Starting phenix.real_space_refine on Sat Jun 14 15:09:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mb3_9065/06_2025/6mb3_9065.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mb3_9065/06_2025/6mb3_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_9065/06_2025/6mb3_9065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mb3_9065/06_2025/6mb3_9065.map" model { file = "/net/cci-nas-00/data/ceres_data/6mb3_9065/06_2025/6mb3_9065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mb3_9065/06_2025/6mb3_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16423 Number of models: 1 Model: "" Number of chains: 19 Chain: "E" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 637 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 23, 'TRANS': 66} Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "A" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "K" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "B" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "M" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "N" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "D" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "O" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "F" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "P" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "G" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "Q" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "I" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "R" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "J" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "S" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Time building chain proxies: 9.81, per 1000 atoms: 0.60 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: 3.89 Conformation dependent library (CDL) restraints added in 2.1 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: 3.00 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'O' and resid 79 through 83 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'S' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.741A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.894A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.549A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.549A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA7, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.182A pdb=" N GLY A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET A 34 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.182A pdb=" N GLY A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA A 96 " --> pdb=" O GLY A 100D" (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLY A 100D" --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.523A pdb=" N VAL K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.523A pdb=" N VAL K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AB4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.370A pdb=" N GLY B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET B 34 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.370A pdb=" N GLY B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR B 102 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA B 96 " --> pdb=" O GLY B 100D" (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLY B 100D" --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.506A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.506A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AC1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.292A pdb=" N GLY C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N MET C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.292A pdb=" N GLY C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA C 96 " --> pdb=" O GLY C 100D" (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLY C 100D" --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.532A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.532A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AC7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.191A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N MET D 34 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.191A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ALA D 96 " --> pdb=" O GLY D 100D" (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLY D 100D" --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 9 through 13 removed outlier: 6.445A pdb=" N VAL O 11 " --> pdb=" O THR O 105 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 9 through 13 removed outlier: 6.445A pdb=" N VAL O 11 " --> pdb=" O THR O 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 19 through 24 Processing sheet with id=AD4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.212A pdb=" N GLY F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET F 34 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.212A pdb=" N GLY F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA F 96 " --> pdb=" O GLY F 100D" (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLY F 100D" --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 9 through 13 removed outlier: 6.583A pdb=" N VAL P 11 " --> pdb=" O THR P 105 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 9 through 13 removed outlier: 6.583A pdb=" N VAL P 11 " --> pdb=" O THR P 105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AE1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.379A pdb=" N GLY G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.379A pdb=" N GLY G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA G 96 " --> pdb=" O GLY G 100D" (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLY G 100D" --> pdb=" O ALA G 96 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 9 through 13 removed outlier: 6.578A pdb=" N VAL Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 9 through 13 removed outlier: 6.578A pdb=" N VAL Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.007A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 10 through 12 removed outlier: 4.433A pdb=" N TYR I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA I 96 " --> pdb=" O GLY I 100D" (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLY I 100D" --> pdb=" O ALA I 96 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'R' and resid 9 through 13 removed outlier: 6.528A pdb=" N VAL R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 9 through 13 removed outlier: 6.528A pdb=" N VAL R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 19 through 24 Processing sheet with id=AF4, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.808A pdb=" N MET J 34 " --> pdb=" O ILE J 50 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 10 through 12 removed outlier: 7.118A pdb=" N CYS J 92 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TRP J 103 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG J 94 " --> pdb=" O ASP J 101 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 9 through 13 removed outlier: 6.544A pdb=" N VAL S 11 " --> pdb=" O THR S 105 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 9 through 13 removed outlier: 6.544A pdb=" N VAL S 11 " --> pdb=" O THR S 105 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 19 through 24 699 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.72 Time building geometry restraints manager: 4.65 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 39.290 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.500 ------------------------------------------------------------------------------- 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 0.187 16859 Z= 1.074 Angle : 1.751 13.266 22990 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 Details of bonding type rmsd hydrogen bonds : bond 0.15806 ( 618) hydrogen bonds : angle 8.04819 ( 1464) SS BOND : bond 0.05612 ( 18) SS BOND : angle 3.27420 ( 36) covalent geometry : bond 0.01996 (16841) covalent geometry : angle 1.74801 (22954) *********************** 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 : 1.775 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: 0.3351 time to fit residues: 242.7613 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 : 1.806 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105928 restraints weight = 25754.242| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.37 r_work: 0.3113 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 16859 Z= 0.149 Angle : 0.683 10.546 22990 Z= 0.372 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 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 618) hydrogen bonds : angle 6.41439 ( 1464) SS BOND : bond 0.00420 ( 18) SS BOND : angle 1.10866 ( 36) covalent geometry : bond 0.00330 (16841) covalent geometry : angle 0.68252 (22954) *********************** 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 : 1.860 Fit side-chains REVERT: A 56 ARG cc_start: 0.8079 (mtt-85) cc_final: 0.7744 (mtt-85) REVERT: K 104 LEU cc_start: 0.6967 (tp) cc_final: 0.6679 (tp) REVERT: C 16 ARG cc_start: 0.8179 (mmm160) cc_final: 0.7953 (mmm160) REVERT: N 5 THR cc_start: 0.8809 (m) cc_final: 0.8408 (p) REVERT: N 47 LEU cc_start: 0.9230 (tp) cc_final: 0.8921 (tt) REVERT: N 103 LYS cc_start: 0.8382 (mtpt) cc_final: 0.8027 (tttp) REVERT: P 32 ASP cc_start: 0.8827 (m-30) cc_final: 0.8598 (m-30) REVERT: Q 17 GLN cc_start: 0.7429 (mt0) cc_final: 0.7106 (mp10) REVERT: I 82 MET cc_start: 0.7561 (mtm) cc_final: 0.7086 (mtm) REVERT: R 27 ASN cc_start: 0.8338 (p0) cc_final: 0.8118 (p0) REVERT: R 54 ARG cc_start: 0.8066 (pmm-80) cc_final: 0.7741 (ptt90) REVERT: J 82 LEU cc_start: 0.8282 (mt) cc_final: 0.8073 (mt) REVERT: J 110 THR cc_start: 0.5798 (m) cc_final: 0.5309 (p) REVERT: S 38 GLN cc_start: 0.6448 (tt0) cc_final: 0.5840 (tt0) outliers start: 39 outliers final: 26 residues processed: 397 average time/residue: 0.3002 time to fit residues: 177.1541 Evaluate side-chains 331 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 305 time to evaluate : 1.812 ------------------------------------------------------------------------------- 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 20 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 135 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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** O 34 HIS P 51 ASN Q 34 HIS ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 GLN I 3 GLN S 6 GLN S 34 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.092985 restraints weight = 26516.464| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.34 r_work: 0.2939 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 16859 Z= 0.331 Angle : 0.793 11.663 22990 Z= 0.424 Chirality : 0.048 0.188 2442 Planarity : 0.006 0.054 3001 Dihedral : 5.160 21.120 2411 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.86 % Favored : 95.05 % Rotamer: Outliers : 3.74 % Allowed : 11.23 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2140 helix: None (None), residues: 0 sheet: 0.69 (0.16), residues: 900 loop : -0.48 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 103 HIS 0.008 0.002 HIS B 35 PHE 0.028 0.003 PHE L 98 TYR 0.028 0.002 TYR G 79 ARG 0.007 0.001 ARG A 16 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 618) hydrogen bonds : angle 5.98489 ( 1464) SS BOND : bond 0.00716 ( 18) SS BOND : angle 2.76848 ( 36) covalent geometry : bond 0.00785 (16841) covalent geometry : angle 0.78600 (22954) *********************** 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 372 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 307 time to evaluate : 1.756 Fit side-chains REVERT: L 89 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8762 (tt0) REVERT: A 16 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7691 (mpp80) REVERT: M 69 THR cc_start: 0.8745 (p) cc_final: 0.8488 (t) REVERT: N 5 THR cc_start: 0.8911 (m) cc_final: 0.8487 (p) REVERT: N 45 LYS cc_start: 0.9211 (tttt) cc_final: 0.8986 (ptmm) REVERT: N 103 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8239 (tttp) REVERT: O 5 THR cc_start: 0.8806 (m) cc_final: 0.8398 (p) REVERT: F 110 THR cc_start: 0.8660 (m) cc_final: 0.8409 (p) REVERT: P 32 ASP cc_start: 0.8955 (m-30) cc_final: 0.8750 (m-30) REVERT: I 79 TYR cc_start: 0.8351 (m-80) cc_final: 0.8145 (m-80) REVERT: R 82 ASP cc_start: 0.7597 (m-30) cc_final: 0.7379 (m-30) REVERT: J 81 GLN cc_start: 0.7250 (tm-30) cc_final: 0.6342 (tm-30) REVERT: J 87 THR cc_start: 0.8162 (m) cc_final: 0.7871 (m) REVERT: J 110 THR cc_start: 0.6547 (m) cc_final: 0.6083 (p) REVERT: S 31 TYR cc_start: 0.8789 (m-80) cc_final: 0.8536 (m-80) outliers start: 65 outliers final: 49 residues processed: 339 average time/residue: 0.2752 time to fit residues: 140.4650 Evaluate side-chains 319 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 267 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 89 GLN 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 5 THR Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 51 ASN 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 C residue 92 CYS Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain 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 Q residue 105 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 62 PHE Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 112 SER 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 14 optimal weight: 0.6980 chunk 208 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 202 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 171 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.126153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.096334 restraints weight = 26415.578| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.13 r_work: 0.2992 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16859 Z= 0.167 Angle : 0.626 11.561 22990 Z= 0.330 Chirality : 0.043 0.155 2442 Planarity : 0.004 0.036 3001 Dihedral : 4.761 20.831 2411 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.75 % Rotamer: Outliers : 2.94 % Allowed : 13.59 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 0.84 (0.16), residues: 882 loop : -0.57 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 47 HIS 0.004 0.001 HIS B 35 PHE 0.023 0.002 PHE I 67 TYR 0.022 0.001 TYR L 49 ARG 0.008 0.001 ARG H 16 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 618) hydrogen bonds : angle 5.56490 ( 1464) SS BOND : bond 0.00458 ( 18) SS BOND : angle 1.92196 ( 36) covalent geometry : bond 0.00385 (16841) covalent geometry : angle 0.62191 (22954) *********************** 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 352 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 301 time to evaluate : 2.007 Fit side-chains REVERT: H 112 SER cc_start: 0.7606 (t) cc_final: 0.7390 (p) REVERT: A 16 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7627 (mpp80) REVERT: A 85 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7644 (tm-30) REVERT: A 105 GLN cc_start: 0.8679 (pp30) cc_final: 0.8123 (pp30) REVERT: B 102 TYR cc_start: 0.8893 (m-80) cc_final: 0.8680 (m-10) REVERT: N 5 THR cc_start: 0.8868 (m) cc_final: 0.8536 (p) REVERT: N 103 LYS cc_start: 0.8704 (mtpt) cc_final: 0.8214 (tttp) REVERT: O 5 THR cc_start: 0.8780 (m) cc_final: 0.8462 (p) REVERT: P 67 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8501 (p) REVERT: P 83 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8241 (mm-30) REVERT: I 75 LYS cc_start: 0.7533 (mmtp) cc_final: 0.7296 (mmtp) REVERT: R 93 ARG cc_start: 0.7395 (ttp80) cc_final: 0.6923 (mtp-110) REVERT: J 87 THR cc_start: 0.8163 (m) cc_final: 0.7881 (m) REVERT: J 110 THR cc_start: 0.6517 (m) cc_final: 0.6181 (p) REVERT: S 31 TYR cc_start: 0.8742 (m-80) cc_final: 0.8370 (m-80) REVERT: S 38 GLN cc_start: 0.6575 (tt0) cc_final: 0.6015 (tt0) outliers start: 51 outliers final: 34 residues processed: 327 average time/residue: 0.2917 time to fit residues: 142.5740 Evaluate side-chains 315 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 279 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 111 VAL 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 110 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain 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 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 110 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain 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 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 21 optimal weight: 0.0000 chunk 165 optimal weight: 10.0000 chunk 159 optimal weight: 0.0770 chunk 174 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 158 optimal weight: 7.9990 chunk 102 optimal weight: 0.0070 overall best weight: 0.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.130093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.099973 restraints weight = 26461.817| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.25 r_work: 0.3067 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16859 Z= 0.096 Angle : 0.567 11.664 22990 Z= 0.292 Chirality : 0.041 0.144 2442 Planarity : 0.004 0.037 3001 Dihedral : 4.323 18.655 2411 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 2.07 % Allowed : 14.92 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.05 (0.16), residues: 882 loop : -0.51 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 36 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE I 67 TYR 0.021 0.001 TYR L 49 ARG 0.006 0.000 ARG B 16 Details of bonding type rmsd hydrogen bonds : bond 0.02856 ( 618) hydrogen bonds : angle 5.22175 ( 1464) SS BOND : bond 0.00376 ( 18) SS BOND : angle 1.42863 ( 36) covalent geometry : bond 0.00210 (16841) covalent geometry : angle 0.56504 (22954) *********************** 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 351 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 315 time to evaluate : 1.719 Fit side-chains REVERT: A 16 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7813 (mpp80) REVERT: A 85 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7643 (tm-30) REVERT: A 105 GLN cc_start: 0.8646 (pp30) cc_final: 0.8088 (pp30) REVERT: K 31 TYR cc_start: 0.9353 (m-10) cc_final: 0.9125 (m-80) REVERT: N 5 THR cc_start: 0.8801 (m) cc_final: 0.8552 (p) REVERT: N 103 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8341 (tttp) REVERT: O 5 THR cc_start: 0.8771 (m) cc_final: 0.8425 (p) REVERT: F 75 LYS cc_start: 0.9264 (mttm) cc_final: 0.9045 (mmtm) REVERT: P 83 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7915 (mm-30) REVERT: R 27 ASN cc_start: 0.7635 (p0) cc_final: 0.7274 (p0) REVERT: R 60 ASP cc_start: 0.7512 (p0) cc_final: 0.7273 (p0) REVERT: J 32 TYR cc_start: 0.8519 (m-80) cc_final: 0.8172 (m-80) REVERT: J 87 THR cc_start: 0.8110 (m) cc_final: 0.7841 (m) REVERT: J 103 TRP cc_start: 0.8870 (m100) cc_final: 0.8495 (m100) REVERT: J 110 THR cc_start: 0.6458 (m) cc_final: 0.6249 (p) outliers start: 36 outliers final: 23 residues processed: 334 average time/residue: 0.2781 time to fit residues: 138.6596 Evaluate side-chains 307 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 282 time to evaluate : 1.954 ------------------------------------------------------------------------------- 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 A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 92 CYS 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 17 SER Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain O residue 85 ASP 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 G residue 105 GLN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain J residue 28 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 89 optimal weight: 0.0370 chunk 122 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 95 optimal weight: 0.1980 chunk 51 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 overall best weight: 3.2464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN P 53 ASN ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.093768 restraints weight = 26479.691| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.22 r_work: 0.2966 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16859 Z= 0.271 Angle : 0.698 11.628 22990 Z= 0.363 Chirality : 0.045 0.177 2442 Planarity : 0.005 0.059 3001 Dihedral : 4.672 21.266 2411 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % Rotamer: Outliers : 2.88 % Allowed : 15.84 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.17), residues: 2140 helix: None (None), residues: 0 sheet: 1.03 (0.16), residues: 873 loop : -0.80 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 47 HIS 0.006 0.002 HIS B 35 PHE 0.021 0.002 PHE I 67 TYR 0.021 0.002 TYR L 49 ARG 0.009 0.001 ARG L 94 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 618) hydrogen bonds : angle 5.39409 ( 1464) SS BOND : bond 0.00731 ( 18) SS BOND : angle 2.07243 ( 36) covalent geometry : bond 0.00640 (16841) covalent geometry : angle 0.69365 (22954) *********************** 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 329 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 279 time to evaluate : 2.361 Fit side-chains REVERT: L 78 LEU cc_start: 0.7739 (tt) cc_final: 0.7413 (mt) REVERT: A 16 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7808 (mpp80) REVERT: A 46 GLU cc_start: 0.7936 (pt0) cc_final: 0.7627 (pt0) REVERT: A 85 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7761 (tm-30) REVERT: A 105 GLN cc_start: 0.8676 (pp30) cc_final: 0.8214 (pp30) REVERT: K 106 LEU cc_start: 0.4550 (pp) cc_final: 0.3515 (mt) REVERT: B 102 TYR cc_start: 0.8845 (m-10) cc_final: 0.8619 (m-10) REVERT: N 5 THR cc_start: 0.8860 (m) cc_final: 0.8601 (p) REVERT: N 103 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8520 (tttp) REVERT: D 16 ARG cc_start: 0.6279 (mmt180) cc_final: 0.5916 (mmm160) REVERT: O 5 THR cc_start: 0.8825 (m) cc_final: 0.8540 (p) REVERT: O 52 ILE cc_start: 0.8906 (mm) cc_final: 0.8448 (mt) REVERT: P 83 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8137 (mm-30) REVERT: R 93 ARG cc_start: 0.7473 (ttp80) cc_final: 0.6912 (mtp-110) REVERT: J 87 THR cc_start: 0.8216 (m) cc_final: 0.7966 (m) REVERT: J 110 THR cc_start: 0.6539 (m) cc_final: 0.6262 (p) REVERT: S 31 TYR cc_start: 0.8682 (m-80) cc_final: 0.8268 (m-80) outliers start: 50 outliers final: 39 residues processed: 311 average time/residue: 0.2883 time to fit residues: 136.2650 Evaluate side-chains 308 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 267 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 42 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain K residue 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 C residue 20 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 103 LYS 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 39 LEU Chi-restraints excluded: chain O residue 85 ASP 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 7 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 67 SER Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain S residue 37 GLN Chi-restraints excluded: chain S residue 72 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 212 optimal weight: 9.9990 chunk 148 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 187 optimal weight: 0.0060 chunk 160 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 overall best weight: 2.5600 ------------------------------------------------------------------------------- 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** J 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.094329 restraints weight = 26447.139| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.30 r_work: 0.2962 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16859 Z= 0.212 Angle : 0.641 11.998 22990 Z= 0.334 Chirality : 0.043 0.140 2442 Planarity : 0.005 0.041 3001 Dihedral : 4.621 20.562 2411 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.63 % Rotamer: Outliers : 3.17 % Allowed : 15.90 % Favored : 80.93 % 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: 0.98 (0.16), residues: 873 loop : -0.92 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 47 HIS 0.005 0.001 HIS B 35 PHE 0.014 0.002 PHE L 98 TYR 0.022 0.002 TYR J 52A ARG 0.006 0.000 ARG B 16 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 618) hydrogen bonds : angle 5.37674 ( 1464) SS BOND : bond 0.00445 ( 18) SS BOND : angle 1.83819 ( 36) covalent geometry : bond 0.00498 (16841) covalent geometry : angle 0.63784 (22954) *********************** 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 334 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 279 time to evaluate : 1.935 Fit side-chains REVERT: L 78 LEU cc_start: 0.7806 (tt) cc_final: 0.7461 (mt) REVERT: A 16 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7793 (mpp80) REVERT: A 46 GLU cc_start: 0.7985 (pt0) cc_final: 0.7689 (pt0) REVERT: A 85 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7810 (tm-30) REVERT: A 105 GLN cc_start: 0.8700 (pp30) cc_final: 0.8220 (pp30) REVERT: K 106 LEU cc_start: 0.4357 (OUTLIER) cc_final: 0.3521 (mt) REVERT: N 5 THR cc_start: 0.8833 (m) cc_final: 0.8576 (p) REVERT: N 103 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8588 (tttp) REVERT: D 16 ARG cc_start: 0.6332 (mmt180) cc_final: 0.5810 (mmm160) REVERT: O 5 THR cc_start: 0.8851 (m) cc_final: 0.8571 (p) REVERT: O 52 ILE cc_start: 0.8816 (mm) cc_final: 0.8388 (mt) REVERT: F 75 LYS cc_start: 0.9242 (mttm) cc_final: 0.9025 (mmtm) REVERT: R 93 ARG cc_start: 0.7470 (ttp80) cc_final: 0.6941 (mtp-110) REVERT: J 32 TYR cc_start: 0.8435 (m-80) cc_final: 0.8082 (m-80) REVERT: J 87 THR cc_start: 0.8192 (m) cc_final: 0.7952 (m) REVERT: J 110 THR cc_start: 0.6747 (m) cc_final: 0.6536 (p) outliers start: 55 outliers final: 46 residues processed: 313 average time/residue: 0.2746 time to fit residues: 129.5189 Evaluate side-chains 315 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 266 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 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 N residue 103 LYS 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 D residue 99 ASP Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain 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 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 99 ASP Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain S residue 37 GLN Chi-restraints excluded: chain S residue 72 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 40 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 185 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.126854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.096457 restraints weight = 26314.672| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.26 r_work: 0.2998 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16859 Z= 0.130 Angle : 0.597 11.780 22990 Z= 0.307 Chirality : 0.042 0.156 2442 Planarity : 0.004 0.042 3001 Dihedral : 4.379 19.887 2411 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.95 % Rotamer: Outliers : 2.59 % Allowed : 16.65 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.05 (0.16), residues: 873 loop : -0.87 (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 0.009 0.001 PHE I 67 TYR 0.023 0.001 TYR L 49 ARG 0.007 0.000 ARG B 16 Details of bonding type rmsd hydrogen bonds : bond 0.03076 ( 618) hydrogen bonds : angle 5.20230 ( 1464) SS BOND : bond 0.00440 ( 18) SS BOND : angle 1.40104 ( 36) covalent geometry : bond 0.00298 (16841) covalent geometry : angle 0.59533 (22954) *********************** 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 329 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 284 time to evaluate : 1.706 Fit side-chains REVERT: L 78 LEU cc_start: 0.7838 (tt) cc_final: 0.7532 (mt) REVERT: L 94 ARG cc_start: 0.9252 (OUTLIER) cc_final: 0.8516 (mtp85) REVERT: A 16 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7847 (mpp80) REVERT: A 46 GLU cc_start: 0.7833 (pt0) cc_final: 0.7595 (pt0) REVERT: A 85 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7710 (tm-30) REVERT: A 105 GLN cc_start: 0.8656 (pp30) cc_final: 0.8180 (pp30) REVERT: K 106 LEU cc_start: 0.4156 (OUTLIER) cc_final: 0.3450 (mt) REVERT: C 82 SER cc_start: 0.9168 (m) cc_final: 0.8835 (t) REVERT: N 5 THR cc_start: 0.8799 (m) cc_final: 0.8583 (p) REVERT: N 103 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8539 (tttp) REVERT: D 16 ARG cc_start: 0.6292 (mmt180) cc_final: 0.5801 (mmm160) REVERT: O 5 THR cc_start: 0.8827 (m) cc_final: 0.8561 (p) REVERT: O 62 PHE cc_start: 0.8891 (m-80) cc_final: 0.8607 (m-80) REVERT: F 75 LYS cc_start: 0.9244 (mttm) cc_final: 0.9023 (mmtm) REVERT: P 83 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8141 (mm-30) REVERT: R 93 ARG cc_start: 0.7430 (ttp80) cc_final: 0.7078 (mtp-110) REVERT: J 32 TYR cc_start: 0.8521 (m-80) cc_final: 0.8156 (m-80) REVERT: J 87 THR cc_start: 0.8108 (m) cc_final: 0.7836 (m) REVERT: J 110 THR cc_start: 0.6564 (m) cc_final: 0.6340 (p) outliers start: 45 outliers final: 35 residues processed: 313 average time/residue: 0.2893 time to fit residues: 135.4118 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 : 1.925 ------------------------------------------------------------------------------- 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 94 ARG Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 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 N residue 103 LYS 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 D residue 99 ASP Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain F residue 62 SER 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 Q residue 20 THR Chi-restraints excluded: chain Q residue 42 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 32 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.124627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.096464 restraints weight = 26355.535| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.50 r_work: 0.2929 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16859 Z= 0.190 Angle : 0.631 12.851 22990 Z= 0.327 Chirality : 0.043 0.153 2442 Planarity : 0.005 0.043 3001 Dihedral : 4.480 20.556 2411 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.63 % Rotamer: Outliers : 2.76 % Allowed : 16.99 % Favored : 80.24 % 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: -0.14 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.01 (0.16), residues: 873 loop : -0.94 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 47 HIS 0.005 0.001 HIS B 35 PHE 0.013 0.002 PHE L 98 TYR 0.022 0.001 TYR L 49 ARG 0.006 0.000 ARG B 16 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 618) hydrogen bonds : angle 5.25263 ( 1464) SS BOND : bond 0.00533 ( 18) SS BOND : angle 1.69448 ( 36) covalent geometry : bond 0.00445 (16841) covalent geometry : angle 0.62784 (22954) *********************** 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 329 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 281 time to evaluate : 1.811 Fit side-chains REVERT: L 78 LEU cc_start: 0.7818 (tt) cc_final: 0.7512 (mt) REVERT: L 94 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8421 (mtp85) REVERT: A 16 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7841 (mpp80) REVERT: A 85 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7632 (tm-30) REVERT: A 105 GLN cc_start: 0.8580 (pp30) cc_final: 0.8140 (pp30) REVERT: K 106 LEU cc_start: 0.4078 (OUTLIER) cc_final: 0.3458 (mt) REVERT: C 82 SER cc_start: 0.9133 (m) cc_final: 0.8810 (t) REVERT: N 103 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8511 (tttp) REVERT: D 16 ARG cc_start: 0.6273 (mmt180) cc_final: 0.5859 (mmm160) REVERT: O 5 THR cc_start: 0.8811 (m) cc_final: 0.8595 (p) REVERT: O 62 PHE cc_start: 0.8804 (m-80) cc_final: 0.8515 (m-80) REVERT: F 75 LYS cc_start: 0.9171 (mttm) cc_final: 0.8947 (mmtm) REVERT: P 83 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8063 (mm-30) REVERT: Q 83 GLU cc_start: 0.7832 (tt0) cc_final: 0.7597 (tp30) REVERT: R 27 ASN cc_start: 0.7452 (p0) cc_final: 0.7000 (p0) REVERT: R 93 ARG cc_start: 0.7416 (ttp80) cc_final: 0.7147 (mtp-110) REVERT: J 6 GLU cc_start: 0.5477 (pm20) cc_final: 0.5035 (pm20) REVERT: J 32 TYR cc_start: 0.8498 (m-80) cc_final: 0.8131 (m-80) REVERT: J 87 THR cc_start: 0.8097 (m) cc_final: 0.7850 (m) REVERT: S 31 TYR cc_start: 0.8594 (m-80) cc_final: 0.8272 (m-80) outliers start: 48 outliers final: 42 residues processed: 313 average time/residue: 0.2849 time to fit residues: 134.6747 Evaluate side-chains 320 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 274 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 94 ARG 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 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 106 LEU 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 N residue 103 LYS 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 39 LEU Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain 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 Q residue 20 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 126 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 90 optimal weight: 0.0000 chunk 170 optimal weight: 9.9990 chunk 163 optimal weight: 0.9980 chunk 193 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.125674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.097911 restraints weight = 26313.986| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.40 r_work: 0.2945 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16859 Z= 0.151 Angle : 0.604 12.053 22990 Z= 0.311 Chirality : 0.042 0.155 2442 Planarity : 0.004 0.043 3001 Dihedral : 4.385 20.098 2411 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.23 % Favored : 94.72 % Rotamer: Outliers : 2.71 % Allowed : 17.22 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.04 (0.17), residues: 873 loop : -0.91 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.004 0.001 HIS B 35 PHE 0.009 0.001 PHE L 98 TYR 0.023 0.001 TYR L 49 ARG 0.006 0.000 ARG B 16 Details of bonding type rmsd hydrogen bonds : bond 0.03057 ( 618) hydrogen bonds : angle 5.16144 ( 1464) SS BOND : bond 0.00459 ( 18) SS BOND : angle 1.46762 ( 36) covalent geometry : bond 0.00352 (16841) covalent geometry : angle 0.60145 (22954) ********************** 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 325 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 278 time to evaluate : 1.986 Fit side-chains REVERT: L 78 LEU cc_start: 0.7778 (tt) cc_final: 0.7504 (mt) REVERT: L 94 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8412 (mtp85) REVERT: A 16 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7840 (mpp80) REVERT: A 85 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7715 (tm-30) REVERT: A 105 GLN cc_start: 0.8609 (pp30) cc_final: 0.8169 (pp30) REVERT: K 106 LEU cc_start: 0.4074 (OUTLIER) cc_final: 0.3523 (mt) REVERT: C 82 SER cc_start: 0.9124 (m) cc_final: 0.8793 (t) REVERT: N 103 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8535 (tttp) REVERT: D 16 ARG cc_start: 0.6215 (mmt180) cc_final: 0.5843 (mmm160) REVERT: F 75 LYS cc_start: 0.9152 (mttm) cc_final: 0.8934 (mmtm) REVERT: P 83 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8211 (mm-30) REVERT: R 93 ARG cc_start: 0.7410 (ttp80) cc_final: 0.7120 (mtp-110) REVERT: J 6 GLU cc_start: 0.5013 (pm20) cc_final: 0.4198 (mp0) REVERT: J 28 THR cc_start: 0.6956 (OUTLIER) cc_final: 0.6398 (m) REVERT: J 32 TYR cc_start: 0.8525 (m-80) cc_final: 0.8188 (m-80) REVERT: J 87 THR cc_start: 0.7995 (m) cc_final: 0.7731 (m) outliers start: 47 outliers final: 39 residues processed: 308 average time/residue: 0.2947 time to fit residues: 136.5629 Evaluate side-chains 316 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 106 LEU 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 N residue 103 LYS 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 39 LEU Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain 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 110 THR Chi-restraints excluded: chain Q residue 20 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 21 optimal weight: 0.1980 chunk 213 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.123295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.091729 restraints weight = 26594.756| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.11 r_work: 0.2961 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16859 Z= 0.206 Angle : 0.635 12.690 22990 Z= 0.329 Chirality : 0.043 0.163 2442 Planarity : 0.005 0.043 3001 Dihedral : 4.511 20.911 2411 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.84 % Favored : 94.11 % Rotamer: Outliers : 3.17 % Allowed : 16.82 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 0.99 (0.17), residues: 873 loop : -0.98 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 47 HIS 0.004 0.001 HIS B 35 PHE 0.012 0.002 PHE L 98 TYR 0.024 0.001 TYR L 49 ARG 0.006 0.000 ARG B 16 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 618) hydrogen bonds : angle 5.25399 ( 1464) SS BOND : bond 0.00508 ( 18) SS BOND : angle 1.75025 ( 36) covalent geometry : bond 0.00483 (16841) covalent geometry : angle 0.63200 (22954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9064.69 seconds wall clock time: 156 minutes 18.36 seconds (9378.36 seconds total)