Starting phenix.real_space_refine on Thu Sep 18 11:09:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mb3_9065/09_2025/6mb3_9065.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mb3_9065/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6mb3_9065/09_2025/6mb3_9065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mb3_9065/09_2025/6mb3_9065.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mb3_9065/09_2025/6mb3_9065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mb3_9065/09_2025/6mb3_9065.map" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.23, per 1000 atoms: 0.26 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: 1.01 Conformation dependent library (CDL) restraints added in 559.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.98 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: 3.21 Time building geometry restraints manager: 1.34 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: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.620 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.670 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG F 66 TYR 0.069 0.010 TYR R 31 PHE 0.029 0.007 PHE D 29 TRP 0.033 0.007 TRP B 36 HIS 0.027 0.008 HIS O 34 Details of bonding type rmsd covalent geometry : bond 0.01996 (16841) covalent geometry : angle 1.74801 (22954) SS BOND : bond 0.05612 ( 18) SS BOND : angle 3.27420 ( 36) hydrogen bonds : bond 0.15806 ( 618) hydrogen bonds : angle 8.04819 ( 1464) *********************** 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 : 0.639 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: 0.8448 (p) REVERT: N 70 SER cc_start: 0.8412 (t) cc_final: 0.8202 (p) REVERT: Q 104 LEU cc_start: 0.8650 (tp) cc_final: 0.8296 (tt) REVERT: I 28 THR cc_start: 0.8960 (m) cc_final: 0.8498 (p) REVERT: I 34 MET cc_start: 0.8501 (mmm) cc_final: 0.8281 (mmm) REVERT: I 98 TYR cc_start: 0.8288 (t80) cc_final: 0.8083 (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: 0.7570 (t80) REVERT: J 12 VAL cc_start: 0.6641 (t) cc_final: 0.6423 (m) REVERT: J 68 THR cc_start: 0.8385 (m) cc_final: 0.8044 (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: 0.1545 time to fit residues: 112.6217 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 : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 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 = 0.3692 r_free = 0.3692 target = 0.134238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.105356 restraints weight = 25684.445| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.39 r_work: 0.3105 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16859 Z= 0.150 Angle : 0.684 10.791 22990 Z= 0.368 Chirality : 0.045 0.176 2442 Planarity : 0.004 0.042 3001 Dihedral : 4.832 20.655 2411 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.74 % Favored : 96.17 % Rotamer: Outliers : 2.30 % Allowed : 8.58 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 0.82 (0.16), residues: 900 loop : 0.06 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 16 TYR 0.022 0.002 TYR G 79 PHE 0.019 0.002 PHE I 29 TRP 0.016 0.001 TRP A 103 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00339 (16841) covalent geometry : angle 0.68257 (22954) SS BOND : bond 0.00498 ( 18) SS BOND : angle 1.18572 ( 36) hydrogen bonds : bond 0.03949 ( 618) hydrogen bonds : angle 6.36197 ( 1464) *********************** 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 428 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 388 time to evaluate : 0.634 Fit side-chains REVERT: A 56 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7766 (mtt-85) REVERT: K 104 LEU cc_start: 0.7004 (tp) cc_final: 0.6732 (tp) REVERT: C 16 ARG cc_start: 0.8220 (mmm160) cc_final: 0.7995 (mmm160) REVERT: N 5 THR cc_start: 0.8821 (m) cc_final: 0.8416 (p) REVERT: N 47 LEU cc_start: 0.9236 (tp) cc_final: 0.8934 (tt) REVERT: N 103 LYS cc_start: 0.8412 (mtpt) cc_final: 0.8046 (tttp) REVERT: P 32 ASP cc_start: 0.8822 (m-30) cc_final: 0.8599 (m-30) REVERT: Q 17 GLN cc_start: 0.7471 (mt0) cc_final: 0.7139 (mp10) REVERT: I 66 ARG cc_start: 0.5440 (mtm110) cc_final: 0.5078 (mtm110) REVERT: I 82 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6530 (mtm) REVERT: R 27 ASN cc_start: 0.8342 (p0) cc_final: 0.8116 (p0) REVERT: R 54 ARG cc_start: 0.8100 (pmm-80) cc_final: 0.7765 (ptt90) REVERT: J 82 LEU cc_start: 0.8297 (mt) cc_final: 0.8096 (mt) REVERT: J 110 THR cc_start: 0.5836 (m) cc_final: 0.5343 (p) REVERT: S 38 GLN cc_start: 0.6455 (tt0) cc_final: 0.5848 (tt0) outliers start: 40 outliers final: 26 residues processed: 402 average time/residue: 0.1417 time to fit residues: 84.8460 Evaluate side-chains 336 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 309 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain A residue 46 GLU 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 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 9 SER Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain I residue 82 MET 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 129 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 P 51 ASN Q 34 HIS ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN I 105 GLN S 34 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.122769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.090800 restraints weight = 26990.217| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.38 r_work: 0.2915 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 16859 Z= 0.262 Angle : 0.717 11.507 22990 Z= 0.383 Chirality : 0.046 0.190 2442 Planarity : 0.005 0.047 3001 Dihedral : 4.863 20.895 2411 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 3.17 % Allowed : 11.46 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 0.79 (0.16), residues: 900 loop : -0.31 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 16 TYR 0.025 0.002 TYR G 79 PHE 0.021 0.003 PHE L 98 TRP 0.021 0.002 TRP H 103 HIS 0.006 0.002 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00616 (16841) covalent geometry : angle 0.71209 (22954) SS BOND : bond 0.00655 ( 18) SS BOND : angle 2.28303 ( 36) hydrogen bonds : bond 0.04129 ( 618) hydrogen bonds : angle 5.86430 ( 1464) *********************** 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 371 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 316 time to evaluate : 0.599 Fit side-chains REVERT: A 16 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7391 (mpp80) REVERT: A 56 ARG cc_start: 0.8499 (mtt-85) cc_final: 0.8294 (mtt-85) REVERT: A 105 GLN cc_start: 0.8608 (pp30) cc_final: 0.8123 (pp30) REVERT: M 69 THR cc_start: 0.8731 (p) cc_final: 0.8454 (t) REVERT: N 5 THR cc_start: 0.8907 (m) cc_final: 0.8470 (p) REVERT: N 45 LYS cc_start: 0.9142 (tttt) cc_final: 0.8908 (ptmm) REVERT: D 18 LEU cc_start: 0.7363 (tp) cc_final: 0.7099 (tp) REVERT: I 66 ARG cc_start: 0.5810 (mtm110) cc_final: 0.5466 (mtm110) REVERT: R 27 ASN cc_start: 0.8223 (p0) cc_final: 0.7895 (p0) REVERT: R 93 ARG cc_start: 0.7291 (ttp-110) cc_final: 0.6817 (mtp-110) REVERT: J 87 THR cc_start: 0.8092 (m) cc_final: 0.7864 (m) REVERT: J 110 THR cc_start: 0.6368 (m) cc_final: 0.5878 (p) REVERT: S 31 TYR cc_start: 0.8724 (m-80) cc_final: 0.8337 (m-80) REVERT: S 38 GLN cc_start: 0.6640 (tt0) cc_final: 0.6002 (tt0) outliers start: 55 outliers final: 41 residues processed: 342 average time/residue: 0.1391 time to fit residues: 71.5385 Evaluate side-chains 315 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 273 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain M residue 76 THR 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 D residue 28 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain O residue 52 ILE Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 62 PHE Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain S residue 37 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 20 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 53 ASN Q 51 ASN ** I 105 GLN ** 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 = 0.3593 r_free = 0.3593 target = 0.126681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.096017 restraints weight = 26411.074| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.21 r_work: 0.3010 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16859 Z= 0.176 Angle : 0.626 11.828 22990 Z= 0.330 Chirality : 0.043 0.161 2442 Planarity : 0.004 0.035 3001 Dihedral : 4.638 20.323 2411 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.65 % Rotamer: Outliers : 3.46 % Allowed : 12.67 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 0.95 (0.16), residues: 882 loop : -0.47 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 16 TYR 0.021 0.001 TYR L 49 PHE 0.014 0.002 PHE L 98 TRP 0.014 0.001 TRP C 47 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00406 (16841) covalent geometry : angle 0.62202 (22954) SS BOND : bond 0.00544 ( 18) SS BOND : angle 1.84026 ( 36) hydrogen bonds : bond 0.03447 ( 618) hydrogen bonds : angle 5.49812 ( 1464) *********************** 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 369 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 309 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8636 (pp30) cc_final: 0.8104 (pp30) REVERT: N 5 THR cc_start: 0.8872 (m) cc_final: 0.8533 (p) REVERT: N 103 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8158 (tttp) REVERT: O 5 THR cc_start: 0.8764 (m) cc_final: 0.8424 (p) REVERT: P 83 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8147 (mm-30) REVERT: I 66 ARG cc_start: 0.6212 (mtm110) cc_final: 0.5574 (mtm110) REVERT: I 79 TYR cc_start: 0.8381 (m-80) cc_final: 0.8158 (m-80) REVERT: R 27 ASN cc_start: 0.7902 (p0) cc_final: 0.7587 (p0) REVERT: R 93 ARG cc_start: 0.7357 (ttp-110) cc_final: 0.6843 (mtp-110) REVERT: J 87 THR cc_start: 0.8183 (m) cc_final: 0.7880 (m) REVERT: J 105 GLN cc_start: 0.7270 (mm-40) cc_final: 0.6966 (mm110) REVERT: J 110 THR cc_start: 0.6490 (m) cc_final: 0.6142 (p) REVERT: S 31 TYR cc_start: 0.8735 (m-80) cc_final: 0.8333 (m-80) outliers start: 60 outliers final: 46 residues processed: 339 average time/residue: 0.1403 time to fit residues: 71.3136 Evaluate side-chains 327 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain A residue 12 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 51 ASN Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain M residue 48 ILE 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 24 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 51 ASN Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain 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 S residue 37 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 96 optimal weight: 9.9990 chunk 10 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 209 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 ASN Q 51 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.127868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.097266 restraints weight = 26291.909| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.32 r_work: 0.3011 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16859 Z= 0.139 Angle : 0.597 11.616 22990 Z= 0.311 Chirality : 0.042 0.144 2442 Planarity : 0.004 0.040 3001 Dihedral : 4.466 19.747 2411 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.39 % Favored : 95.51 % Rotamer: Outliers : 3.34 % Allowed : 13.48 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.02 (0.16), residues: 882 loop : -0.51 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 16 TYR 0.021 0.001 TYR L 49 PHE 0.012 0.001 PHE L 98 TRP 0.011 0.001 TRP C 47 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00319 (16841) covalent geometry : angle 0.59414 (22954) SS BOND : bond 0.00472 ( 18) SS BOND : angle 1.49650 ( 36) hydrogen bonds : bond 0.03203 ( 618) hydrogen bonds : angle 5.32565 ( 1464) *********************** 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: 58 poor density : 293 time to evaluate : 0.645 Fit side-chains REVERT: A 16 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7731 (mpp80) REVERT: A 105 GLN cc_start: 0.8664 (pp30) cc_final: 0.8151 (pp30) REVERT: N 5 THR cc_start: 0.8834 (m) cc_final: 0.8520 (p) REVERT: N 103 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8311 (tttp) REVERT: O 5 THR cc_start: 0.8762 (m) cc_final: 0.8417 (p) REVERT: P 83 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7958 (mm-30) REVERT: I 66 ARG cc_start: 0.6347 (mtm110) cc_final: 0.6040 (mtm180) REVERT: R 27 ASN cc_start: 0.7857 (p0) cc_final: 0.7521 (p0) REVERT: R 93 ARG cc_start: 0.7341 (ttp-110) cc_final: 0.6812 (mtp-110) REVERT: J 87 THR cc_start: 0.8177 (m) cc_final: 0.7900 (m) REVERT: J 105 GLN cc_start: 0.7238 (mm-40) cc_final: 0.7010 (mm110) REVERT: J 110 THR cc_start: 0.6580 (m) cc_final: 0.6326 (p) REVERT: S 31 TYR cc_start: 0.8732 (m-80) cc_final: 0.8286 (m-80) outliers start: 58 outliers final: 48 residues processed: 325 average time/residue: 0.1377 time to fit residues: 67.5918 Evaluate side-chains 330 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 280 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain 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 46 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain K residue 51 ASN Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 51 ASN Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain S residue 37 GLN Chi-restraints excluded: chain S residue 72 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 170 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 34 HIS Q 51 ASN Q 89 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.092104 restraints weight = 26515.134| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.21 r_work: 0.2938 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 16859 Z= 0.311 Angle : 0.717 11.900 22990 Z= 0.376 Chirality : 0.046 0.172 2442 Planarity : 0.005 0.044 3001 Dihedral : 4.840 21.174 2411 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.61 % Favored : 94.30 % Rotamer: Outliers : 3.97 % Allowed : 14.46 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 0.81 (0.16), residues: 882 loop : -0.81 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 94 TYR 0.024 0.002 TYR L 49 PHE 0.020 0.002 PHE L 98 TRP 0.020 0.002 TRP C 47 HIS 0.007 0.002 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00732 (16841) covalent geometry : angle 0.71209 (22954) SS BOND : bond 0.00700 ( 18) SS BOND : angle 2.20674 ( 36) hydrogen bonds : bond 0.03985 ( 618) hydrogen bonds : angle 5.61117 ( 1464) *********************** 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 343 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 274 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8717 (pp30) cc_final: 0.8259 (pp30) REVERT: B 102 TYR cc_start: 0.8834 (m-10) cc_final: 0.8601 (m-10) REVERT: M 60 ASP cc_start: 0.7759 (t0) cc_final: 0.7551 (t0) REVERT: N 5 THR cc_start: 0.8842 (m) cc_final: 0.8542 (p) REVERT: N 103 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8479 (tttp) REVERT: D 16 ARG cc_start: 0.6346 (mmt180) cc_final: 0.5748 (mmm160) REVERT: O 5 THR cc_start: 0.8844 (m) cc_final: 0.8565 (p) REVERT: I 66 ARG cc_start: 0.6415 (mtm110) cc_final: 0.5985 (mtm180) REVERT: R 27 ASN cc_start: 0.7783 (p0) cc_final: 0.7381 (p0) REVERT: R 93 ARG cc_start: 0.7346 (ttp-110) cc_final: 0.6935 (mtp-110) REVERT: J 87 THR cc_start: 0.8243 (m) cc_final: 0.7990 (m) REVERT: J 105 GLN cc_start: 0.7264 (mm-40) cc_final: 0.6898 (mm110) REVERT: J 110 THR cc_start: 0.6693 (m) cc_final: 0.6428 (p) REVERT: S 31 TYR cc_start: 0.8722 (m-80) cc_final: 0.8390 (m-80) outliers start: 69 outliers final: 57 residues processed: 315 average time/residue: 0.1262 time to fit residues: 60.5224 Evaluate side-chains 323 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 265 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 42 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 51 ASN Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 102 THR 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 110 THR Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain S residue 37 GLN Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 72 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 46 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 192 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.096359 restraints weight = 26049.671| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.22 r_work: 0.3046 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16859 Z= 0.112 Angle : 0.585 11.476 22990 Z= 0.302 Chirality : 0.041 0.138 2442 Planarity : 0.004 0.040 3001 Dihedral : 4.420 19.976 2411 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.30 % Favored : 95.65 % Rotamer: Outliers : 2.07 % Allowed : 16.30 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.04 (0.16), residues: 873 loop : -0.80 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 16 TYR 0.022 0.001 TYR L 49 PHE 0.007 0.001 PHE L 98 TRP 0.009 0.001 TRP C 47 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00254 (16841) covalent geometry : angle 0.58439 (22954) SS BOND : bond 0.00371 ( 18) SS BOND : angle 0.97810 ( 36) hydrogen bonds : bond 0.03011 ( 618) hydrogen bonds : angle 5.25858 ( 1464) *********************** 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 333 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 297 time to evaluate : 0.620 Fit side-chains REVERT: H 16 ARG cc_start: 0.7878 (mtm-85) cc_final: 0.7615 (mtp85) REVERT: L 78 LEU cc_start: 0.7746 (tt) cc_final: 0.7365 (mt) REVERT: A 16 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7823 (mpp80) REVERT: A 105 GLN cc_start: 0.8668 (pp30) cc_final: 0.8174 (pp30) REVERT: N 5 THR cc_start: 0.8830 (m) cc_final: 0.8594 (p) REVERT: N 103 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8432 (tttp) REVERT: D 16 ARG cc_start: 0.6147 (mmt180) cc_final: 0.5764 (mmm160) REVERT: O 5 THR cc_start: 0.8832 (m) cc_final: 0.8546 (p) REVERT: O 52 ILE cc_start: 0.8788 (mm) cc_final: 0.8370 (mt) REVERT: O 62 PHE cc_start: 0.8926 (m-80) cc_final: 0.8712 (m-80) REVERT: I 66 ARG cc_start: 0.6354 (mtm110) cc_final: 0.6103 (mtm180) REVERT: R 27 ASN cc_start: 0.7702 (p0) cc_final: 0.7282 (p0) REVERT: R 93 ARG cc_start: 0.7340 (ttp-110) cc_final: 0.7093 (mtp-110) REVERT: J 6 GLU cc_start: 0.5691 (mp0) cc_final: 0.5243 (mp0) REVERT: J 32 TYR cc_start: 0.8579 (m-80) cc_final: 0.8179 (m-80) REVERT: J 87 THR cc_start: 0.8145 (m) cc_final: 0.7895 (m) REVERT: J 110 THR cc_start: 0.6509 (m) cc_final: 0.6302 (p) outliers start: 36 outliers final: 23 residues processed: 318 average time/residue: 0.1322 time to fit residues: 62.9988 Evaluate side-chains 299 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain M residue 48 ILE 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 28 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain S residue 37 GLN Chi-restraints excluded: chain S residue 72 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 148 optimal weight: 0.0060 chunk 99 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 95 optimal weight: 0.0060 overall best weight: 1.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 3 GLN I 105 GLN J 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.098376 restraints weight = 26452.424| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.45 r_work: 0.2969 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16859 Z= 0.138 Angle : 0.600 11.464 22990 Z= 0.309 Chirality : 0.042 0.155 2442 Planarity : 0.004 0.042 3001 Dihedral : 4.315 19.526 2411 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.91 % Favored : 95.05 % Rotamer: Outliers : 2.25 % Allowed : 16.36 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.08 (0.16), residues: 873 loop : -0.83 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 16 TYR 0.020 0.001 TYR L 49 PHE 0.010 0.001 PHE I 67 TRP 0.012 0.001 TRP J 47 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00319 (16841) covalent geometry : angle 0.59866 (22954) SS BOND : bond 0.00485 ( 18) SS BOND : angle 1.09024 ( 36) hydrogen bonds : bond 0.03154 ( 618) hydrogen bonds : angle 5.17585 ( 1464) *********************** 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 321 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 282 time to evaluate : 0.453 Fit side-chains REVERT: L 78 LEU cc_start: 0.7767 (tt) cc_final: 0.7399 (mt) REVERT: A 85 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7395 (tm-30) REVERT: A 105 GLN cc_start: 0.8591 (pp30) cc_final: 0.8090 (pp30) REVERT: N 103 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8460 (tttp) REVERT: O 5 THR cc_start: 0.8818 (m) cc_final: 0.8563 (p) REVERT: O 52 ILE cc_start: 0.8675 (mm) cc_final: 0.8252 (mt) REVERT: I 66 ARG cc_start: 0.6481 (mtm110) cc_final: 0.6000 (mtm180) REVERT: R 27 ASN cc_start: 0.7601 (p0) cc_final: 0.7193 (p0) REVERT: R 93 ARG cc_start: 0.7291 (ttp-110) cc_final: 0.7079 (mtp-110) REVERT: J 6 GLU cc_start: 0.5566 (mp0) cc_final: 0.5175 (mp0) REVERT: J 32 TYR cc_start: 0.8521 (m-80) cc_final: 0.8096 (m-80) REVERT: J 46 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7168 (mm-30) REVERT: J 87 THR cc_start: 0.8094 (m) cc_final: 0.7863 (m) outliers start: 39 outliers final: 31 residues processed: 306 average time/residue: 0.1286 time to fit residues: 59.5067 Evaluate side-chains 307 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 275 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 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 R residue 95 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain S residue 37 GLN Chi-restraints excluded: chain S residue 72 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 127 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 212 optimal weight: 10.0000 chunk 5 optimal weight: 0.0050 chunk 211 optimal weight: 5.9990 chunk 195 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 94 optimal weight: 0.2980 overall best weight: 2.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.095982 restraints weight = 26406.975| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.13 r_work: 0.2984 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16859 Z= 0.192 Angle : 0.636 12.494 22990 Z= 0.329 Chirality : 0.043 0.164 2442 Planarity : 0.005 0.053 3001 Dihedral : 4.444 20.528 2411 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.51 % Favored : 94.44 % Rotamer: Outliers : 2.25 % Allowed : 17.05 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.05 (0.16), residues: 873 loop : -0.94 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 16 TYR 0.023 0.001 TYR L 49 PHE 0.013 0.002 PHE L 98 TRP 0.014 0.001 TRP C 47 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00450 (16841) covalent geometry : angle 0.63424 (22954) SS BOND : bond 0.00494 ( 18) SS BOND : angle 1.30175 ( 36) hydrogen bonds : bond 0.03406 ( 618) hydrogen bonds : angle 5.24425 ( 1464) *********************** 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 320 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 281 time to evaluate : 0.645 Fit side-chains REVERT: L 78 LEU cc_start: 0.7800 (tt) cc_final: 0.7445 (mt) REVERT: A 16 ARG cc_start: 0.8143 (mpp80) cc_final: 0.7800 (mtt90) REVERT: A 46 GLU cc_start: 0.7752 (pt0) cc_final: 0.7503 (pt0) REVERT: A 85 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7616 (tm-30) REVERT: A 105 GLN cc_start: 0.8618 (pp30) cc_final: 0.8171 (pp30) REVERT: K 94 ARG cc_start: 0.8824 (mtt-85) cc_final: 0.8461 (mtt-85) REVERT: N 103 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8596 (tttp) REVERT: D 16 ARG cc_start: 0.6256 (mmt180) cc_final: 0.5706 (mmm160) REVERT: O 5 THR cc_start: 0.8835 (m) cc_final: 0.8591 (p) REVERT: Q 83 GLU cc_start: 0.7956 (tt0) cc_final: 0.7606 (tp30) REVERT: I 66 ARG cc_start: 0.6576 (mtm110) cc_final: 0.6138 (mtm180) REVERT: R 27 ASN cc_start: 0.7579 (p0) cc_final: 0.7132 (p0) REVERT: R 93 ARG cc_start: 0.7360 (ttp-110) cc_final: 0.7116 (mtp-110) REVERT: J 32 TYR cc_start: 0.8564 (m-80) cc_final: 0.8165 (m-80) REVERT: J 87 THR cc_start: 0.8107 (m) cc_final: 0.7861 (m) outliers start: 39 outliers final: 32 residues processed: 306 average time/residue: 0.1344 time to fit residues: 61.8169 Evaluate side-chains 306 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 273 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain S residue 37 GLN Chi-restraints excluded: chain S residue 72 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 96 optimal weight: 0.0170 chunk 38 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.097957 restraints weight = 26198.683| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.13 r_work: 0.3023 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16859 Z= 0.111 Angle : 0.589 11.017 22990 Z= 0.302 Chirality : 0.042 0.148 2442 Planarity : 0.004 0.044 3001 Dihedral : 4.218 19.077 2411 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.81 % Favored : 95.14 % Rotamer: Outliers : 2.02 % Allowed : 17.63 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.13 (0.16), residues: 873 loop : -0.85 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 16 TYR 0.022 0.001 TYR L 49 PHE 0.008 0.001 PHE O 62 TRP 0.010 0.001 TRP I 36 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00253 (16841) covalent geometry : angle 0.58868 (22954) SS BOND : bond 0.00414 ( 18) SS BOND : angle 0.88143 ( 36) hydrogen bonds : bond 0.02935 ( 618) hydrogen bonds : angle 5.07844 ( 1464) ********************** 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 319 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 284 time to evaluate : 0.633 Fit side-chains REVERT: L 78 LEU cc_start: 0.7776 (tt) cc_final: 0.7473 (mt) REVERT: A 46 GLU cc_start: 0.7742 (pt0) cc_final: 0.7491 (pt0) REVERT: A 105 GLN cc_start: 0.8600 (pp30) cc_final: 0.8138 (pp30) REVERT: K 12 SER cc_start: 0.6483 (OUTLIER) cc_final: 0.6263 (t) REVERT: K 94 ARG cc_start: 0.8779 (mtt180) cc_final: 0.8542 (mtt180) REVERT: B 81 GLN cc_start: 0.8970 (tp40) cc_final: 0.8633 (tp40) REVERT: C 82 SER cc_start: 0.9105 (m) cc_final: 0.8794 (t) REVERT: N 103 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8567 (tttp) REVERT: O 5 THR cc_start: 0.8835 (m) cc_final: 0.8604 (p) REVERT: I 66 ARG cc_start: 0.6409 (mtm110) cc_final: 0.5892 (mtm180) REVERT: I 97 TYR cc_start: 0.8549 (t80) cc_final: 0.8285 (t80) REVERT: R 27 ASN cc_start: 0.7510 (p0) cc_final: 0.7064 (p0) REVERT: R 46 LEU cc_start: 0.8433 (tp) cc_final: 0.8198 (tp) REVERT: R 93 ARG cc_start: 0.7338 (ttp-110) cc_final: 0.7108 (mtp-110) REVERT: J 32 TYR cc_start: 0.8575 (m-80) cc_final: 0.8209 (m-80) REVERT: J 87 THR cc_start: 0.8043 (m) cc_final: 0.7779 (m) outliers start: 35 outliers final: 28 residues processed: 307 average time/residue: 0.1229 time to fit residues: 56.9019 Evaluate side-chains 304 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 274 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain N residue 51 ASN 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 84 VAL Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain S residue 37 GLN Chi-restraints excluded: chain S residue 72 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 54 optimal weight: 0.8980 chunk 178 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 123 optimal weight: 0.4980 chunk 192 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.092336 restraints weight = 26834.107| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.27 r_work: 0.2952 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16859 Z= 0.129 Angle : 0.596 11.646 22990 Z= 0.305 Chirality : 0.042 0.154 2442 Planarity : 0.004 0.044 3001 Dihedral : 4.200 19.154 2411 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.95 % Rotamer: Outliers : 2.13 % Allowed : 17.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.18), residues: 2140 helix: None (None), residues: 0 sheet: 1.17 (0.17), residues: 873 loop : -0.84 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 16 TYR 0.022 0.001 TYR L 49 PHE 0.008 0.001 PHE L 98 TRP 0.010 0.001 TRP C 47 HIS 0.003 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00299 (16841) covalent geometry : angle 0.59513 (22954) SS BOND : bond 0.00437 ( 18) SS BOND : angle 1.00519 ( 36) hydrogen bonds : bond 0.03008 ( 618) hydrogen bonds : angle 5.05786 ( 1464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4496.70 seconds wall clock time: 77 minutes 35.29 seconds (4655.29 seconds total)