Starting phenix.real_space_refine on Sat Jun 7 16:46:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dz5_27789/06_2025/8dz5_27789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dz5_27789/06_2025/8dz5_27789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dz5_27789/06_2025/8dz5_27789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dz5_27789/06_2025/8dz5_27789.map" model { file = "/net/cci-nas-00/data/ceres_data/8dz5_27789/06_2025/8dz5_27789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dz5_27789/06_2025/8dz5_27789.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.050 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 35 5.16 5 C 5655 2.51 5 N 1530 2.21 5 O 1730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8950 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 280 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 10, 'TRANS': 29} Chain: "H" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "L" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "B" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "D" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "E" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "F" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "N" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Time building chain proxies: 5.85, per 1000 atoms: 0.65 Number of scatterers: 8950 At special positions: 0 Unit cell: (72.45, 112.7, 115, 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 35 16.00 O 1730 8.00 N 1530 7.00 C 5655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 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: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 31 sheets defined 8.5% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.520A pdb=" N GLN H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.699A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.701A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 61 through 64 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 'B' and resid 79 through 83 removed outlier: 3.594A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.601A pdb=" N GLN C 64 " --> pdb=" O ASP C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.565A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.532A pdb=" N GLN E 64 " --> pdb=" O ASP E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.773A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 removed outlier: 3.556A pdb=" N GLN M 64 " --> pdb=" O ASP M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.547A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.389A pdb=" N GLY H 10 " --> pdb=" O THR H 109 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA H 93 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.649A 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 11 removed outlier: 6.389A pdb=" N GLY H 10 " --> pdb=" O THR H 109 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N CYS H 92 " --> pdb=" O TRP H 102 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TRP H 102 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS H 94 " --> pdb=" O ASP H 100C" (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.703A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA6, first strand: chain 'L' and resid 33 through 35 removed outlier: 4.151A pdb=" N GLN L 89 " --> pdb=" O ALA L 34 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AA8, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.916A pdb=" N SER A 21 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.275A pdb=" N GLY A 10 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N MET A 34 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.275A pdb=" N GLY A 10 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N CYS A 92 " --> pdb=" O TRP A 102 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TRP A 102 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS A 94 " --> pdb=" O ASP A 100C" (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.805A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.554A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN B 89 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.732A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 80 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER C 70 " --> pdb=" O PHE C 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.788A pdb=" N ALA C 93 " --> pdb=" O HIS C 35 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N MET C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ILE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.785A pdb=" N CYS C 92 " --> pdb=" O TRP C 102 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TRP C 102 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS C 94 " --> pdb=" O ASP C 100C" (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.535A pdb=" N THR D 102 " --> pdb=" O TYR D 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 35 through 37 removed outlier: 6.432A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN D 37 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.937A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 80 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.509A pdb=" N ALA E 93 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N MET E 34 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.591A pdb=" N CYS E 92 " --> pdb=" O TRP E 102 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TRP E 102 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS E 94 " --> pdb=" O ASP E 100C" (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'F' and resid 10 through 13 Processing sheet with id=AC7, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.481A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN F 89 " --> pdb=" O ALA F 34 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.776A pdb=" N SER M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU M 80 " --> pdb=" O LEU M 20 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.492A pdb=" N GLY M 10 " --> pdb=" O THR M 109 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N MET M 34 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.492A pdb=" N GLY M 10 " --> pdb=" O THR M 109 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N CYS M 92 " --> pdb=" O TRP M 102 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TRP M 102 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS M 94 " --> pdb=" O ASP M 100C" (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AD4, first strand: chain 'N' and resid 53 through 54 removed outlier: 3.506A pdb=" N GLN N 37 " --> pdb=" O LYS N 45 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU N 47 " --> pdb=" O TRP N 35 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN N 89 " --> pdb=" O ALA N 34 " (cutoff:3.500A) 335 hydrogen bonds defined for protein. 750 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: 2.39 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2879 1.34 - 1.46: 2279 1.46 - 1.58: 3956 1.58 - 1.70: 0 1.70 - 1.81: 50 Bond restraints: 9164 Sorted by residual: bond pdb=" N GLY F 64 " pdb=" CA GLY F 64 " ideal model delta sigma weight residual 1.454 1.443 0.012 9.90e-03 1.02e+04 1.35e+00 bond pdb=" CA ASP C 100C" pdb=" C ASP C 100C" ideal model delta sigma weight residual 1.521 1.532 -0.011 9.90e-03 1.02e+04 1.35e+00 bond pdb=" CB ASP H 100C" pdb=" CG ASP H 100C" ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.14e+00 bond pdb=" CB PRO I 50 " pdb=" CG PRO I 50 " ideal model delta sigma weight residual 1.492 1.544 -0.052 5.00e-02 4.00e+02 1.07e+00 bond pdb=" CB GLU N 81 " pdb=" CG GLU N 81 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.62e-01 ... (remaining 9159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 11832 1.50 - 3.00: 498 3.00 - 4.50: 76 4.50 - 6.00: 16 6.00 - 7.50: 5 Bond angle restraints: 12427 Sorted by residual: angle pdb=" CA GLU N 105 " pdb=" CB GLU N 105 " pdb=" CG GLU N 105 " ideal model delta sigma weight residual 114.10 121.39 -7.29 2.00e+00 2.50e-01 1.33e+01 angle pdb=" CA GLU N 81 " pdb=" CB GLU N 81 " pdb=" CG GLU N 81 " ideal model delta sigma weight residual 114.10 119.55 -5.45 2.00e+00 2.50e-01 7.44e+00 angle pdb=" N ILE F 29 " pdb=" CA ILE F 29 " pdb=" CB ILE F 29 " ideal model delta sigma weight residual 111.64 109.47 2.17 8.20e-01 1.49e+00 7.02e+00 angle pdb=" N LYS D 50 " pdb=" CA LYS D 50 " pdb=" C LYS D 50 " ideal model delta sigma weight residual 112.86 109.71 3.15 1.22e+00 6.72e-01 6.68e+00 angle pdb=" C ASP F 17 " pdb=" CA ASP F 17 " pdb=" CB ASP F 17 " ideal model delta sigma weight residual 109.76 114.84 -5.08 1.99e+00 2.53e-01 6.53e+00 ... (remaining 12422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4789 17.78 - 35.56: 459 35.56 - 53.34: 98 53.34 - 71.11: 26 71.11 - 88.89: 12 Dihedral angle restraints: 5384 sinusoidal: 2100 harmonic: 3284 Sorted by residual: dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual -86.00 -128.94 42.94 1 1.00e+01 1.00e-02 2.57e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual -86.00 -126.77 40.77 1 1.00e+01 1.00e-02 2.33e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 88 " pdb=" CB CYS D 88 " ideal model delta sinusoidal sigma weight residual -86.00 -123.86 37.86 1 1.00e+01 1.00e-02 2.02e+01 ... (remaining 5381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 823 0.029 - 0.059: 332 0.059 - 0.088: 81 0.088 - 0.117: 77 0.117 - 0.147: 22 Chirality restraints: 1335 Sorted by residual: chirality pdb=" CA VAL A 40 " pdb=" N VAL A 40 " pdb=" C VAL A 40 " pdb=" CB VAL A 40 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ASP C 100C" pdb=" N ASP C 100C" pdb=" C ASP C 100C" pdb=" CB ASP C 100C" both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CG LEU D 33 " pdb=" CB LEU D 33 " pdb=" CD1 LEU D 33 " pdb=" CD2 LEU D 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1332 not shown) Planarity restraints: 1594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 40 " -0.054 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO A 41 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 91 " 0.016 2.00e-02 2.50e+03 1.29e-02 3.33e+00 pdb=" CG TYR N 91 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR N 91 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR N 91 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR N 91 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR N 91 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR N 91 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR N 91 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 39 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO B 40 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 40 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 40 " 0.021 5.00e-02 4.00e+02 ... (remaining 1591 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 431 2.71 - 3.26: 8584 3.26 - 3.81: 14663 3.81 - 4.35: 17872 4.35 - 4.90: 30731 Nonbonded interactions: 72281 Sorted by model distance: nonbonded pdb=" OD1 ASP C 100C" pdb=" N TYR C 101 " model vdw 2.167 3.120 nonbonded pdb=" O TYR H 32 " pdb=" NH1 ARG H 71 " model vdw 2.221 3.120 nonbonded pdb=" O TYR C 32 " pdb=" NH1 ARG C 71 " model vdw 2.231 3.120 nonbonded pdb=" ND2 ASN I 43 " pdb=" O TYR L 91 " model vdw 2.246 3.120 nonbonded pdb=" OG1 THR E 28 " pdb=" OD2 ASP N 1 " model vdw 2.247 3.040 ... (remaining 72276 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 'C' selection = chain 'E' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'L' selection = chain 'N' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.660 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.003 0.052 9174 Z= 0.149 Angle : 0.713 7.497 12447 Z= 0.400 Chirality : 0.042 0.147 1335 Planarity : 0.004 0.081 1594 Dihedral : 15.288 88.892 3274 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.62 % Allowed : 18.34 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.27), residues: 1133 helix: None (None), residues: 0 sheet: -0.97 (0.23), residues: 495 loop : 0.25 (0.28), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 102 HIS 0.005 0.002 HIS M 35 PHE 0.016 0.002 PHE A 79 TYR 0.028 0.002 TYR N 91 ARG 0.011 0.001 ARG F 18 Details of bonding type rmsd hydrogen bonds : bond 0.26958 ( 311) hydrogen bonds : angle 11.85273 ( 750) SS BOND : bond 0.00192 ( 10) SS BOND : angle 1.01381 ( 20) covalent geometry : bond 0.00304 ( 9164) covalent geometry : angle 0.71256 (12427) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.7682 (ptpp) cc_final: 0.7476 (ptpp) REVERT: A 80 LEU cc_start: 0.7136 (tt) cc_final: 0.6845 (tt) outliers start: 6 outliers final: 5 residues processed: 138 average time/residue: 0.2491 time to fit residues: 45.2976 Evaluate side-chains 122 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 28 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN D 90 GLN M 3 GLN N 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.087856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.068158 restraints weight = 21946.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.070460 restraints weight = 13808.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.072062 restraints weight = 10014.151| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9174 Z= 0.236 Angle : 0.659 6.904 12447 Z= 0.353 Chirality : 0.045 0.166 1335 Planarity : 0.004 0.050 1594 Dihedral : 5.667 49.351 1263 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.04 % Allowed : 16.58 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.27), residues: 1133 helix: None (None), residues: 0 sheet: -1.03 (0.22), residues: 535 loop : 0.05 (0.28), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 102 HIS 0.005 0.002 HIS M 96 PHE 0.016 0.002 PHE A 79 TYR 0.018 0.002 TYR E 90 ARG 0.004 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 311) hydrogen bonds : angle 8.02671 ( 750) SS BOND : bond 0.00245 ( 10) SS BOND : angle 0.71377 ( 20) covalent geometry : bond 0.00544 ( 9164) covalent geometry : angle 0.65856 (12427) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.7434 (m-10) cc_final: 0.6515 (m-10) REVERT: B 27 GLN cc_start: 0.7069 (mm110) cc_final: 0.6847 (mm-40) REVERT: C 45 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7394 (mt) REVERT: C 100 ASP cc_start: 0.8102 (p0) cc_final: 0.7604 (p0) REVERT: C 102 TRP cc_start: 0.8862 (OUTLIER) cc_final: 0.8643 (m100) REVERT: E 100 ASP cc_start: 0.7876 (p0) cc_final: 0.7429 (t0) REVERT: N 105 GLU cc_start: 0.7147 (tp30) cc_final: 0.6393 (tm-30) outliers start: 39 outliers final: 19 residues processed: 146 average time/residue: 0.2352 time to fit residues: 46.5529 Evaluate side-chains 131 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 102 TRP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 91 TYR Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 78 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN N 89 GLN N 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.090880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.071335 restraints weight = 21593.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.073825 restraints weight = 14407.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.074750 restraints weight = 9603.790| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9174 Z= 0.115 Angle : 0.585 7.726 12447 Z= 0.310 Chirality : 0.043 0.141 1335 Planarity : 0.003 0.038 1594 Dihedral : 5.358 58.189 1260 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.01 % Allowed : 17.20 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -0.72 (0.23), residues: 515 loop : 0.12 (0.28), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 102 HIS 0.003 0.001 HIS M 35 PHE 0.011 0.001 PHE B 71 TYR 0.012 0.001 TYR E 101 ARG 0.005 0.000 ARG F 18 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 311) hydrogen bonds : angle 7.12026 ( 750) SS BOND : bond 0.00299 ( 10) SS BOND : angle 0.64970 ( 20) covalent geometry : bond 0.00261 ( 9164) covalent geometry : angle 0.58442 (12427) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 2 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8456 (mm) REVERT: A 67 PHE cc_start: 0.7377 (m-10) cc_final: 0.7135 (m-10) REVERT: C 45 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7166 (mt) REVERT: C 53 ASP cc_start: 0.7254 (p0) cc_final: 0.7014 (p0) REVERT: C 100 ASP cc_start: 0.8046 (p0) cc_final: 0.7762 (p0) REVERT: E 53 ASP cc_start: 0.8162 (p0) cc_final: 0.7614 (p0) REVERT: F 17 ASP cc_start: 0.7851 (t0) cc_final: 0.7647 (t0) REVERT: N 46 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8639 (tt) REVERT: N 90 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7460 (pm20) REVERT: N 105 GLU cc_start: 0.7340 (tp30) cc_final: 0.6894 (tm-30) outliers start: 29 outliers final: 15 residues processed: 146 average time/residue: 0.2648 time to fit residues: 50.7190 Evaluate side-chains 132 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 90 GLN Chi-restraints excluded: chain N residue 91 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 13 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN D 90 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN M 3 GLN N 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.089546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.069983 restraints weight = 21999.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.072311 restraints weight = 13586.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.073942 restraints weight = 9738.777| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9174 Z= 0.187 Angle : 0.608 6.229 12447 Z= 0.322 Chirality : 0.043 0.142 1335 Planarity : 0.004 0.034 1594 Dihedral : 5.482 57.057 1260 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.15 % Allowed : 17.51 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -0.91 (0.22), residues: 535 loop : 0.22 (0.28), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 102 HIS 0.004 0.001 HIS A 35 PHE 0.011 0.001 PHE B 71 TYR 0.015 0.002 TYR M 91 ARG 0.006 0.001 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03280 ( 311) hydrogen bonds : angle 6.94744 ( 750) SS BOND : bond 0.00265 ( 10) SS BOND : angle 0.90908 ( 20) covalent geometry : bond 0.00434 ( 9164) covalent geometry : angle 0.60774 (12427) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 2 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8536 (mm) REVERT: B 17 ASP cc_start: 0.7062 (t0) cc_final: 0.6159 (m-30) REVERT: B 24 ARG cc_start: 0.7948 (ttm110) cc_final: 0.7710 (ttm-80) REVERT: C 45 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7291 (mt) REVERT: C 53 ASP cc_start: 0.7339 (p0) cc_final: 0.7109 (p0) REVERT: E 53 ASP cc_start: 0.8232 (p0) cc_final: 0.7708 (p0) REVERT: E 82 MET cc_start: 0.8619 (tpp) cc_final: 0.8230 (mmt) REVERT: E 100 ASP cc_start: 0.7783 (p0) cc_final: 0.7554 (t0) REVERT: F 18 ARG cc_start: 0.8621 (tmm-80) cc_final: 0.8320 (ttp80) REVERT: M 11 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8463 (m) REVERT: M 82 MET cc_start: 0.7898 (mtt) cc_final: 0.7672 (mtt) REVERT: N 46 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8643 (tt) REVERT: N 58 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7937 (p) REVERT: N 105 GLU cc_start: 0.7374 (tp30) cc_final: 0.6932 (tm-30) outliers start: 40 outliers final: 26 residues processed: 140 average time/residue: 0.2466 time to fit residues: 46.4321 Evaluate side-chains 136 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 91 TYR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 63 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN N 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.088809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.069285 restraints weight = 22033.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.071595 restraints weight = 13666.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.073186 restraints weight = 9829.667| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9174 Z= 0.209 Angle : 0.615 7.676 12447 Z= 0.327 Chirality : 0.044 0.211 1335 Planarity : 0.004 0.033 1594 Dihedral : 5.383 58.824 1258 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.77 % Allowed : 17.62 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -0.95 (0.22), residues: 535 loop : 0.16 (0.28), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 35 HIS 0.004 0.001 HIS A 35 PHE 0.016 0.002 PHE A 79 TYR 0.017 0.002 TYR B 91 ARG 0.006 0.000 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 311) hydrogen bonds : angle 6.84040 ( 750) SS BOND : bond 0.00308 ( 10) SS BOND : angle 0.89500 ( 20) covalent geometry : bond 0.00483 ( 9164) covalent geometry : angle 0.61476 (12427) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 2 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8507 (mm) REVERT: L 45 LYS cc_start: 0.8774 (pttt) cc_final: 0.8371 (pttm) REVERT: B 17 ASP cc_start: 0.7234 (t0) cc_final: 0.6203 (m-30) REVERT: B 105 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7804 (mm-30) REVERT: C 45 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7420 (mt) REVERT: C 100 ASP cc_start: 0.7820 (p0) cc_final: 0.7571 (p0) REVERT: E 53 ASP cc_start: 0.8278 (p0) cc_final: 0.7718 (p0) REVERT: E 82 MET cc_start: 0.8610 (tpp) cc_final: 0.8188 (mmt) REVERT: E 100 ASP cc_start: 0.7818 (p0) cc_final: 0.7507 (t0) REVERT: M 82 MET cc_start: 0.7915 (mtt) cc_final: 0.7713 (mtt) REVERT: N 105 GLU cc_start: 0.7193 (tp30) cc_final: 0.6602 (tm-30) outliers start: 46 outliers final: 29 residues processed: 158 average time/residue: 0.2537 time to fit residues: 53.4052 Evaluate side-chains 142 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 91 TYR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 94 optimal weight: 0.0010 overall best weight: 1.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN M 3 GLN N 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.097601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.076873 restraints weight = 21109.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.079138 restraints weight = 13927.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.080688 restraints weight = 10349.067| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9174 Z= 0.142 Angle : 0.603 8.403 12447 Z= 0.315 Chirality : 0.043 0.163 1335 Planarity : 0.003 0.030 1594 Dihedral : 5.149 56.655 1258 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.15 % Allowed : 18.03 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -0.90 (0.22), residues: 530 loop : 0.24 (0.28), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 35 HIS 0.003 0.001 HIS A 35 PHE 0.013 0.001 PHE A 79 TYR 0.015 0.002 TYR H 90 ARG 0.007 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03010 ( 311) hydrogen bonds : angle 6.54432 ( 750) SS BOND : bond 0.00254 ( 10) SS BOND : angle 0.92358 ( 20) covalent geometry : bond 0.00332 ( 9164) covalent geometry : angle 0.60257 (12427) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 2 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8436 (mm) REVERT: L 45 LYS cc_start: 0.8782 (pttt) cc_final: 0.8371 (pttm) REVERT: B 17 ASP cc_start: 0.7233 (t0) cc_final: 0.6138 (m-30) REVERT: B 105 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7768 (mm-30) REVERT: C 45 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7219 (mt) REVERT: C 53 ASP cc_start: 0.7606 (p0) cc_final: 0.7301 (p0) REVERT: E 53 ASP cc_start: 0.8251 (p0) cc_final: 0.7683 (p0) REVERT: E 82 MET cc_start: 0.8591 (tpp) cc_final: 0.8168 (mmt) REVERT: F 18 ARG cc_start: 0.8609 (tmm-80) cc_final: 0.8393 (ttp80) outliers start: 40 outliers final: 28 residues processed: 158 average time/residue: 0.2651 time to fit residues: 55.4055 Evaluate side-chains 149 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 91 TYR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 84 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 0.0020 chunk 107 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 27 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN M 3 GLN N 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.091969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.072466 restraints weight = 21733.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.074892 restraints weight = 13280.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076554 restraints weight = 9429.100| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9174 Z= 0.118 Angle : 0.618 9.756 12447 Z= 0.318 Chirality : 0.043 0.222 1335 Planarity : 0.003 0.028 1594 Dihedral : 4.953 54.324 1258 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.32 % Allowed : 18.96 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.27), residues: 1133 helix: None (None), residues: 0 sheet: -0.79 (0.23), residues: 530 loop : 0.31 (0.28), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 35 HIS 0.002 0.001 HIS A 35 PHE 0.009 0.001 PHE H 52A TYR 0.021 0.001 TYR B 91 ARG 0.006 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.02840 ( 311) hydrogen bonds : angle 6.34553 ( 750) SS BOND : bond 0.00280 ( 10) SS BOND : angle 1.00851 ( 20) covalent geometry : bond 0.00277 ( 9164) covalent geometry : angle 0.61742 (12427) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 2 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8355 (mm) REVERT: L 45 LYS cc_start: 0.8709 (pttt) cc_final: 0.8331 (pttm) REVERT: A 19 ARG cc_start: 0.7310 (ttt-90) cc_final: 0.6580 (ttt-90) REVERT: B 17 ASP cc_start: 0.7288 (t0) cc_final: 0.6252 (m-30) REVERT: B 105 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7717 (tm-30) REVERT: C 45 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7158 (mt) REVERT: C 53 ASP cc_start: 0.7342 (p0) cc_final: 0.7090 (p0) REVERT: E 17 SER cc_start: 0.9098 (m) cc_final: 0.8839 (p) REVERT: E 53 ASP cc_start: 0.8254 (p0) cc_final: 0.7699 (p0) REVERT: E 82 MET cc_start: 0.8555 (tpp) cc_final: 0.8147 (mmt) REVERT: N 90 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7293 (pm20) outliers start: 32 outliers final: 24 residues processed: 158 average time/residue: 0.2398 time to fit residues: 50.9348 Evaluate side-chains 152 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 90 GLN Chi-restraints excluded: chain N residue 91 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 40 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN M 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.089425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.069595 restraints weight = 22038.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.071940 restraints weight = 13655.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.073593 restraints weight = 9854.165| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9174 Z= 0.175 Angle : 0.649 10.036 12447 Z= 0.334 Chirality : 0.043 0.235 1335 Planarity : 0.004 0.062 1594 Dihedral : 5.116 52.349 1258 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.94 % Allowed : 19.38 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.27), residues: 1133 helix: None (None), residues: 0 sheet: -0.77 (0.23), residues: 530 loop : 0.27 (0.28), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 35 HIS 0.004 0.001 HIS A 35 PHE 0.013 0.001 PHE A 67 TYR 0.019 0.002 TYR B 91 ARG 0.019 0.001 ARG M 83 Details of bonding type rmsd hydrogen bonds : bond 0.02947 ( 311) hydrogen bonds : angle 6.42297 ( 750) SS BOND : bond 0.00219 ( 10) SS BOND : angle 1.17331 ( 20) covalent geometry : bond 0.00409 ( 9164) covalent geometry : angle 0.64769 (12427) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8796 (pttt) cc_final: 0.8431 (pttm) REVERT: A 19 ARG cc_start: 0.7376 (ttt-90) cc_final: 0.6746 (ttt-90) REVERT: A 100 GLN cc_start: 0.7043 (OUTLIER) cc_final: 0.4258 (mp10) REVERT: B 17 ASP cc_start: 0.7349 (t0) cc_final: 0.6381 (m-30) REVERT: B 105 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7636 (tm-30) REVERT: C 45 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7152 (mt) REVERT: C 53 ASP cc_start: 0.7465 (p0) cc_final: 0.7177 (p0) REVERT: E 17 SER cc_start: 0.9065 (m) cc_final: 0.8815 (p) REVERT: E 53 ASP cc_start: 0.8309 (p0) cc_final: 0.7699 (p0) REVERT: E 82 MET cc_start: 0.8524 (tpp) cc_final: 0.8125 (mmt) REVERT: N 30 SER cc_start: 0.7351 (OUTLIER) cc_final: 0.7097 (p) outliers start: 38 outliers final: 31 residues processed: 156 average time/residue: 0.2393 time to fit residues: 50.0302 Evaluate side-chains 154 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 91 TYR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN M 3 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.098167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.077770 restraints weight = 21316.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.080356 restraints weight = 14389.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.080986 restraints weight = 10325.446| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9174 Z= 0.159 Angle : 0.659 10.424 12447 Z= 0.338 Chirality : 0.043 0.222 1335 Planarity : 0.004 0.048 1594 Dihedral : 5.101 52.293 1258 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.52 % Allowed : 20.21 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.27), residues: 1133 helix: None (None), residues: 0 sheet: -0.67 (0.23), residues: 520 loop : 0.16 (0.28), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 35 HIS 0.004 0.001 HIS A 35 PHE 0.009 0.001 PHE B 71 TYR 0.023 0.002 TYR B 91 ARG 0.015 0.001 ARG M 83 Details of bonding type rmsd hydrogen bonds : bond 0.02882 ( 311) hydrogen bonds : angle 6.37267 ( 750) SS BOND : bond 0.00241 ( 10) SS BOND : angle 1.02153 ( 20) covalent geometry : bond 0.00373 ( 9164) covalent geometry : angle 0.65825 (12427) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8790 (pttt) cc_final: 0.8379 (pttm) REVERT: A 19 ARG cc_start: 0.7335 (ttt-90) cc_final: 0.6872 (ttt-90) REVERT: A 57 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7436 (ptmt) REVERT: B 17 ASP cc_start: 0.7333 (t0) cc_final: 0.6305 (m-30) REVERT: B 105 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7745 (tm-30) REVERT: C 45 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7134 (mt) REVERT: C 53 ASP cc_start: 0.7636 (p0) cc_final: 0.7372 (p0) REVERT: E 17 SER cc_start: 0.9052 (m) cc_final: 0.8815 (p) REVERT: E 53 ASP cc_start: 0.8310 (p0) cc_final: 0.7991 (p0) REVERT: E 82 MET cc_start: 0.8560 (tpp) cc_final: 0.8108 (mmt) REVERT: E 100 ASP cc_start: 0.7868 (p0) cc_final: 0.7663 (t0) REVERT: N 30 SER cc_start: 0.7425 (OUTLIER) cc_final: 0.7173 (p) outliers start: 34 outliers final: 29 residues processed: 155 average time/residue: 0.2541 time to fit residues: 52.5922 Evaluate side-chains 154 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 chunk 67 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.096264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.076653 restraints weight = 22038.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.078223 restraints weight = 15485.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.079524 restraints weight = 11733.221| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 9174 Z= 0.242 Angle : 0.686 8.189 12447 Z= 0.358 Chirality : 0.045 0.230 1335 Planarity : 0.004 0.051 1594 Dihedral : 5.382 50.953 1258 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.25 % Allowed : 19.48 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -0.80 (0.23), residues: 520 loop : -0.00 (0.28), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 35 HIS 0.005 0.002 HIS A 35 PHE 0.011 0.002 PHE A 29 TYR 0.022 0.002 TYR B 91 ARG 0.014 0.001 ARG M 83 Details of bonding type rmsd hydrogen bonds : bond 0.03120 ( 311) hydrogen bonds : angle 6.59364 ( 750) SS BOND : bond 0.00197 ( 10) SS BOND : angle 1.16313 ( 20) covalent geometry : bond 0.00563 ( 9164) covalent geometry : angle 0.68480 (12427) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8854 (pttt) cc_final: 0.8407 (pttm) REVERT: A 19 ARG cc_start: 0.7410 (ttt-90) cc_final: 0.6816 (ttt-90) REVERT: A 57 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7625 (ptmt) REVERT: A 100 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.4205 (mp10) REVERT: B 17 ASP cc_start: 0.7493 (t0) cc_final: 0.6331 (m-30) REVERT: B 105 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7781 (tm-30) REVERT: C 45 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7593 (mt) REVERT: C 53 ASP cc_start: 0.7713 (p0) cc_final: 0.7454 (p0) REVERT: E 17 SER cc_start: 0.9109 (m) cc_final: 0.8835 (p) REVERT: E 53 ASP cc_start: 0.8307 (p0) cc_final: 0.7966 (p0) REVERT: E 82 MET cc_start: 0.8586 (tpp) cc_final: 0.8112 (mmt) outliers start: 41 outliers final: 32 residues processed: 158 average time/residue: 0.2408 time to fit residues: 51.0192 Evaluate side-chains 154 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 91 TYR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 45 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN M 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.094461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.074532 restraints weight = 21743.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.076951 restraints weight = 13482.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.078588 restraints weight = 9690.688| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9174 Z= 0.121 Angle : 0.655 8.929 12447 Z= 0.334 Chirality : 0.043 0.207 1335 Planarity : 0.004 0.042 1594 Dihedral : 5.015 52.331 1258 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.59 % Allowed : 20.73 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.27), residues: 1133 helix: None (None), residues: 0 sheet: -0.67 (0.23), residues: 520 loop : 0.17 (0.28), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.003 0.001 HIS A 35 PHE 0.011 0.001 PHE H 52A TYR 0.021 0.001 TYR B 91 ARG 0.014 0.001 ARG M 83 Details of bonding type rmsd hydrogen bonds : bond 0.02790 ( 311) hydrogen bonds : angle 6.30534 ( 750) SS BOND : bond 0.00239 ( 10) SS BOND : angle 1.09527 ( 20) covalent geometry : bond 0.00285 ( 9164) covalent geometry : angle 0.65358 (12427) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3008.11 seconds wall clock time: 53 minutes 5.79 seconds (3185.79 seconds total)