Starting phenix.real_space_refine on Thu Mar 13 11:45:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dz5_27789/03_2025/8dz5_27789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dz5_27789/03_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_27789/03_2025/8dz5_27789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dz5_27789/03_2025/8dz5_27789.map" model { file = "/net/cci-nas-00/data/ceres_data/8dz5_27789/03_2025/8dz5_27789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dz5_27789/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.83, 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: 2.21 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: 1.49 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: 2.68 Time building geometry restraints manager: 2.63 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.220 Find NCS groups from input model: 0.390 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.890 ------------------------------------------------------------------------------- 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 9164 Z= 0.189 Angle : 0.713 7.497 12427 Z= 0.399 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 *********************** 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 : 1.027 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: 0.2653 time to fit residues: 48.1162 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 : 1.074 ------------------------------------------------------------------------------- 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 9164 Z= 0.355 Angle : 0.659 6.904 12427 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 *********************** 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 : 1.022 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: 0.2377 time to fit residues: 46.7972 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 : 1.021 ------------------------------------------------------------------------------- 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: 9.9990 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 9164 Z= 0.166 Angle : 0.584 7.726 12427 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 *********************** 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 : 1.004 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: 0.2751 time to fit residues: 52.2844 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 : 1.163 ------------------------------------------------------------------------------- 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: 9.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 95 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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** ** L 90 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.090025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.070207 restraints weight = 21600.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072616 restraints weight = 13383.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.074249 restraints weight = 9591.047| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9164 Z= 0.212 Angle : 0.585 6.326 12427 Z= 0.308 Chirality : 0.043 0.141 1335 Planarity : 0.003 0.033 1594 Dihedral : 5.345 57.702 1260 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.52 % Allowed : 17.93 % Favored : 78.55 % 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 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -0.78 (0.23), residues: 530 loop : 0.29 (0.28), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 102 HIS 0.003 0.001 HIS A 35 PHE 0.011 0.001 PHE B 71 TYR 0.012 0.002 TYR M 91 ARG 0.005 0.000 ARG A 19 *********************** 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 153 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 ASP cc_start: 0.6982 (t0) cc_final: 0.6141 (m-30) REVERT: C 45 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7118 (mt) REVERT: C 53 ASP cc_start: 0.7306 (p0) cc_final: 0.7076 (p0) REVERT: E 53 ASP cc_start: 0.8184 (p0) cc_final: 0.7666 (p0) REVERT: E 82 MET cc_start: 0.8560 (tpp) cc_final: 0.8215 (mmt) REVERT: E 100 ASP cc_start: 0.7757 (p0) cc_final: 0.7514 (t0) REVERT: F 18 ARG cc_start: 0.8559 (tmm-80) cc_final: 0.8263 (ttp80) REVERT: M 11 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8428 (m) REVERT: N 58 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7973 (p) outliers start: 34 outliers final: 22 residues processed: 143 average time/residue: 0.2525 time to fit residues: 48.1184 Evaluate side-chains 134 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 TYR 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 B residue 106 ILE 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 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 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: 8.9990 chunk 81 optimal weight: 7.9990 chunk 61 optimal weight: 0.0000 chunk 90 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.088514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.069077 restraints weight = 22006.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.071357 restraints weight = 13669.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.072930 restraints weight = 9855.744| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9164 Z= 0.352 Angle : 0.645 7.462 12427 Z= 0.340 Chirality : 0.044 0.207 1335 Planarity : 0.004 0.033 1594 Dihedral : 5.466 59.223 1258 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.46 % Allowed : 17.72 % 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: -0.73 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -0.93 (0.22), residues: 535 loop : 0.16 (0.28), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 35 HIS 0.004 0.002 HIS A 35 PHE 0.016 0.002 PHE A 79 TYR 0.019 0.002 TYR B 91 ARG 0.006 0.000 ARG F 24 *********************** 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 161 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 ASP cc_start: 0.7165 (t0) cc_final: 0.6116 (m-30) REVERT: B 105 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7775 (mm-30) REVERT: C 45 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7450 (mt) REVERT: C 53 ASP cc_start: 0.7646 (p0) cc_final: 0.7427 (p0) REVERT: C 100 ASP cc_start: 0.7877 (p0) cc_final: 0.7593 (p0) REVERT: E 53 ASP cc_start: 0.8285 (p0) cc_final: 0.7727 (p0) REVERT: E 82 MET cc_start: 0.8628 (tpp) cc_final: 0.8186 (mmt) REVERT: E 100 ASP cc_start: 0.7770 (p0) cc_final: 0.7467 (t0) REVERT: M 82 SER cc_start: 0.9293 (m) cc_final: 0.9060 (p) outliers start: 43 outliers final: 29 residues processed: 149 average time/residue: 0.2529 time to fit residues: 49.9175 Evaluate side-chains 140 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 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 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 91 TYR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 ILE 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 Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.097372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.077095 restraints weight = 21134.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.079884 restraints weight = 14450.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.080577 restraints weight = 10220.688| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9164 Z= 0.230 Angle : 0.610 8.765 12427 Z= 0.318 Chirality : 0.043 0.158 1335 Planarity : 0.004 0.030 1594 Dihedral : 5.197 57.392 1258 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.73 % Allowed : 18.24 % Favored : 78.03 % 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: -0.65 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -0.86 (0.23), residues: 530 loop : 0.18 (0.28), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 35 HIS 0.003 0.001 HIS A 35 PHE 0.014 0.001 PHE A 79 TYR 0.026 0.002 TYR B 91 ARG 0.007 0.000 ARG F 24 *********************** 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 162 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8820 (pttt) cc_final: 0.8401 (pttm) REVERT: A 19 ARG cc_start: 0.7284 (ttt-90) cc_final: 0.6814 (ttt-90) REVERT: B 11 LEU cc_start: 0.7920 (tp) cc_final: 0.7719 (tp) REVERT: B 17 ASP cc_start: 0.7255 (t0) cc_final: 0.6105 (m-30) REVERT: B 24 ARG cc_start: 0.7799 (ttm-80) cc_final: 0.7510 (ttm-80) REVERT: B 105 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7796 (mm-30) REVERT: C 45 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7233 (mt) REVERT: C 53 ASP cc_start: 0.7404 (p0) cc_final: 0.7169 (p0) REVERT: E 53 ASP cc_start: 0.8314 (p0) cc_final: 0.7732 (p0) REVERT: E 82 MET cc_start: 0.8570 (tpp) cc_final: 0.8121 (mmt) REVERT: F 18 ARG cc_start: 0.8663 (tmm-80) cc_final: 0.8408 (ttp80) REVERT: M 82 SER cc_start: 0.9379 (m) cc_final: 0.9106 (p) outliers start: 36 outliers final: 29 residues processed: 152 average time/residue: 0.2455 time to fit residues: 49.3542 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 : 0.962 ------------------------------------------------------------------------------- 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 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 33 LEU 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 D residue 106 ILE Chi-restraints excluded: chain E residue 50 ILE 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 45 LEU Chi-restraints excluded: chain M residue 99 GLU 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: 5.9990 chunk 63 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 105 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.089970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.070568 restraints weight = 21966.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.072873 restraints weight = 13555.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.074476 restraints weight = 9726.714| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9164 Z= 0.249 Angle : 0.618 7.666 12427 Z= 0.324 Chirality : 0.044 0.231 1335 Planarity : 0.003 0.029 1594 Dihedral : 5.150 54.904 1258 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.94 % Allowed : 18.34 % 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: -0.63 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -0.84 (0.23), residues: 530 loop : 0.19 (0.28), residues: 603 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 0.018 0.002 TYR B 91 ARG 0.005 0.000 ARG A 19 *********************** 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 162 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8826 (pttt) cc_final: 0.8398 (pttm) REVERT: A 19 ARG cc_start: 0.7345 (ttt-90) cc_final: 0.6705 (ttt-90) REVERT: A 100 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.4207 (mp10) REVERT: B 17 ASP cc_start: 0.7379 (t0) cc_final: 0.6416 (m-30) REVERT: B 105 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7707 (tm-30) REVERT: C 45 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7261 (mt) REVERT: C 53 ASP cc_start: 0.7369 (p0) cc_final: 0.7119 (p0) REVERT: E 53 ASP cc_start: 0.8303 (p0) cc_final: 0.7991 (p0) REVERT: E 82 MET cc_start: 0.8581 (tpp) cc_final: 0.8134 (mmt) REVERT: F 18 ARG cc_start: 0.8416 (tmm-80) cc_final: 0.8157 (ttp80) REVERT: M 82 SER cc_start: 0.9321 (m) cc_final: 0.9063 (p) REVERT: M 99 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6621 (tt0) REVERT: N 30 SER cc_start: 0.7392 (OUTLIER) cc_final: 0.7172 (p) outliers start: 38 outliers final: 31 residues processed: 152 average time/residue: 0.2431 time to fit residues: 49.0890 Evaluate side-chains 149 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 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 97 THR 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 102 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 50 ILE 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 45 LEU Chi-restraints excluded: chain M residue 99 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.088807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.069624 restraints weight = 22325.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.071909 restraints weight = 13715.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.073480 restraints weight = 9815.978| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9164 Z= 0.307 Angle : 0.663 10.455 12427 Z= 0.341 Chirality : 0.044 0.241 1335 Planarity : 0.004 0.030 1594 Dihedral : 5.269 53.172 1258 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.46 % Allowed : 18.65 % Favored : 76.89 % 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: -0.71 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -0.81 (0.23), residues: 525 loop : 0.04 (0.28), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 35 HIS 0.005 0.001 HIS A 35 PHE 0.013 0.001 PHE A 67 TYR 0.022 0.002 TYR B 91 ARG 0.005 0.000 ARG A 19 *********************** 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 160 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8835 (pttt) cc_final: 0.8405 (pttm) REVERT: A 57 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7430 (ptmt) REVERT: A 75 LYS cc_start: 0.7759 (ptpp) cc_final: 0.7554 (ptpp) REVERT: A 100 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.4099 (mp10) REVERT: B 17 ASP cc_start: 0.7451 (t0) cc_final: 0.6404 (m-30) REVERT: B 105 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7653 (tm-30) REVERT: C 45 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7522 (mt) REVERT: C 53 ASP cc_start: 0.7545 (p0) cc_final: 0.7293 (p0) REVERT: E 17 SER cc_start: 0.9031 (m) cc_final: 0.8768 (p) REVERT: E 53 ASP cc_start: 0.8333 (p0) cc_final: 0.7996 (p0) REVERT: E 82 MET cc_start: 0.8536 (tpp) cc_final: 0.8097 (mmt) REVERT: M 3 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8584 (pp30) REVERT: M 82 SER cc_start: 0.9322 (m) cc_final: 0.9066 (p) outliers start: 43 outliers final: 37 residues processed: 153 average time/residue: 0.2353 time to fit residues: 48.1231 Evaluate side-chains 153 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 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 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 97 THR 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 D residue 106 ILE Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 69 ILE 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 3 GLN 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 M residue 99 GLU 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: 0.1980 chunk 36 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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** ** 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 ** 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 = 0.3525 r_free = 0.3525 target = 0.089697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.070029 restraints weight = 22264.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.072290 restraints weight = 13919.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.073865 restraints weight = 10098.023| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9164 Z= 0.279 Angle : 0.663 10.521 12427 Z= 0.341 Chirality : 0.044 0.230 1335 Planarity : 0.004 0.046 1594 Dihedral : 5.248 51.138 1258 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.56 % Allowed : 18.96 % Favored : 76.48 % 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: -0.77 (0.23), residues: 520 loop : 0.03 (0.28), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 35 HIS 0.004 0.001 HIS A 35 PHE 0.009 0.001 PHE A 29 TYR 0.021 0.002 TYR B 91 ARG 0.009 0.000 ARG F 18 *********************** 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 160 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 116 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8823 (pttt) cc_final: 0.8393 (pttm) REVERT: A 19 ARG cc_start: 0.7522 (mmm-85) cc_final: 0.6913 (ttt-90) REVERT: A 57 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7363 (ptmt) REVERT: A 75 LYS cc_start: 0.7742 (ptpp) cc_final: 0.7464 (pttm) REVERT: A 100 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.4062 (mp10) REVERT: B 17 ASP cc_start: 0.7495 (t0) cc_final: 0.6405 (m-30) REVERT: B 105 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7702 (tm-30) REVERT: C 45 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7515 (mt) REVERT: C 53 ASP cc_start: 0.7572 (p0) cc_final: 0.7309 (p0) REVERT: E 17 SER cc_start: 0.9094 (m) cc_final: 0.8832 (p) REVERT: E 53 ASP cc_start: 0.8274 (p0) cc_final: 0.7947 (p0) REVERT: E 72 ASP cc_start: 0.8591 (t0) cc_final: 0.8391 (t70) REVERT: E 82 MET cc_start: 0.8545 (tpp) cc_final: 0.8084 (mmt) REVERT: M 82 SER cc_start: 0.9339 (m) cc_final: 0.9090 (p) REVERT: M 99 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6655 (tt0) REVERT: N 30 SER cc_start: 0.7242 (OUTLIER) cc_final: 0.7022 (p) outliers start: 44 outliers final: 34 residues processed: 152 average time/residue: 0.2331 time to fit residues: 47.6780 Evaluate side-chains 151 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 88 CYS Chi-restraints excluded: chain B residue 97 THR 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 D residue 106 ILE Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 69 ILE 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 45 LEU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 99 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** ** 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 ** 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 = 0.3512 r_free = 0.3512 target = 0.088440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.068554 restraints weight = 21989.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.070949 restraints weight = 13569.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.072582 restraints weight = 9710.022| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9164 Z= 0.293 Angle : 0.669 8.879 12427 Z= 0.344 Chirality : 0.044 0.226 1335 Planarity : 0.004 0.063 1594 Dihedral : 5.252 50.246 1258 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.56 % Allowed : 18.96 % Favored : 76.48 % 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: -0.71 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -0.81 (0.23), residues: 520 loop : 0.02 (0.28), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 35 HIS 0.005 0.001 HIS A 35 PHE 0.017 0.001 PHE A 67 TYR 0.019 0.002 TYR B 91 ARG 0.015 0.001 ARG M 83 ********************** 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: 44 poor density : 119 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8823 (pttt) cc_final: 0.8386 (pttm) REVERT: A 19 ARG cc_start: 0.7616 (mmm-85) cc_final: 0.6960 (ttt-90) REVERT: A 57 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7352 (ptmt) REVERT: A 75 LYS cc_start: 0.7742 (ptpp) cc_final: 0.7468 (pttm) REVERT: A 100 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.4063 (mp10) REVERT: B 17 ASP cc_start: 0.7579 (t0) cc_final: 0.6395 (m-30) REVERT: B 105 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7734 (tm-30) REVERT: C 45 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7529 (mt) REVERT: E 17 SER cc_start: 0.9097 (m) cc_final: 0.8818 (p) REVERT: E 53 ASP cc_start: 0.8297 (p0) cc_final: 0.7956 (p0) REVERT: E 72 ASP cc_start: 0.8606 (t0) cc_final: 0.8395 (t70) REVERT: E 82 MET cc_start: 0.8567 (tpp) cc_final: 0.8107 (mmt) REVERT: M 82 SER cc_start: 0.9342 (m) cc_final: 0.9078 (p) REVERT: N 30 SER cc_start: 0.7317 (OUTLIER) cc_final: 0.7035 (p) outliers start: 44 outliers final: 37 residues processed: 156 average time/residue: 0.2520 time to fit residues: 52.3429 Evaluate side-chains 158 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 88 CYS Chi-restraints excluded: chain B residue 97 THR 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 D residue 106 ILE Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 69 ILE 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 28 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 99 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 45 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 103 optimal weight: 0.0470 chunk 5 optimal weight: 0.0770 chunk 84 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.9840 ------------------------------------------------------------------------------- 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** ** B 90 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.089452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.069537 restraints weight = 21994.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.071910 restraints weight = 13718.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.073549 restraints weight = 9887.697| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9164 Z= 0.248 Angle : 0.674 10.311 12427 Z= 0.342 Chirality : 0.044 0.221 1335 Planarity : 0.004 0.058 1594 Dihedral : 5.143 50.138 1258 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.25 % Allowed : 19.17 % Favored : 76.58 % 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: -0.66 (0.26), residues: 1133 helix: None (None), residues: 0 sheet: -0.79 (0.23), residues: 520 loop : 0.07 (0.28), residues: 613 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 0.009 0.001 PHE H 52A TYR 0.018 0.002 TYR H 90 ARG 0.016 0.001 ARG M 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2874.50 seconds wall clock time: 50 minutes 53.56 seconds (3053.56 seconds total)