8247 (tttp) REVERT: O 5 THR cc_start: 0.8843 (m) cc_final: 0.8637 (p) REVERT: P 83 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8745 (mm-30) REVERT: Q 17 GLN cc_start: 0.7817 (mp10) cc_final: 0.6393 (tt0) REVERT: J 82 LEU cc_start: 0.8324 (mt) cc_final: 0.7963 (mp) REVERT: J 87 THR cc_start: 0.7846 (m) cc_final: 0.7617 (m) REVERT: S 93 ARG cc_start: 0.8298 (ttp-170) cc_final: 0.8026 (ttp-170) outliers start: 54 outliers final: 46 residues processed: 315 average time/residue: 0.2846 time to fit residues: 134.7400 Evaluate side-chains 317 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 269 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain S residue 37 GLN Chi-restraints excluded: chain S residue 72 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 ASN ** 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: 0.8522 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16841 Z= 0.260 Angle : 0.600 12.057 22954 Z= 0.312 Chirality : 0.042 0.146 2442 Planarity : 0.004 0.040 3001 Dihedral : 4.466 20.131 2411 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.84 % Favored : 94.11 % Rotamer: Outliers : 3.40 % Allowed : 15.55 % Favored : 81.05 % 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: -0.00 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.01 (0.16), residues: 882 loop : -0.77 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 47 HIS 0.004 0.001 HIS B 35 PHE 0.021 0.002 PHE I 67 TYR 0.024 0.001 TYR L 49 ARG 0.006 0.000 ARG B 16 *********************** 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 338 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 279 time to evaluate : 2.058 Fit side-chains revert: symmetry clash REVERT: L 66 LYS cc_start: 0.7785 (tttt) cc_final: 0.7508 (ttpt) REVERT: L 78 LEU cc_start: 0.7830 (tt) cc_final: 0.7562 (mt) REVERT: A 85 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7482 (tm-30) REVERT: A 105 GLN cc_start: 0.8699 (pp30) cc_final: 0.8332 (pp30) REVERT: K 106 LEU cc_start: 0.4260 (OUTLIER) cc_final: 0.3281 (tp) REVERT: O 5 THR cc_start: 0.8866 (m) cc_final: 0.8665 (p) REVERT: Q 17 GLN cc_start: 0.7770 (mp10) cc_final: 0.6377 (tt0) REVERT: R 27 ASN cc_start: 0.8124 (p0) cc_final: 0.7741 (p0) REVERT: J 28 THR cc_start: 0.7275 (OUTLIER) cc_final: 0.6996 (m) REVERT: J 82 LEU cc_start: 0.8299 (mt) cc_final: 0.7926 (mp) REVERT: J 87 THR cc_start: 0.7757 (m) cc_final: 0.7498 (m) REVERT: J 105 GLN cc_start: 0.7108 (mm-40) cc_final: 0.6885 (mm110) outliers start: 59 outliers final: 47 residues processed: 315 average time/residue: 0.2863 time to fit residues: 135.4549 Evaluate side-chains 320 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 271 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain S residue 37 GLN Chi-restraints excluded: chain S residue 72 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 141 optimal weight: 0.0070 chunk 102 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8510 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16841 Z= 0.218 Angle : 0.574 12.212 22954 Z= 0.297 Chirality : 0.041 0.143 2442 Planarity : 0.004 0.041 3001 Dihedral : 4.336 19.714 2411 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.63 % Rotamer: Outliers : 2.82 % Allowed : 16.71 % Favored : 80.47 % 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: 0.01 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.04 (0.16), residues: 882 loop : -0.78 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.003 0.001 HIS B 35 PHE 0.016 0.001 PHE I 67 TYR 0.023 0.001 TYR L 49 ARG 0.007 0.000 ARG B 16 *********************** 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 331 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 282 time to evaluate : 2.036 Fit side-chains revert: symmetry clash REVERT: H 16 ARG cc_start: 0.7644 (mtm-85) cc_final: 0.7304 (mtm-85) REVERT: L 78 LEU cc_start: 0.7788 (tt) cc_final: 0.7572 (mt) REVERT: A 85 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7483 (tm-30) REVERT: A 105 GLN cc_start: 0.8722 (pp30) cc_final: 0.8325 (pp30) REVERT: K 106 LEU cc_start: 0.3957 (OUTLIER) cc_final: 0.3011 (mt) REVERT: D 16 ARG cc_start: 0.6537 (mmt180) cc_final: 0.6024 (mmm160) REVERT: O 52 ILE cc_start: 0.8699 (mm) cc_final: 0.8255 (mt) REVERT: P 83 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8569 (mm-30) REVERT: Q 17 GLN cc_start: 0.7823 (mp10) cc_final: 0.6455 (tt0) REVERT: R 27 ASN cc_start: 0.8000 (p0) cc_final: 0.7560 (p0) REVERT: R 46 LEU cc_start: 0.8360 (tp) cc_final: 0.8142 (tp) REVERT: R 60 ASP cc_start: 0.7710 (p0) cc_final: 0.7506 (p0) REVERT: J 28 THR cc_start: 0.7120 (OUTLIER) cc_final: 0.6830 (m) REVERT: J 82 LEU cc_start: 0.8275 (mt) cc_final: 0.7906 (mp) REVERT: J 87 THR cc_start: 0.7723 (m) cc_final: 0.7465 (m) REVERT: J 105 GLN cc_start: 0.7272 (mm-40) cc_final: 0.7070 (mm110) outliers start: 49 outliers final: 45 residues processed: 312 average time/residue: 0.2860 time to fit residues: 133.9841 Evaluate side-chains 317 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 270 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain S residue 37 GLN Chi-restraints excluded: chain S residue 72 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** 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: 0.8545 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16841 Z= 0.325 Angle : 0.623 11.982 22954 Z= 0.325 Chirality : 0.043 0.160 2442 Planarity : 0.005 0.055 3001 Dihedral : 4.547 21.354 2411 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.50 % Favored : 93.46 % Rotamer: Outliers : 2.88 % Allowed : 17.11 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.06 (0.16), residues: 873 loop : -0.93 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 47 HIS 0.005 0.001 HIS B 35 PHE 0.016 0.002 PHE I 67 TYR 0.024 0.001 TYR L 49 ARG 0.007 0.000 ARG B 16 *********************** 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 325 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 275 time to evaluate : 2.013 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7569 (tm-30) REVERT: A 105 GLN cc_start: 0.8717 (pp30) cc_final: 0.8344 (pp30) REVERT: K 106 LEU cc_start: 0.3904 (OUTLIER) cc_final: 0.3073 (mt) REVERT: B 102 TYR cc_start: 0.8655 (m-80) cc_final: 0.8294 (m-80) REVERT: C 82 SER cc_start: 0.9067 (m) cc_final: 0.8808 (t) REVERT: D 16 ARG cc_start: 0.6547 (mmt180) cc_final: 0.6007 (mmm160) REVERT: O 52 ILE cc_start: 0.8694 (mm) cc_final: 0.8241 (mt) REVERT: P 83 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8592 (mm-30) REVERT: Q 17 GLN cc_start: 0.7822 (mp10) cc_final: 0.6513 (tt0) REVERT: R 27 ASN cc_start: 0.7732 (p0) cc_final: 0.7298 (p0) REVERT: J 28 THR cc_start: 0.7178 (OUTLIER) cc_final: 0.6926 (m) REVERT: J 82 LEU cc_start: 0.8279 (mt) cc_final: 0.7903 (mp) REVERT: J 87 THR cc_start: 0.7703 (m) cc_final: 0.7457 (m) outliers start: 50 outliers final: 44 residues processed: 307 average time/residue: 0.2844 time to fit residues: 131.8946 Evaluate side-chains 317 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 271 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain S residue 37 GLN Chi-restraints excluded: chain S residue 72 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 142 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 198 optimal weight: 0.0470 chunk 171 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 136 optimal weight: 0.2980 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** 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: 0.8490 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16841 Z= 0.156 Angle : 0.556 11.539 22954 Z= 0.286 Chirality : 0.041 0.138 2442 Planarity : 0.004 0.042 3001 Dihedral : 4.249 18.968 2411 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.67 % Rotamer: Outliers : 2.13 % Allowed : 18.20 % Favored : 79.67 % 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: 0.02 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.15 (0.17), residues: 873 loop : -0.86 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 103 HIS 0.002 0.001 HIS B 35 PHE 0.012 0.001 PHE I 67 TYR 0.023 0.001 TYR L 49 ARG 0.007 0.000 ARG B 16 ********************** 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 330 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 293 time to evaluate : 2.191 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8733 (pp30) cc_final: 0.8336 (pp30) REVERT: K 106 LEU cc_start: 0.3610 (OUTLIER) cc_final: 0.3009 (mt) REVERT: B 102 TYR cc_start: 0.8623 (m-80) cc_final: 0.8261 (m-80) REVERT: C 82 SER cc_start: 0.9002 (m) cc_final: 0.8737 (t) REVERT: D 16 ARG cc_start: 0.6526 (mmt180) cc_final: 0.5990 (mmm160) REVERT: O 62 PHE cc_start: 0.8727 (m-80) cc_final: 0.8414 (m-80) REVERT: P 83 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8507 (mm-30) REVERT: Q 17 GLN cc_start: 0.7809 (mp10) cc_final: 0.6496 (tt0) REVERT: I 79 TYR cc_start: 0.8169 (m-80) cc_final: 0.7686 (m-80) REVERT: R 27 ASN cc_start: 0.7879 (p0) cc_final: 0.7436 (p0) REVERT: R 46 LEU cc_start: 0.8352 (tp) cc_final: 0.8150 (tp) REVERT: J 6 GLU cc_start: 0.5768 (mp0) cc_final: 0.5285 (mp0) REVERT: J 28 THR cc_start: 0.7137 (OUTLIER) cc_final: 0.6886 (m) REVERT: J 82 LEU cc_start: 0.8318 (mt) cc_final: 0.7951 (mp) REVERT: J 87 THR cc_start: 0.7684 (m) cc_final: 0.7456 (m) outliers start: 37 outliers final: 32 residues processed: 315 average time/residue: 0.2783 time to fit residues: 132.6211 Evaluate side-chains 313 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 279 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain S residue 37 GLN Chi-restraints excluded: chain S residue 72 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 0.4980 chunk 71 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 21 optimal weight: 0.0470 chunk 31 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.126812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.099376 restraints weight = 26321.911| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.51 r_work: 0.2976 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.4712 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= 0.171 Angle : 0.560 11.229 22954 Z= 0.287 Chirality : 0.041 0.145 2442 Planarity : 0.004 0.043 3001 Dihedral : 4.137 19.158 2411 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.37 % Favored : 94.58 % Rotamer: Outliers : 2.30 % Allowed : 18.03 % Favored : 79.67 % 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 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.18 (0.17), residues: 873 loop : -0.83 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 47 HIS 0.003 0.001 HIS B 35 PHE 0.013 0.001 PHE I 67 TYR 0.022 0.001 TYR L 49 ARG 0.007 0.000 ARG B 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3915.76 seconds wall clock time: 72 minutes 4.91 seconds (4324.91 seconds total)