Starting phenix.real_space_refine on Mon Dec 30 05:48:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d64_27216/12_2024/8d64_27216.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d64_27216/12_2024/8d64_27216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d64_27216/12_2024/8d64_27216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d64_27216/12_2024/8d64_27216.map" model { file = "/net/cci-nas-00/data/ceres_data/8d64_27216/12_2024/8d64_27216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d64_27216/12_2024/8d64_27216.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 8175 2.51 5 N 2085 2.21 5 O 2250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12545 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'DHL': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D Time building chain proxies: 5.19, per 1000 atoms: 0.41 Number of scatterers: 12545 At special positions: 0 Unit cell: (90.2, 90.2, 123.2, 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 2250 8.00 N 2085 7.00 C 8175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 1.6 seconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 32.5% alpha, 36.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 62 through 69 removed outlier: 3.654A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 208 through 221 removed outlier: 3.531A pdb=" N LEU A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 249 Processing helix chain 'A' and resid 260 through 286 Processing helix chain 'A' and resid 302 through 317 Processing helix chain 'B' and resid 62 through 69 removed outlier: 3.653A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.531A pdb=" N LEU B 212 " --> pdb=" O PHE B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 249 Processing helix chain 'B' and resid 260 through 286 Processing helix chain 'B' and resid 302 through 317 Processing helix chain 'C' and resid 62 through 69 removed outlier: 3.653A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN C 69 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.531A pdb=" N LEU C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 249 Processing helix chain 'C' and resid 260 through 286 Processing helix chain 'C' and resid 302 through 317 Processing helix chain 'D' and resid 62 through 69 removed outlier: 3.653A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 208 through 221 removed outlier: 3.530A pdb=" N LEU D 212 " --> pdb=" O PHE D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 249 Processing helix chain 'D' and resid 260 through 286 Processing helix chain 'D' and resid 302 through 317 Processing helix chain 'E' and resid 62 through 69 removed outlier: 3.653A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 208 through 221 removed outlier: 3.531A pdb=" N LEU E 212 " --> pdb=" O PHE E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 249 Processing helix chain 'E' and resid 260 through 286 Processing helix chain 'E' and resid 302 through 317 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 5.294A pdb=" N THR A 87 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 107 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASN A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR A 32 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 26 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR A 38 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE A 20 " --> pdb=" O TYR A 38 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL A 40 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE A 18 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLN A 42 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL A 16 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N THR A 44 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL A 14 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL A 12 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N SER A 143 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL A 14 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE A 145 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL A 16 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 147 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE A 18 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.521A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.521A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 58 removed outlier: 5.293A pdb=" N THR B 87 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 107 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASN B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR B 32 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL B 26 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR B 38 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE B 20 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL B 40 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE B 18 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLN B 42 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL B 16 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR B 44 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL B 14 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL B 12 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N SER B 143 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL B 14 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 145 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL B 16 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 147 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE B 18 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.521A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.521A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 58 removed outlier: 5.293A pdb=" N THR C 87 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU C 107 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASN C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL C 26 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR C 38 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE C 20 " --> pdb=" O TYR C 38 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL C 40 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE C 18 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLN C 42 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL C 16 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N THR C 44 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL C 14 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL C 12 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N SER C 143 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL C 14 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE C 145 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL C 16 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL C 147 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE C 18 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.521A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.521A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 58 removed outlier: 5.294A pdb=" N THR D 87 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU D 107 " --> pdb=" O THR D 87 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASN D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR D 32 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL D 26 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TYR D 38 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILE D 20 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL D 40 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE D 18 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLN D 42 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL D 16 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR D 44 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL D 14 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL D 12 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N SER D 143 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL D 14 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE D 145 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL D 16 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL D 147 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE D 18 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.522A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.522A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 56 through 58 removed outlier: 5.293A pdb=" N THR E 87 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU E 107 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASN E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR E 32 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL E 26 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TYR E 38 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE E 20 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL E 40 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE E 18 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLN E 42 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL E 16 " --> pdb=" O GLN E 42 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR E 44 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL E 14 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL E 12 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N SER E 143 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL E 14 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE E 145 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL E 16 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL E 147 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE E 18 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.521A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.521A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1830 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 3.52 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: 3947 1.34 - 1.46: 2403 1.46 - 1.57: 6475 1.57 - 1.69: 0 1.69 - 1.81: 55 Bond restraints: 12880 Sorted by residual: bond pdb=" N ASP D 158 " pdb=" CA ASP D 158 " ideal model delta sigma weight residual 1.458 1.488 -0.030 6.30e-03 2.52e+04 2.20e+01 bond pdb=" N ASP E 158 " pdb=" CA ASP E 158 " ideal model delta sigma weight residual 1.458 1.488 -0.029 6.30e-03 2.52e+04 2.19e+01 bond pdb=" N ASP A 158 " pdb=" CA ASP A 158 " ideal model delta sigma weight residual 1.458 1.488 -0.029 6.30e-03 2.52e+04 2.15e+01 bond pdb=" N ASP B 158 " pdb=" CA ASP B 158 " ideal model delta sigma weight residual 1.458 1.487 -0.029 6.30e-03 2.52e+04 2.11e+01 bond pdb=" N ASP C 158 " pdb=" CA ASP C 158 " ideal model delta sigma weight residual 1.458 1.487 -0.029 6.30e-03 2.52e+04 2.08e+01 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 16567 1.52 - 3.05: 802 3.05 - 4.57: 121 4.57 - 6.10: 25 6.10 - 7.62: 30 Bond angle restraints: 17545 Sorted by residual: angle pdb=" C ASP B 158 " pdb=" CA ASP B 158 " pdb=" CB ASP B 158 " ideal model delta sigma weight residual 116.54 110.76 5.78 1.46e+00 4.69e-01 1.57e+01 angle pdb=" C ASP E 158 " pdb=" CA ASP E 158 " pdb=" CB ASP E 158 " ideal model delta sigma weight residual 116.54 110.79 5.75 1.46e+00 4.69e-01 1.55e+01 angle pdb=" C ASP C 158 " pdb=" CA ASP C 158 " pdb=" CB ASP C 158 " ideal model delta sigma weight residual 116.54 110.80 5.74 1.46e+00 4.69e-01 1.55e+01 angle pdb=" C ASP A 158 " pdb=" CA ASP A 158 " pdb=" CB ASP A 158 " ideal model delta sigma weight residual 116.54 110.81 5.73 1.46e+00 4.69e-01 1.54e+01 angle pdb=" C ASP D 158 " pdb=" CA ASP D 158 " pdb=" CB ASP D 158 " ideal model delta sigma weight residual 116.54 110.82 5.72 1.46e+00 4.69e-01 1.54e+01 ... (remaining 17540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 6702 16.95 - 33.89: 703 33.89 - 50.84: 100 50.84 - 67.78: 15 67.78 - 84.73: 10 Dihedral angle restraints: 7530 sinusoidal: 3025 harmonic: 4505 Sorted by residual: dihedral pdb=" CA LEU C 118 " pdb=" C LEU C 118 " pdb=" N PHE C 119 " pdb=" CA PHE C 119 " ideal model delta harmonic sigma weight residual 180.00 -151.43 -28.57 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA LEU E 118 " pdb=" C LEU E 118 " pdb=" N PHE E 119 " pdb=" CA PHE E 119 " ideal model delta harmonic sigma weight residual -180.00 -151.45 -28.55 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA LEU A 118 " pdb=" C LEU A 118 " pdb=" N PHE A 119 " pdb=" CA PHE A 119 " ideal model delta harmonic sigma weight residual -180.00 -151.45 -28.55 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 7527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1323 0.050 - 0.100: 453 0.100 - 0.150: 137 0.150 - 0.200: 26 0.200 - 0.250: 11 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CA GLU B 156 " pdb=" N GLU B 156 " pdb=" C GLU B 156 " pdb=" CB GLU B 156 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA GLU A 156 " pdb=" N GLU A 156 " pdb=" C GLU A 156 " pdb=" CB GLU A 156 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA GLU E 156 " pdb=" N GLU E 156 " pdb=" C GLU E 156 " pdb=" CB GLU E 156 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1947 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 54 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO D 55 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 55 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 55 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 54 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.52e+00 pdb=" N PRO C 55 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 54 " 0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO E 55 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 55 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 55 " 0.033 5.00e-02 4.00e+02 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3289 2.80 - 3.32: 10426 3.32 - 3.85: 20050 3.85 - 4.37: 24068 4.37 - 4.90: 43065 Nonbonded interactions: 100898 Sorted by model distance: nonbonded pdb=" OE2 GLU A 59 " pdb=" OG SER B 134 " model vdw 2.275 3.040 nonbonded pdb=" OG SER A 227 " pdb=" CG GLU A 230 " model vdw 2.289 3.440 nonbonded pdb=" OG SER C 227 " pdb=" CG GLU C 230 " model vdw 2.289 3.440 nonbonded pdb=" OG SER E 227 " pdb=" CG GLU E 230 " model vdw 2.289 3.440 nonbonded pdb=" OG SER B 227 " pdb=" CG GLU B 230 " model vdw 2.289 3.440 ... (remaining 100893 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 27.270 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.007 0.045 12880 Z= 0.458 Angle : 0.809 7.624 17545 Z= 0.470 Chirality : 0.058 0.250 1950 Planarity : 0.006 0.059 2235 Dihedral : 13.690 84.726 4620 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.18), residues: 1525 helix: -1.79 (0.18), residues: 535 sheet: -1.46 (0.22), residues: 505 loop : -3.92 (0.20), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 206 HIS 0.005 0.001 HIS D 177 PHE 0.014 0.002 PHE C 106 TYR 0.016 0.002 TYR B 245 ARG 0.003 0.000 ARG E 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.313 Fit side-chains REVERT: B 38 TYR cc_start: 0.8893 (m-80) cc_final: 0.8508 (m-80) REVERT: B 131 GLU cc_start: 0.8794 (tt0) cc_final: 0.8481 (tt0) REVERT: C 38 TYR cc_start: 0.8912 (m-80) cc_final: 0.8611 (m-80) REVERT: C 90 LYS cc_start: 0.8893 (pttt) cc_final: 0.8600 (pttm) REVERT: C 146 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7878 (mm-40) REVERT: D 38 TYR cc_start: 0.8771 (m-80) cc_final: 0.8506 (m-80) REVERT: E 65 ARG cc_start: 0.8483 (mtp-110) cc_final: 0.8266 (mtm110) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2969 time to fit residues: 79.8538 Evaluate side-chains 121 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 182 GLN B 139 GLN C 139 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 12880 Z= 0.167 Angle : 0.539 5.848 17545 Z= 0.283 Chirality : 0.046 0.147 1950 Planarity : 0.004 0.046 2235 Dihedral : 4.958 20.817 1690 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.25 % Allowed : 11.85 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.20), residues: 1525 helix: 0.04 (0.21), residues: 510 sheet: -0.62 (0.27), residues: 395 loop : -3.02 (0.20), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 206 HIS 0.004 0.001 HIS C 177 PHE 0.011 0.001 PHE D 247 TYR 0.011 0.001 TYR A 245 ARG 0.008 0.001 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.486 Fit side-chains REVERT: A 90 LYS cc_start: 0.8957 (ptpp) cc_final: 0.8723 (pttm) REVERT: A 245 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.6505 (t80) REVERT: B 38 TYR cc_start: 0.8872 (m-80) cc_final: 0.8501 (m-80) REVERT: C 38 TYR cc_start: 0.8870 (m-80) cc_final: 0.8578 (m-80) REVERT: C 90 LYS cc_start: 0.8882 (pttt) cc_final: 0.8587 (pttm) REVERT: C 146 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7906 (mm-40) REVERT: D 38 TYR cc_start: 0.8826 (m-80) cc_final: 0.8519 (m-80) REVERT: D 65 ARG cc_start: 0.8186 (mtp-110) cc_final: 0.7920 (mtm110) REVERT: E 65 ARG cc_start: 0.8485 (mtp-110) cc_final: 0.8233 (mtm110) REVERT: E 245 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.6751 (t80) outliers start: 31 outliers final: 22 residues processed: 185 average time/residue: 0.2569 time to fit residues: 68.3288 Evaluate side-chains 159 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 136 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12880 Z= 0.279 Angle : 0.570 5.915 17545 Z= 0.297 Chirality : 0.048 0.145 1950 Planarity : 0.004 0.043 2235 Dihedral : 5.104 23.867 1690 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.25 % Allowed : 14.25 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1525 helix: 1.04 (0.22), residues: 500 sheet: -0.39 (0.27), residues: 425 loop : -3.04 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 224 HIS 0.006 0.001 HIS E 177 PHE 0.015 0.002 PHE A 121 TYR 0.016 0.002 TYR C 245 ARG 0.004 0.000 ARG E 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.436 Fit side-chains REVERT: B 38 TYR cc_start: 0.8901 (m-80) cc_final: 0.8643 (m-80) REVERT: B 287 GLN cc_start: 0.1240 (OUTLIER) cc_final: 0.0868 (mm110) REVERT: C 38 TYR cc_start: 0.8890 (m-80) cc_final: 0.8607 (m-80) REVERT: C 90 LYS cc_start: 0.8877 (pttt) cc_final: 0.8595 (pttm) REVERT: C 146 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7937 (mm-40) REVERT: D 38 TYR cc_start: 0.8858 (m-80) cc_final: 0.8595 (m-80) REVERT: D 65 ARG cc_start: 0.8390 (mtp-110) cc_final: 0.8144 (mtm110) REVERT: E 65 ARG cc_start: 0.8548 (mtp-110) cc_final: 0.8339 (mtm110) outliers start: 31 outliers final: 27 residues processed: 164 average time/residue: 0.2726 time to fit residues: 63.4794 Evaluate side-chains 165 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12880 Z= 0.192 Angle : 0.523 5.673 17545 Z= 0.272 Chirality : 0.046 0.145 1950 Planarity : 0.004 0.039 2235 Dihedral : 4.795 20.943 1690 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.69 % Allowed : 15.42 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1525 helix: 1.48 (0.23), residues: 500 sheet: -0.19 (0.28), residues: 395 loop : -2.70 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 206 HIS 0.004 0.001 HIS C 177 PHE 0.011 0.001 PHE D 247 TYR 0.012 0.001 TYR C 245 ARG 0.005 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.6748 (t80) REVERT: B 38 TYR cc_start: 0.8882 (m-80) cc_final: 0.8590 (m-80) REVERT: B 287 GLN cc_start: 0.1217 (OUTLIER) cc_final: 0.0885 (mm110) REVERT: C 38 TYR cc_start: 0.8873 (m-80) cc_final: 0.8592 (m-80) REVERT: C 146 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7935 (mm-40) REVERT: D 38 TYR cc_start: 0.8793 (m-80) cc_final: 0.8545 (m-80) REVERT: D 65 ARG cc_start: 0.8398 (mtp-110) cc_final: 0.8149 (mtm110) REVERT: E 65 ARG cc_start: 0.8564 (mtp-110) cc_final: 0.8350 (mtm110) REVERT: E 287 GLN cc_start: 0.1808 (OUTLIER) cc_final: 0.0752 (mm110) outliers start: 37 outliers final: 28 residues processed: 173 average time/residue: 0.2679 time to fit residues: 65.9917 Evaluate side-chains 172 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN B 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12880 Z= 0.249 Angle : 0.547 5.750 17545 Z= 0.285 Chirality : 0.047 0.144 1950 Planarity : 0.004 0.038 2235 Dihedral : 4.895 22.824 1690 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.84 % Allowed : 16.07 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1525 helix: 1.65 (0.23), residues: 500 sheet: -0.18 (0.28), residues: 410 loop : -2.61 (0.22), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 206 HIS 0.005 0.001 HIS E 177 PHE 0.013 0.001 PHE B 247 TYR 0.015 0.001 TYR C 245 ARG 0.005 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.8808 (tp) REVERT: B 38 TYR cc_start: 0.8891 (m-80) cc_final: 0.8606 (m-80) REVERT: B 145 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.8829 (tp) REVERT: B 287 GLN cc_start: 0.1163 (OUTLIER) cc_final: 0.0797 (mm110) REVERT: C 38 TYR cc_start: 0.8896 (m-80) cc_final: 0.8609 (m-80) REVERT: C 146 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7956 (mm-40) REVERT: D 38 TYR cc_start: 0.8823 (m-80) cc_final: 0.8558 (m-80) REVERT: E 65 ARG cc_start: 0.8600 (mtp-110) cc_final: 0.8389 (mtm110) REVERT: E 287 GLN cc_start: 0.1880 (OUTLIER) cc_final: 0.0836 (mm110) outliers start: 39 outliers final: 31 residues processed: 174 average time/residue: 0.2655 time to fit residues: 66.5146 Evaluate side-chains 178 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 139 GLN B 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12880 Z= 0.272 Angle : 0.559 5.775 17545 Z= 0.291 Chirality : 0.048 0.145 1950 Planarity : 0.004 0.046 2235 Dihedral : 4.946 23.644 1690 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.98 % Allowed : 16.29 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.22), residues: 1525 helix: 1.36 (0.23), residues: 530 sheet: -0.02 (0.27), residues: 425 loop : -2.79 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 206 HIS 0.005 0.001 HIS B 177 PHE 0.013 0.001 PHE B 247 TYR 0.015 0.002 TYR C 245 ARG 0.010 0.000 ARG E 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 TYR cc_start: 0.8893 (m-80) cc_final: 0.8608 (m-80) REVERT: B 145 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.8832 (tp) REVERT: B 287 GLN cc_start: 0.1208 (OUTLIER) cc_final: 0.0865 (mm110) REVERT: C 38 TYR cc_start: 0.8895 (m-80) cc_final: 0.8616 (m-80) REVERT: C 146 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7965 (mm-40) REVERT: D 38 TYR cc_start: 0.8854 (m-80) cc_final: 0.8633 (m-80) REVERT: D 65 ARG cc_start: 0.8432 (mtp-110) cc_final: 0.8161 (mtm110) REVERT: D 145 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9038 (tp) REVERT: D 239 MET cc_start: 0.7350 (ttt) cc_final: 0.7048 (mtt) REVERT: E 65 ARG cc_start: 0.8624 (mtp-110) cc_final: 0.8418 (mtm110) REVERT: E 145 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.8835 (tp) outliers start: 41 outliers final: 34 residues processed: 175 average time/residue: 0.2530 time to fit residues: 64.1149 Evaluate side-chains 179 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 144 optimal weight: 0.4980 chunk 90 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 182 GLN B 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12880 Z= 0.198 Angle : 0.521 5.649 17545 Z= 0.270 Chirality : 0.046 0.145 1950 Planarity : 0.004 0.044 2235 Dihedral : 4.730 21.216 1690 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.84 % Allowed : 16.73 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.22), residues: 1525 helix: 1.81 (0.23), residues: 500 sheet: 0.50 (0.26), residues: 430 loop : -2.89 (0.22), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 206 HIS 0.004 0.001 HIS B 177 PHE 0.011 0.001 PHE E 236 TYR 0.012 0.001 TYR C 245 ARG 0.006 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.8784 (tp) REVERT: B 38 TYR cc_start: 0.8863 (m-80) cc_final: 0.8565 (m-80) REVERT: B 287 GLN cc_start: 0.1210 (OUTLIER) cc_final: 0.0885 (mm110) REVERT: C 38 TYR cc_start: 0.8880 (m-80) cc_final: 0.8565 (m-80) REVERT: C 146 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7970 (mm-40) REVERT: D 38 TYR cc_start: 0.8825 (m-80) cc_final: 0.8572 (m-80) REVERT: D 65 ARG cc_start: 0.8419 (mtp-110) cc_final: 0.8128 (mtm110) REVERT: D 145 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9060 (tp) REVERT: E 65 ARG cc_start: 0.8623 (mtp-110) cc_final: 0.8415 (mtm110) REVERT: E 145 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.8798 (tp) REVERT: E 287 GLN cc_start: 0.1755 (OUTLIER) cc_final: 0.0800 (mm110) outliers start: 39 outliers final: 32 residues processed: 183 average time/residue: 0.2569 time to fit residues: 67.9551 Evaluate side-chains 186 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12880 Z= 0.232 Angle : 0.555 15.001 17545 Z= 0.284 Chirality : 0.047 0.152 1950 Planarity : 0.004 0.047 2235 Dihedral : 4.777 21.805 1690 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.05 % Allowed : 17.09 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.22), residues: 1525 helix: 1.46 (0.23), residues: 530 sheet: 0.50 (0.26), residues: 445 loop : -2.79 (0.22), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 206 HIS 0.005 0.001 HIS E 177 PHE 0.012 0.001 PHE D 247 TYR 0.013 0.001 TYR C 245 ARG 0.012 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.8792 (tp) REVERT: B 38 TYR cc_start: 0.8872 (m-80) cc_final: 0.8591 (m-80) REVERT: B 145 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.8822 (tp) REVERT: B 287 GLN cc_start: 0.1224 (OUTLIER) cc_final: 0.0902 (mm110) REVERT: C 38 TYR cc_start: 0.8888 (m-80) cc_final: 0.8602 (m-80) REVERT: C 146 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7957 (mm-40) REVERT: D 38 TYR cc_start: 0.8830 (m-80) cc_final: 0.8615 (m-80) REVERT: D 145 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9029 (tp) REVERT: E 145 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.8811 (tp) REVERT: E 287 GLN cc_start: 0.1397 (OUTLIER) cc_final: 0.0446 (mm110) outliers start: 42 outliers final: 33 residues processed: 182 average time/residue: 0.2494 time to fit residues: 65.4998 Evaluate side-chains 184 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN B 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 12880 Z= 0.443 Angle : 0.649 11.679 17545 Z= 0.336 Chirality : 0.051 0.182 1950 Planarity : 0.005 0.045 2235 Dihedral : 5.267 27.496 1690 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.62 % Allowed : 17.82 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.22), residues: 1525 helix: 1.26 (0.23), residues: 530 sheet: 0.45 (0.25), residues: 460 loop : -3.19 (0.21), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 206 HIS 0.007 0.002 HIS E 177 PHE 0.018 0.002 PHE E 121 TYR 0.021 0.002 TYR C 245 ARG 0.011 0.001 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: A 145 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.8824 (tp) REVERT: B 38 TYR cc_start: 0.8914 (m-80) cc_final: 0.8696 (m-80) REVERT: B 145 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.8834 (tp) REVERT: C 38 TYR cc_start: 0.8912 (m-80) cc_final: 0.8632 (m-80) REVERT: C 146 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7953 (mm-40) REVERT: D 145 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.9062 (tp) REVERT: E 145 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.8866 (tp) outliers start: 36 outliers final: 29 residues processed: 170 average time/residue: 0.2433 time to fit residues: 60.6429 Evaluate side-chains 171 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.0030 chunk 99 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 12 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN B 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12880 Z= 0.144 Angle : 0.526 12.865 17545 Z= 0.268 Chirality : 0.046 0.158 1950 Planarity : 0.004 0.041 2235 Dihedral : 4.567 19.887 1690 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.67 % Allowed : 19.05 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.22), residues: 1525 helix: 1.43 (0.23), residues: 540 sheet: 0.72 (0.25), residues: 460 loop : -3.04 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 206 HIS 0.004 0.001 HIS B 177 PHE 0.011 0.001 PHE E 106 TYR 0.008 0.001 TYR E 245 ARG 0.010 0.000 ARG B 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8912 (ptpp) cc_final: 0.8663 (pttm) REVERT: B 38 TYR cc_start: 0.8853 (m-80) cc_final: 0.8533 (m-80) REVERT: C 38 TYR cc_start: 0.8848 (m-80) cc_final: 0.8507 (m-80) REVERT: C 146 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7937 (mm-40) REVERT: D 38 TYR cc_start: 0.8778 (m-80) cc_final: 0.8544 (m-80) REVERT: D 90 LYS cc_start: 0.8807 (pttm) cc_final: 0.8547 (pttt) REVERT: D 93 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.8076 (mtt) outliers start: 23 outliers final: 19 residues processed: 166 average time/residue: 0.2346 time to fit residues: 57.8966 Evaluate side-chains 163 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 281 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 15 optimal weight: 0.0870 chunk 21 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 6 optimal weight: 0.0670 chunk 86 optimal weight: 9.9990 overall best weight: 1.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN B 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.148131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.109625 restraints weight = 14307.552| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.66 r_work: 0.2946 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12880 Z= 0.223 Angle : 0.551 11.371 17545 Z= 0.283 Chirality : 0.047 0.162 1950 Planarity : 0.004 0.040 2235 Dihedral : 4.691 20.617 1690 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.75 % Allowed : 19.05 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.22), residues: 1525 helix: 1.45 (0.23), residues: 540 sheet: 0.76 (0.26), residues: 460 loop : -3.02 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 206 HIS 0.004 0.001 HIS C 177 PHE 0.012 0.001 PHE B 236 TYR 0.013 0.001 TYR C 245 ARG 0.010 0.000 ARG B 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2392.23 seconds wall clock time: 44 minutes 36.21 seconds (2676.21 seconds total)