Starting phenix.real_space_refine on Tue Dec 31 17:21:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mb3_9065/12_2024/6mb3_9065.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mb3_9065/12_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/cci-nas-00/data/ceres_data/6mb3_9065/12_2024/6mb3_9065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mb3_9065/12_2024/6mb3_9065.map" model { file = "/net/cci-nas-00/data/ceres_data/6mb3_9065/12_2024/6mb3_9065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mb3_9065/12_2024/6mb3_9065.cif" } 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. Time to flip 13 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 10.27, per 1000 atoms: 0.63 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 - 3.00 Amino acid : True - 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: 4.11 Conformation dependent library (CDL) restraints added in 2.2 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: 3.45 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: 6.26 Time building geometry restraints manager: 4.76 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: 0.00 - 2.65: 20310 2.65 - 5.31: 2356 5.31 - 7.96: 260 7.96 - 10.61: 21 10.61 - 13.27: 7 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 3.120 nonbonded pdb=" OD2 ASP C 72 " pdb=" NZ LYS C 75 " model vdw 2.379 3.120 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 Time spend for trying shortcut: 0.00 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 39.930 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.220 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 505 time to evaluate : 1.800 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: 0.3282 time to fit residues: 237.6136 Evaluate side-chains 319 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.879 ------------------------------------------------------------------------------- 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: 0.6980 chunk 163 optimal weight: 0.9990 chunk 90 optimal weight: 0.0270 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 HIS L 38 GLN L 89 GLN B 105 GLN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 38 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16841 Z= 0.214 Angle : 0.683 10.546 22954 Z= 0.371 Chirality : 0.046 0.158 2442 Planarity : 0.005 0.041 3001 Dihedral : 4.834 20.529 2411 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.21 % Rotamer: Outliers : 2.25 % Allowed : 8.70 % Favored : 89.06 % 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: 0.82 (0.16), residues: 900 loop : 0.09 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 103 HIS 0.003 0.001 HIS C 35 PHE 0.019 0.002 PHE I 29 TYR 0.022 0.002 TYR G 79 ARG 0.005 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 385 time to evaluate : 1.783 Fit side-chains REVERT: H 105 GLN cc_start: 0.8509 (pm20) cc_final: 0.8250 (pm20) REVERT: A 56 ARG cc_start: 0.8153 (mtt-85) cc_final: 0.7754 (mtt-85) REVERT: K 104 LEU cc_start: 0.7005 (tp) cc_final: 0.6710 (tp) REVERT: N 5 THR cc_start: 0.8719 (m) cc_final: 0.8414 (p) REVERT: N 47 LEU cc_start: 0.9215 (tp) cc_final: 0.8902 (tt) REVERT: N 103 LYS cc_start: 0.8477 (mtpt) cc_final: 0.8157 (tttp) REVERT: P 32 ASP cc_start: 0.8768 (m-30) cc_final: 0.8548 (m-30) REVERT: I 82 MET cc_start: 0.7480 (mtm) cc_final: 0.7059 (mtm) REVERT: R 27 ASN cc_start: 0.8212 (p0) cc_final: 0.8009 (p0) REVERT: R 54 ARG cc_start: 0.8088 (pmm-80) cc_final: 0.7755 (ptt90) REVERT: J 110 THR cc_start: 0.5666 (m) cc_final: 0.5263 (p) REVERT: S 38 GLN cc_start: 0.6454 (tt0) cc_final: 0.5759 (tt0) outliers start: 39 outliers final: 26 residues processed: 397 average time/residue: 0.2960 time to fit residues: 173.4202 Evaluate side-chains 330 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 304 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain A residue 108 LEU 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 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 51 ASN Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain G residue 105 GLN 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 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: 2.9990 chunk 133 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 196 optimal weight: 8.9990 chunk 212 optimal weight: 8.9990 chunk 175 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 3 GLN S 6 GLN S 34 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 16841 Z= 0.353 Angle : 0.690 11.107 22954 Z= 0.369 Chirality : 0.045 0.190 2442 Planarity : 0.005 0.045 3001 Dihedral : 4.787 20.586 2411 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.35 % Favored : 95.56 % Rotamer: Outliers : 2.94 % Allowed : 11.12 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 0.83 (0.16), residues: 900 loop : -0.24 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 103 HIS 0.006 0.001 HIS B 35 PHE 0.019 0.002 PHE L 98 TYR 0.024 0.002 TYR J 52A ARG 0.007 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 370 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 319 time to evaluate : 1.818 Fit side-chains REVERT: A 16 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7593 (mpp80) REVERT: A 105 GLN cc_start: 0.8633 (pp30) cc_final: 0.8240 (pp30) REVERT: N 5 THR cc_start: 0.8727 (m) cc_final: 0.8470 (p) REVERT: N 45 LYS cc_start: 0.9145 (tttt) cc_final: 0.8919 (ptmm) REVERT: I 79 TYR cc_start: 0.8294 (m-80) cc_final: 0.7997 (m-80) REVERT: I 80 LEU cc_start: 0.8226 (tp) cc_final: 0.8018 (tp) REVERT: R 27 ASN cc_start: 0.8040 (p0) cc_final: 0.7748 (p0) REVERT: J 82 LEU cc_start: 0.8279 (mt) cc_final: 0.8043 (mp) REVERT: J 87 THR cc_start: 0.7900 (m) cc_final: 0.7693 (m) REVERT: J 110 THR cc_start: 0.6010 (m) cc_final: 0.5745 (p) REVERT: S 31 TYR cc_start: 0.8579 (m-80) cc_final: 0.8290 (m-80) REVERT: S 38 GLN cc_start: 0.6622 (tt0) cc_final: 0.5914 (tt0) outliers start: 51 outliers final: 38 residues processed: 342 average time/residue: 0.2862 time to fit residues: 147.6337 Evaluate side-chains 313 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 274 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 46 GLU 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 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 76 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain O residue 52 ILE Chi-restraints excluded: chain O residue 85 ASP 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 110 THR 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 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 37 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 17 GLN N 51 ASN P 51 ASN P 53 ASN ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 16841 Z= 0.358 Angle : 0.668 11.912 22954 Z= 0.354 Chirality : 0.045 0.176 2442 Planarity : 0.005 0.037 3001 Dihedral : 4.808 20.669 2411 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.77 % Favored : 95.14 % Rotamer: Outliers : 4.03 % Allowed : 12.27 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2140 helix: None (None), residues: 0 sheet: 0.79 (0.17), residues: 819 loop : -0.49 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 47 HIS 0.006 0.002 HIS B 35 PHE 0.028 0.002 PHE I 67 TYR 0.021 0.002 TYR L 49 ARG 0.007 0.001 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 372 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 302 time to evaluate : 1.887 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8702 (pp30) cc_final: 0.8205 (pp30) REVERT: M 60 ASP cc_start: 0.7385 (t0) cc_final: 0.7142 (t0) REVERT: N 103 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8367 (tttp) REVERT: O 5 THR cc_start: 0.8773 (m) cc_final: 0.8543 (p) REVERT: F 75 LYS cc_start: 0.9094 (mttm) cc_final: 0.8893 (mmtm) REVERT: P 67 SER cc_start: 0.8825 (OUTLIER) cc_final: 0.8572 (p) REVERT: P 83 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8481 (mm-30) REVERT: I 79 TYR cc_start: 0.8387 (m-80) cc_final: 0.8152 (m-80) REVERT: R 27 ASN cc_start: 0.7634 (p0) cc_final: 0.7358 (p0) REVERT: R 93 ARG cc_start: 0.7323 (ttp-110) cc_final: 0.6879 (mtp-110) REVERT: J 82 LEU cc_start: 0.8253 (mt) cc_final: 0.7899 (mp) REVERT: J 87 THR cc_start: 0.8048 (m) cc_final: 0.7752 (m) REVERT: S 31 TYR cc_start: 0.8651 (m-80) cc_final: 0.8327 (m-80) outliers start: 70 outliers final: 50 residues processed: 338 average time/residue: 0.2853 time to fit residues: 145.6177 Evaluate side-chains 324 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 272 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 46 GLU 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 5 THR Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 51 ASN Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 69 THR 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 N residue 52 ILE 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 82 MET Chi-restraints excluded: chain D residue 84 VAL 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 67 SER 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 42 THR Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain R residue 33 VAL 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 37 GLN Chi-restraints excluded: chain S residue 72 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 ASN ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16841 Z= 0.267 Angle : 0.614 11.493 22954 Z= 0.322 Chirality : 0.043 0.150 2442 Planarity : 0.004 0.039 3001 Dihedral : 4.616 20.356 2411 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.09 % Rotamer: Outliers : 3.23 % Allowed : 14.00 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 0.95 (0.16), residues: 882 loop : -0.66 (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 0.013 0.002 PHE L 98 TYR 0.021 0.001 TYR L 49 ARG 0.006 0.000 ARG B 16 *********************** 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 343 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 287 time to evaluate : 2.082 Fit side-chains REVERT: A 16 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7820 (mpp80) REVERT: A 105 GLN cc_start: 0.8749 (pp30) cc_final: 0.8281 (pp30) REVERT: N 103 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8225 (tttp) REVERT: O 5 THR cc_start: 0.8790 (m) cc_final: 0.8578 (p) REVERT: P 83 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8317 (mm-30) REVERT: Q 17 GLN cc_start: 0.7753 (mp10) cc_final: 0.6441 (tt0) REVERT: R 27 ASN cc_start: 0.7649 (p0) cc_final: 0.7333 (p0) REVERT: R 93 ARG cc_start: 0.7337 (ttp-110) cc_final: 0.6936 (mtp-110) REVERT: J 6 GLU cc_start: 0.5502 (mp0) cc_final: 0.5243 (mp0) REVERT: J 82 LEU cc_start: 0.8331 (mt) cc_final: 0.8005 (mp) REVERT: J 87 THR cc_start: 0.7920 (m) cc_final: 0.7667 (m) REVERT: S 31 TYR cc_start: 0.8671 (m-80) cc_final: 0.8332 (m-80) outliers start: 56 outliers final: 44 residues processed: 317 average time/residue: 0.2833 time to fit residues: 134.9390 Evaluate side-chains 321 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 275 time to evaluate : 1.843 ------------------------------------------------------------------------------- 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 111 VAL Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR 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 51 ASN Chi-restraints excluded: chain K residue 63 SER 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 C residue 11 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 82 MET 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 9 SER 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 67 SER Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 VAL 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 37 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 17 optimal weight: 0.2980 chunk 69 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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** ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16841 Z= 0.361 Angle : 0.659 11.986 22954 Z= 0.345 Chirality : 0.044 0.166 2442 Planarity : 0.005 0.041 3001 Dihedral : 4.731 20.918 2411 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.56 % Favored : 94.35 % Rotamer: Outliers : 3.74 % Allowed : 14.63 % Favored : 81.62 % 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: -0.15 (0.17), residues: 2140 helix: None (None), residues: 0 sheet: 0.94 (0.16), residues: 873 loop : -0.89 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 47 HIS 0.006 0.001 HIS B 35 PHE 0.017 0.002 PHE L 98 TYR 0.021 0.002 TYR L 49 ARG 0.007 0.001 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 349 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 284 time to evaluate : 1.829 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7622 (tm-30) REVERT: A 105 GLN cc_start: 0.8726 (pp30) cc_final: 0.8269 (pp30) REVERT: P 83 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8414 (mm-30) REVERT: I 66 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.5576 (mtp85) REVERT: R 27 ASN cc_start: 0.7683 (p0) cc_final: 0.7328 (p0) REVERT: R 93 ARG cc_start: 0.7294 (ttp-110) cc_final: 0.7083 (mtp-110) REVERT: J 82 LEU cc_start: 0.8351 (mt) cc_final: 0.7979 (mp) REVERT: J 87 THR cc_start: 0.8052 (m) cc_final: 0.7816 (m) REVERT: S 31 TYR cc_start: 0.8597 (m-80) cc_final: 0.8291 (m-80) outliers start: 65 outliers final: 54 residues processed: 325 average time/residue: 0.2887 time to fit residues: 140.7855 Evaluate side-chains 323 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 268 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 45 LYS 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 51 ASN Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 72 SER 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 C residue 20 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain D residue 17 SER 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 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 78 LEU Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 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 42 THR Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 66 ARG Chi-restraints excluded: chain I residue 109 VAL 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 37 GLN Chi-restraints excluded: chain S residue 58 VAL 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: 10.0000 chunk 23 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16841 Z= 0.352 Angle : 0.653 12.606 22954 Z= 0.342 Chirality : 0.044 0.159 2442 Planarity : 0.005 0.041 3001 Dihedral : 4.732 20.971 2411 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.30 % Rotamer: Outliers : 3.51 % Allowed : 15.61 % Favored : 80.88 % 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: -0.30 (0.17), residues: 2140 helix: None (None), residues: 0 sheet: 0.88 (0.16), residues: 873 loop : -1.03 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 47 HIS 0.005 0.001 HIS B 35 PHE 0.019 0.002 PHE I 67 TYR 0.021 0.002 TYR L 49 ARG 0.007 0.001 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 336 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 275 time to evaluate : 1.771 Fit side-chains REVERT: L 78 LEU cc_start: 0.7722 (tt) cc_final: 0.7402 (mt) REVERT: A 85 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7615 (tm-30) REVERT: A 105 GLN cc_start: 0.8741 (pp30) cc_final: 0.8311 (pp30) REVERT: B 102 TYR cc_start: 0.8630 (m-10) cc_final: 0.8351 (m-10) REVERT: Q 17 GLN cc_start: 0.7650 (mp10) cc_final: 0.6480 (tt0) REVERT: R 82 ASP cc_start: 0.7483 (m-30) cc_final: 0.7231 (m-30) REVERT: J 32 TYR cc_start: 0.8471 (m-80) cc_final: 0.8216 (m-80) REVERT: J 82 LEU cc_start: 0.8406 (mt) cc_final: 0.8047 (mp) REVERT: J 87 THR cc_start: 0.8014 (m) cc_final: 0.7786 (m) REVERT: S 31 TYR cc_start: 0.8576 (m-80) cc_final: 0.8277 (m-80) outliers start: 61 outliers final: 53 residues processed: 314 average time/residue: 0.2834 time to fit residues: 134.1520 Evaluate side-chains 313 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 260 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 12 VAL 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 B residue 11 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 67 SER 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 N residue 51 ASN Chi-restraints excluded: chain D residue 17 SER 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 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 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 67 SER Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 109 VAL 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 99 ASP Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain S residue 37 GLN Chi-restraints excluded: chain S residue 58 VAL 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: 0.8980 chunk 83 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16841 Z= 0.247 Angle : 0.618 12.737 22954 Z= 0.320 Chirality : 0.043 0.156 2442 Planarity : 0.004 0.048 3001 Dihedral : 4.553 20.649 2411 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.37 % Favored : 94.58 % Rotamer: Outliers : 2.88 % Allowed : 16.82 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.17), residues: 2140 helix: None (None), residues: 0 sheet: 0.94 (0.16), residues: 873 loop : -1.02 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 47 HIS 0.004 0.001 HIS B 35 PHE 0.011 0.001 PHE L 98 TYR 0.024 0.001 TYR L 49 ARG 0.018 0.001 ARG A 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 333 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 283 time to evaluate : 1.751 Fit side-chains REVERT: L 78 LEU cc_start: 0.7772 (tt) cc_final: 0.7419 (mt) REVERT: A 85 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7592 (tm-30) REVERT: A 105 GLN cc_start: 0.8714 (pp30) cc_final: 0.8304 (pp30) REVERT: O 62 PHE cc_start: 0.8779 (m-80) cc_final: 0.8494 (m-80) REVERT: P 83 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8474 (mm-30) REVERT: Q 17 GLN cc_start: 0.7799 (mp10) cc_final: 0.6513 (tt0) REVERT: R 27 ASN cc_start: 0.7588 (p0) cc_final: 0.7209 (p0) REVERT: R 82 ASP cc_start: 0.7492 (m-30) cc_final: 0.7268 (m-30) REVERT: J 32 TYR cc_start: 0.8497 (m-80) cc_final: 0.8221 (m-80) REVERT: J 82 LEU cc_start: 0.8404 (mt) cc_final: 0.8049 (mp) REVERT: J 87 THR cc_start: 0.7936 (m) cc_final: 0.7670 (m) REVERT: S 31 TYR cc_start: 0.8571 (m-80) cc_final: 0.8283 (m-80) outliers start: 50 outliers final: 44 residues processed: 315 average time/residue: 0.2813 time to fit residues: 134.0377 Evaluate side-chains 313 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 269 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain A residue 12 VAL 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 12 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 M residue 76 THR 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 17 SER 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 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 G residue 11 VAL Chi-restraints excluded: chain G residue 37 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 67 SER Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain I residue 24 THR 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 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: 5.9990 chunk 181 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16841 Z= 0.348 Angle : 0.657 13.091 22954 Z= 0.342 Chirality : 0.044 0.168 2442 Planarity : 0.005 0.047 3001 Dihedral : 4.677 21.165 2411 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.12 % Favored : 93.83 % Rotamer: Outliers : 3.05 % Allowed : 17.05 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 0.89 (0.16), residues: 873 loop : -1.09 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 47 HIS 0.005 0.001 HIS B 35 PHE 0.014 0.002 PHE L 98 TYR 0.023 0.002 TYR L 49 ARG 0.009 0.001 ARG A 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 321 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 268 time to evaluate : 1.830 Fit side-chains REVERT: L 78 LEU cc_start: 0.7700 (tt) cc_final: 0.7388 (mt) REVERT: A 16 ARG cc_start: 0.8347 (mpp80) cc_final: 0.7958 (mtt90) REVERT: A 85 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7645 (tm-30) REVERT: A 105 GLN cc_start: 0.8713 (pp30) cc_final: 0.8298 (pp30) REVERT: C 82 SER cc_start: 0.9110 (m) cc_final: 0.8827 (t) REVERT: P 83 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8422 (mm-30) REVERT: Q 17 GLN cc_start: 0.7690 (mp10) cc_final: 0.6437 (tt0) REVERT: R 27 ASN cc_start: 0.7865 (p0) cc_final: 0.7484 (p0) REVERT: R 82 ASP cc_start: 0.7458 (m-30) cc_final: 0.7244 (m-30) REVERT: J 32 TYR cc_start: 0.8501 (m-80) cc_final: 0.8233 (m-80) REVERT: J 82 LEU cc_start: 0.8369 (mt) cc_final: 0.8013 (mp) REVERT: J 87 THR cc_start: 0.7961 (m) cc_final: 0.7707 (m) REVERT: S 31 TYR cc_start: 0.8572 (m-80) cc_final: 0.8318 (m-80) outliers start: 53 outliers final: 51 residues processed: 302 average time/residue: 0.2817 time to fit residues: 128.2354 Evaluate side-chains 310 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 259 time to evaluate : 1.866 ------------------------------------------------------------------------------- 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 111 VAL Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 108 LEU 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 B residue 11 VAL Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 67 SER 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 N residue 51 ASN Chi-restraints excluded: chain D residue 17 SER 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 82 MET Chi-restraints excluded: chain D residue 84 VAL 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 78 LEU Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 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 67 SER Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain I residue 24 THR 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 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: 2.9990 chunk 125 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 215 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 53 ASN J 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16841 Z= 0.206 Angle : 0.604 12.130 22954 Z= 0.312 Chirality : 0.042 0.152 2442 Planarity : 0.004 0.044 3001 Dihedral : 4.457 20.318 2411 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.95 % Rotamer: Outliers : 2.25 % Allowed : 17.80 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 0.96 (0.17), residues: 873 loop : -1.04 (0.17), residues: 1267 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 0.009 0.001 PHE L 98 TYR 0.022 0.001 TYR L 49 ARG 0.006 0.000 ARG A 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 318 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 279 time to evaluate : 1.780 Fit side-chains REVERT: L 78 LEU cc_start: 0.7679 (tt) cc_final: 0.7383 (mt) REVERT: A 16 ARG cc_start: 0.8273 (mpp80) cc_final: 0.8010 (mtt90) REVERT: A 85 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7558 (tm-30) REVERT: A 105 GLN cc_start: 0.8780 (pp30) cc_final: 0.8367 (pp30) REVERT: C 82 SER cc_start: 0.9072 (m) cc_final: 0.8777 (t) REVERT: Q 17 GLN cc_start: 0.7693 (mp10) cc_final: 0.6454 (tt0) REVERT: R 27 ASN cc_start: 0.7690 (p0) cc_final: 0.7321 (p0) REVERT: R 82 ASP cc_start: 0.7502 (m-30) cc_final: 0.7273 (m-30) REVERT: J 6 GLU cc_start: 0.5427 (mp0) cc_final: 0.5090 (mp0) REVERT: J 28 THR cc_start: 0.7079 (OUTLIER) cc_final: 0.6731 (m) REVERT: J 32 TYR cc_start: 0.8444 (m-80) cc_final: 0.8178 (m-80) REVERT: J 82 LEU cc_start: 0.8372 (mt) cc_final: 0.8023 (mp) REVERT: J 87 THR cc_start: 0.7780 (m) cc_final: 0.7510 (m) outliers start: 39 outliers final: 38 residues processed: 304 average time/residue: 0.2888 time to fit residues: 132.1788 Evaluate side-chains 304 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 1.661 ------------------------------------------------------------------------------- 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 111 VAL Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain A residue 12 VAL 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 B residue 11 VAL Chi-restraints excluded: chain M residue 37 GLN 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 N residue 51 ASN Chi-restraints excluded: chain D residue 17 SER 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 82 MET 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 9 SER Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain G residue 11 VAL 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 I residue 24 THR Chi-restraints excluded: chain R residue 95 SER 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: 0.6980 chunk 52 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 171 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 21 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.126111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.096700 restraints weight = 26427.122| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.18 r_work: 0.3004 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.4787 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= 0.190 Angle : 0.596 11.626 22954 Z= 0.306 Chirality : 0.042 0.154 2442 Planarity : 0.004 0.045 3001 Dihedral : 4.314 19.657 2411 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.63 % Rotamer: Outliers : 2.36 % Allowed : 17.86 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.06 (0.17), residues: 873 loop : -0.99 (0.17), residues: 1267 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 0.008 0.001 PHE I 67 TYR 0.022 0.001 TYR L 49 ARG 0.005 0.000 ARG A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3799.36 seconds wall clock time: 70 minutes 10.01 seconds (4210.01 seconds total)