Starting phenix.real_space_refine on Mon Jul 28 20:15:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8twk_41669/07_2025/8twk_41669.cif Found real_map, /net/cci-nas-00/data/ceres_data/8twk_41669/07_2025/8twk_41669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8twk_41669/07_2025/8twk_41669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8twk_41669/07_2025/8twk_41669.map" model { file = "/net/cci-nas-00/data/ceres_data/8twk_41669/07_2025/8twk_41669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8twk_41669/07_2025/8twk_41669.cif" } resolution = 2.6 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= -0.000 sd= 0.069 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 44 5.16 5 C 6588 2.51 5 N 1860 2.21 5 O 2308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10800 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "D" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Time building chain proxies: 6.70, per 1000 atoms: 0.62 Number of scatterers: 10800 At special positions: 0 Unit cell: (103.53, 79.17, 94.83, 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 44 16.00 O 2308 8.00 N 1860 7.00 C 6588 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: 2.52 Conformation dependent library (CDL) restraints added in 1.7 seconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 53.6% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.604A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 180 Processing helix chain 'A' and resid 197 through 219 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 244 through 260 Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 319 through 340 Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 37 through 45 removed outlier: 3.630A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 180 Processing helix chain 'B' and resid 197 through 219 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 244 through 260 Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 306 through 314 Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 319 through 340 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 37 through 45 removed outlier: 3.645A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 180 Processing helix chain 'C' and resid 197 through 219 Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 244 through 260 Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 306 through 314 Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 319 through 340 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 37 through 45 removed outlier: 3.761A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 180 Processing helix chain 'D' and resid 197 through 219 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 244 through 260 Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 306 through 314 Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 319 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.511A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLY A 105 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL A 76 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LYS A 107 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU A 78 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL A 104 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ALA A 145 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE A 106 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TRP A 147 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP A 147 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL A 267 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER A 300 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N PHE A 269 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.448A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLY B 74 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLY B 105 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LYS B 107 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU B 78 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL B 104 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ALA B 145 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE B 106 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N TRP B 147 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP B 147 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL B 267 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER B 300 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N PHE B 269 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.465A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY C 74 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLY C 105 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL C 76 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LYS C 107 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU C 78 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL C 104 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA C 145 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE C 106 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N TRP C 147 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP C 147 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL C 267 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER C 300 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N PHE C 269 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32 removed outlier: 6.464A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA D 32 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY D 74 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY D 105 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL D 76 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LYS D 107 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU D 78 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL D 104 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ALA D 145 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE D 106 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N TRP D 147 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP D 147 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL D 267 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER D 300 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N PHE D 269 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 560 hydrogen bonds defined for protein. 1596 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: 3.55 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3515 1.34 - 1.46: 1836 1.46 - 1.58: 5265 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" CB PRO D 158 " pdb=" CG PRO D 158 " ideal model delta sigma weight residual 1.506 1.476 0.030 3.90e-02 6.57e+02 6.00e-01 bond pdb=" CB PRO C 158 " pdb=" CG PRO C 158 " ideal model delta sigma weight residual 1.506 1.476 0.030 3.90e-02 6.57e+02 5.98e-01 bond pdb=" CB PRO A 158 " pdb=" CG PRO A 158 " ideal model delta sigma weight residual 1.506 1.476 0.030 3.90e-02 6.57e+02 5.81e-01 bond pdb=" CB PRO B 158 " pdb=" CG PRO B 158 " ideal model delta sigma weight residual 1.506 1.477 0.029 3.90e-02 6.57e+02 5.72e-01 bond pdb=" CG1 ILE D 221 " pdb=" CD1 ILE D 221 " ideal model delta sigma weight residual 1.513 1.489 0.024 3.90e-02 6.57e+02 3.89e-01 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 14243 1.68 - 3.36: 186 3.36 - 5.04: 21 5.04 - 6.73: 13 6.73 - 8.41: 1 Bond angle restraints: 14464 Sorted by residual: angle pdb=" CA LEU A 292 " pdb=" CB LEU A 292 " pdb=" CG LEU A 292 " ideal model delta sigma weight residual 116.30 124.71 -8.41 3.50e+00 8.16e-02 5.77e+00 angle pdb=" CA LEU A 61 " pdb=" CB LEU A 61 " pdb=" CG LEU A 61 " ideal model delta sigma weight residual 116.30 122.85 -6.55 3.50e+00 8.16e-02 3.50e+00 angle pdb=" CA LEU D 61 " pdb=" CB LEU D 61 " pdb=" CG LEU D 61 " ideal model delta sigma weight residual 116.30 122.77 -6.47 3.50e+00 8.16e-02 3.42e+00 angle pdb=" CA TYR C 213 " pdb=" CB TYR C 213 " pdb=" CG TYR C 213 " ideal model delta sigma weight residual 113.90 110.58 3.32 1.80e+00 3.09e-01 3.41e+00 angle pdb=" CA TYR B 213 " pdb=" CB TYR B 213 " pdb=" CG TYR B 213 " ideal model delta sigma weight residual 113.90 110.58 3.32 1.80e+00 3.09e-01 3.40e+00 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 5666 17.29 - 34.58: 561 34.58 - 51.87: 218 51.87 - 69.17: 48 69.17 - 86.46: 11 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" CG ARG A 59 " pdb=" CD ARG A 59 " pdb=" NE ARG A 59 " pdb=" CZ ARG A 59 " ideal model delta sinusoidal sigma weight residual -90.00 -135.00 45.00 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG D 59 " pdb=" CD ARG D 59 " pdb=" NE ARG D 59 " pdb=" CZ ARG D 59 " ideal model delta sinusoidal sigma weight residual -180.00 -135.17 -44.83 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG C 59 " pdb=" CD ARG C 59 " pdb=" NE ARG C 59 " pdb=" CZ ARG C 59 " ideal model delta sinusoidal sigma weight residual -180.00 -135.23 -44.77 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 913 0.023 - 0.046: 387 0.046 - 0.070: 175 0.070 - 0.093: 100 0.093 - 0.116: 69 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA ILE A 73 " pdb=" N ILE A 73 " pdb=" C ILE A 73 " pdb=" CB ILE A 73 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.36e-01 chirality pdb=" CA ILE C 77 " pdb=" N ILE C 77 " pdb=" C ILE C 77 " pdb=" CB ILE C 77 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA ILE D 73 " pdb=" N ILE D 73 " pdb=" C ILE D 73 " pdb=" CB ILE D 73 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.27e-01 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 8 " 0.019 5.00e-02 4.00e+02 2.90e-02 1.34e+00 pdb=" N PRO B 9 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 9 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 9 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 8 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO D 9 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 9 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 9 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 8 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO C 9 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO C 9 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 9 " -0.016 5.00e-02 4.00e+02 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 493 2.69 - 3.24: 10905 3.24 - 3.80: 21040 3.80 - 4.35: 27788 4.35 - 4.90: 43721 Nonbonded interactions: 103947 Sorted by model distance: nonbonded pdb=" O GLY D 154 " pdb=" NH2 ARG D 200 " model vdw 2.140 3.120 nonbonded pdb=" O GLY C 154 " pdb=" NH2 ARG C 200 " model vdw 2.149 3.120 nonbonded pdb=" O GLY B 154 " pdb=" NH2 ARG B 200 " model vdw 2.149 3.120 nonbonded pdb=" O GLY A 154 " pdb=" NH2 ARG A 200 " model vdw 2.152 3.120 nonbonded pdb=" NZ LYS A 207 " pdb=" O SER B 217 " model vdw 2.210 3.120 ... (remaining 103942 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.940 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 0.030 10672 Z= 0.123 Angle : 0.514 8.408 14464 Z= 0.258 Chirality : 0.039 0.116 1644 Planarity : 0.003 0.029 1880 Dihedral : 16.482 86.456 3984 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.34 % Allowed : 17.27 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.70 (0.23), residues: 1364 helix: 2.49 (0.19), residues: 692 sheet: -1.51 (0.34), residues: 184 loop : 0.30 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 147 HIS 0.002 0.001 HIS C 4 PHE 0.011 0.001 PHE A 144 TYR 0.014 0.002 TYR C 213 ARG 0.002 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.13602 ( 560) hydrogen bonds : angle 5.54651 ( 1596) covalent geometry : bond 0.00283 (10672) covalent geometry : angle 0.51441 (14464) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 1.105 Fit side-chains REVERT: A 169 VAL cc_start: 0.8320 (t) cc_final: 0.8088 (p) REVERT: A 341 LYS cc_start: 0.7347 (pttt) cc_final: 0.7144 (pttt) REVERT: B 169 VAL cc_start: 0.8323 (t) cc_final: 0.8077 (p) REVERT: B 341 LYS cc_start: 0.7404 (pttt) cc_final: 0.7161 (pttt) REVERT: C 169 VAL cc_start: 0.8334 (t) cc_final: 0.8096 (p) REVERT: C 276 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7213 (mt-10) REVERT: C 339 GLN cc_start: 0.6710 (mt0) cc_final: 0.6430 (mt0) REVERT: D 169 VAL cc_start: 0.8323 (t) cc_final: 0.8087 (p) REVERT: D 341 LYS cc_start: 0.7280 (pttt) cc_final: 0.7074 (pttt) outliers start: 26 outliers final: 22 residues processed: 111 average time/residue: 1.3552 time to fit residues: 161.8330 Evaluate side-chains 98 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 271 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 0.0060 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN A 324 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 ASN D 324 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.140364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116057 restraints weight = 10763.229| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.47 r_work: 0.3317 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10672 Z= 0.188 Angle : 0.577 6.932 14464 Z= 0.290 Chirality : 0.043 0.139 1644 Planarity : 0.004 0.029 1880 Dihedral : 5.603 47.011 1498 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.14 % Allowed : 13.94 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.37 (0.23), residues: 1364 helix: 2.22 (0.19), residues: 720 sheet: -1.81 (0.29), residues: 216 loop : 0.27 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 147 HIS 0.003 0.001 HIS A 80 PHE 0.014 0.002 PHE A 144 TYR 0.021 0.002 TYR C 213 ARG 0.002 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 560) hydrogen bonds : angle 4.68198 ( 1596) covalent geometry : bond 0.00444 (10672) covalent geometry : angle 0.57710 (14464) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 89 time to evaluate : 1.146 Fit side-chains REVERT: A 169 VAL cc_start: 0.8704 (t) cc_final: 0.8479 (p) REVERT: A 295 TRP cc_start: 0.8730 (OUTLIER) cc_final: 0.7082 (m-90) REVERT: A 341 LYS cc_start: 0.7617 (pttt) cc_final: 0.7364 (pttt) REVERT: B 295 TRP cc_start: 0.8730 (OUTLIER) cc_final: 0.7110 (m-90) REVERT: B 303 ARG cc_start: 0.6261 (OUTLIER) cc_final: 0.5366 (ttp80) REVERT: C 295 TRP cc_start: 0.8696 (OUTLIER) cc_final: 0.7126 (m-90) REVERT: D 169 VAL cc_start: 0.8714 (t) cc_final: 0.8492 (p) REVERT: D 276 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7740 (mt-10) REVERT: D 295 TRP cc_start: 0.8721 (OUTLIER) cc_final: 0.7047 (m-90) REVERT: D 303 ARG cc_start: 0.6224 (mtp-110) cc_final: 0.5251 (ttp80) outliers start: 46 outliers final: 14 residues processed: 125 average time/residue: 1.5587 time to fit residues: 207.4258 Evaluate side-chains 106 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 7 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.139240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.114854 restraints weight = 10867.114| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.48 r_work: 0.3295 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10672 Z= 0.181 Angle : 0.562 7.303 14464 Z= 0.281 Chirality : 0.042 0.138 1644 Planarity : 0.004 0.029 1880 Dihedral : 5.352 47.294 1488 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.42 % Allowed : 14.66 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.22 (0.23), residues: 1364 helix: 2.21 (0.19), residues: 716 sheet: -1.93 (0.29), residues: 216 loop : 0.04 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 147 HIS 0.004 0.001 HIS D 80 PHE 0.014 0.002 PHE B 144 TYR 0.020 0.002 TYR A 213 ARG 0.002 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 560) hydrogen bonds : angle 4.54596 ( 1596) covalent geometry : bond 0.00431 (10672) covalent geometry : angle 0.56231 (14464) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 91 time to evaluate : 1.230 Fit side-chains REVERT: A 169 VAL cc_start: 0.8709 (t) cc_final: 0.8500 (p) REVERT: A 295 TRP cc_start: 0.8829 (OUTLIER) cc_final: 0.7058 (m-90) REVERT: A 325 GLU cc_start: 0.6069 (OUTLIER) cc_final: 0.5581 (tp30) REVERT: A 326 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6590 (tp30) REVERT: A 329 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.6614 (ptpt) REVERT: A 341 LYS cc_start: 0.7635 (pttt) cc_final: 0.7401 (pttt) REVERT: B 98 LYS cc_start: 0.7964 (mttp) cc_final: 0.7710 (mttp) REVERT: B 295 TRP cc_start: 0.8810 (OUTLIER) cc_final: 0.7072 (m-90) REVERT: B 303 ARG cc_start: 0.6413 (mtp-110) cc_final: 0.5543 (ttp80) REVERT: C 295 TRP cc_start: 0.8791 (OUTLIER) cc_final: 0.7066 (m-90) REVERT: D 295 TRP cc_start: 0.8817 (OUTLIER) cc_final: 0.7030 (m-90) REVERT: D 303 ARG cc_start: 0.6379 (mtp-110) cc_final: 0.5439 (ttp80) outliers start: 38 outliers final: 10 residues processed: 119 average time/residue: 1.5769 time to fit residues: 200.5473 Evaluate side-chains 100 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 134 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 117 optimal weight: 8.9990 chunk 133 optimal weight: 0.3980 chunk 102 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.133408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108961 restraints weight = 10872.209| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.46 r_work: 0.3245 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10672 Z= 0.262 Angle : 0.627 7.261 14464 Z= 0.318 Chirality : 0.045 0.143 1644 Planarity : 0.004 0.029 1880 Dihedral : 5.422 46.731 1482 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.15 % Allowed : 15.56 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.98 (0.23), residues: 1364 helix: 2.10 (0.19), residues: 692 sheet: -1.94 (0.29), residues: 216 loop : -0.18 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 147 HIS 0.004 0.001 HIS C 4 PHE 0.014 0.002 PHE C 144 TYR 0.026 0.002 TYR B 213 ARG 0.003 0.001 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 560) hydrogen bonds : angle 4.65271 ( 1596) covalent geometry : bond 0.00628 (10672) covalent geometry : angle 0.62674 (14464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 1.173 Fit side-chains REVERT: A 66 ASP cc_start: 0.8032 (p0) cc_final: 0.7803 (p0) REVERT: A 295 TRP cc_start: 0.8914 (OUTLIER) cc_final: 0.7077 (m-90) REVERT: A 303 ARG cc_start: 0.7003 (ptm160) cc_final: 0.6382 (ptm-80) REVERT: A 325 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5915 (tp30) REVERT: A 341 LYS cc_start: 0.7690 (pttt) cc_final: 0.7451 (pttp) REVERT: B 295 TRP cc_start: 0.8902 (OUTLIER) cc_final: 0.7089 (m-90) REVERT: B 303 ARG cc_start: 0.6514 (mtp-110) cc_final: 0.5690 (ttp80) REVERT: B 325 GLU cc_start: 0.7481 (tp30) cc_final: 0.7108 (tp30) REVERT: C 295 TRP cc_start: 0.8891 (OUTLIER) cc_final: 0.7143 (m-90) REVERT: C 303 ARG cc_start: 0.6821 (ptm160) cc_final: 0.6022 (ptm-80) REVERT: C 325 GLU cc_start: 0.7495 (tp30) cc_final: 0.7107 (tp30) REVERT: D 295 TRP cc_start: 0.8911 (OUTLIER) cc_final: 0.7084 (m-90) REVERT: D 303 ARG cc_start: 0.6410 (mtp-110) cc_final: 0.5430 (ttp80) outliers start: 35 outliers final: 16 residues processed: 120 average time/residue: 1.4982 time to fit residues: 192.5245 Evaluate side-chains 105 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 100 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.137001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.112785 restraints weight = 10710.860| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.45 r_work: 0.3274 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10672 Z= 0.189 Angle : 0.571 7.225 14464 Z= 0.287 Chirality : 0.043 0.137 1644 Planarity : 0.004 0.028 1880 Dihedral : 5.253 47.223 1482 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.60 % Allowed : 15.20 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.05 (0.23), residues: 1364 helix: 2.18 (0.19), residues: 692 sheet: -2.01 (0.29), residues: 216 loop : -0.12 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 147 HIS 0.003 0.001 HIS C 4 PHE 0.014 0.002 PHE B 144 TYR 0.019 0.002 TYR C 213 ARG 0.003 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 560) hydrogen bonds : angle 4.57214 ( 1596) covalent geometry : bond 0.00452 (10672) covalent geometry : angle 0.57091 (14464) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 1.260 Fit side-chains REVERT: A 295 TRP cc_start: 0.8874 (OUTLIER) cc_final: 0.6971 (m-90) REVERT: A 303 ARG cc_start: 0.6897 (ptm160) cc_final: 0.6283 (ptm-80) REVERT: A 325 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5756 (tp30) REVERT: A 329 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6786 (ptpt) REVERT: A 341 LYS cc_start: 0.7610 (pttt) cc_final: 0.7368 (pttm) REVERT: B 295 TRP cc_start: 0.8864 (OUTLIER) cc_final: 0.6968 (m-90) REVERT: B 303 ARG cc_start: 0.6386 (mtp-110) cc_final: 0.5510 (ttp80) REVERT: B 326 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6533 (mm-30) REVERT: B 329 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.6863 (ptpp) REVERT: C 295 TRP cc_start: 0.8852 (OUTLIER) cc_final: 0.7014 (m-90) REVERT: C 326 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6505 (mm-30) REVERT: C 329 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6854 (ptpp) REVERT: D 295 TRP cc_start: 0.8882 (OUTLIER) cc_final: 0.6977 (m-90) REVERT: D 303 ARG cc_start: 0.6414 (mtp-110) cc_final: 0.5428 (ttp80) outliers start: 40 outliers final: 18 residues processed: 127 average time/residue: 1.4248 time to fit residues: 193.7990 Evaluate side-chains 114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 128 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.140329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116080 restraints weight = 10839.201| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.48 r_work: 0.3316 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10672 Z= 0.140 Angle : 0.530 7.311 14464 Z= 0.264 Chirality : 0.041 0.140 1644 Planarity : 0.004 0.028 1880 Dihedral : 5.008 46.850 1482 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.15 % Allowed : 15.83 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.20 (0.23), residues: 1364 helix: 2.17 (0.19), residues: 720 sheet: -2.02 (0.29), residues: 216 loop : 0.11 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 147 HIS 0.002 0.001 HIS D 80 PHE 0.013 0.002 PHE A 144 TYR 0.016 0.002 TYR A 213 ARG 0.002 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 560) hydrogen bonds : angle 4.42589 ( 1596) covalent geometry : bond 0.00334 (10672) covalent geometry : angle 0.52968 (14464) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 1.011 Fit side-chains REVERT: A 295 TRP cc_start: 0.8794 (OUTLIER) cc_final: 0.6810 (m-90) REVERT: A 303 ARG cc_start: 0.6782 (ptm160) cc_final: 0.6207 (ptm-80) REVERT: A 325 GLU cc_start: 0.6034 (OUTLIER) cc_final: 0.5773 (tp30) REVERT: A 341 LYS cc_start: 0.7620 (pttt) cc_final: 0.7407 (pttm) REVERT: B 98 LYS cc_start: 0.7938 (mttp) cc_final: 0.7707 (mttp) REVERT: B 295 TRP cc_start: 0.8777 (OUTLIER) cc_final: 0.6785 (m-90) REVERT: B 303 ARG cc_start: 0.6246 (mtp-110) cc_final: 0.5221 (tmm160) REVERT: C 295 TRP cc_start: 0.8761 (OUTLIER) cc_final: 0.6827 (m-90) REVERT: D 295 TRP cc_start: 0.8802 (OUTLIER) cc_final: 0.6807 (m-90) REVERT: D 303 ARG cc_start: 0.6272 (mtp-110) cc_final: 0.5288 (ttp80) outliers start: 35 outliers final: 19 residues processed: 112 average time/residue: 2.0227 time to fit residues: 242.1410 Evaluate side-chains 104 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 125 optimal weight: 0.0370 chunk 59 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.142375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118068 restraints weight = 10851.022| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.49 r_work: 0.3327 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10672 Z= 0.124 Angle : 0.514 7.315 14464 Z= 0.255 Chirality : 0.041 0.138 1644 Planarity : 0.003 0.028 1880 Dihedral : 4.895 46.777 1482 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.42 % Allowed : 15.65 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.30 (0.23), residues: 1364 helix: 2.26 (0.19), residues: 720 sheet: -2.03 (0.28), residues: 216 loop : 0.17 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 147 HIS 0.002 0.001 HIS C 4 PHE 0.013 0.002 PHE A 144 TYR 0.015 0.002 TYR A 213 ARG 0.002 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 560) hydrogen bonds : angle 4.33099 ( 1596) covalent geometry : bond 0.00290 (10672) covalent geometry : angle 0.51363 (14464) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 86 time to evaluate : 2.254 Fit side-chains REVERT: A 242 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8456 (mmtt) REVERT: A 295 TRP cc_start: 0.8790 (OUTLIER) cc_final: 0.6804 (m-90) REVERT: B 98 LYS cc_start: 0.7949 (mttp) cc_final: 0.7743 (mttp) REVERT: B 295 TRP cc_start: 0.8767 (OUTLIER) cc_final: 0.6760 (m-90) REVERT: C 42 ARG cc_start: 0.6226 (mmm160) cc_final: 0.5926 (mtp180) REVERT: C 295 TRP cc_start: 0.8777 (OUTLIER) cc_final: 0.6855 (m-90) REVERT: D 295 TRP cc_start: 0.8782 (OUTLIER) cc_final: 0.6789 (m-90) REVERT: D 303 ARG cc_start: 0.6216 (mtp-110) cc_final: 0.5188 (tmm160) outliers start: 38 outliers final: 16 residues processed: 115 average time/residue: 2.2511 time to fit residues: 277.5660 Evaluate side-chains 98 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 83 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 125 optimal weight: 0.4980 chunk 30 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.142202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117867 restraints weight = 10703.764| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.48 r_work: 0.3334 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10672 Z= 0.133 Angle : 0.519 7.400 14464 Z= 0.257 Chirality : 0.041 0.140 1644 Planarity : 0.003 0.028 1880 Dihedral : 4.890 46.248 1482 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.97 % Allowed : 16.28 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.33 (0.23), residues: 1364 helix: 2.29 (0.20), residues: 720 sheet: -2.00 (0.28), residues: 216 loop : 0.16 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 147 HIS 0.002 0.001 HIS B 80 PHE 0.012 0.002 PHE C 144 TYR 0.016 0.002 TYR A 213 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 560) hydrogen bonds : angle 4.30121 ( 1596) covalent geometry : bond 0.00315 (10672) covalent geometry : angle 0.51853 (14464) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 1.252 Fit side-chains REVERT: A 242 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8461 (mmtt) REVERT: A 295 TRP cc_start: 0.8806 (OUTLIER) cc_final: 0.6822 (m-90) REVERT: B 295 TRP cc_start: 0.8777 (OUTLIER) cc_final: 0.6776 (m-90) REVERT: B 303 ARG cc_start: 0.6285 (mtp-110) cc_final: 0.5436 (ttp80) REVERT: C 34 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: C 42 ARG cc_start: 0.6257 (mmm160) cc_final: 0.5902 (mtt180) REVERT: C 295 TRP cc_start: 0.8786 (OUTLIER) cc_final: 0.6872 (m-90) REVERT: D 295 TRP cc_start: 0.8813 (OUTLIER) cc_final: 0.6822 (m-90) REVERT: D 303 ARG cc_start: 0.6228 (mtp-110) cc_final: 0.5199 (tmm160) outliers start: 33 outliers final: 20 residues processed: 108 average time/residue: 1.6201 time to fit residues: 186.9141 Evaluate side-chains 102 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 92 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 57 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.142861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.118485 restraints weight = 10768.260| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.48 r_work: 0.3332 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10672 Z= 0.125 Angle : 0.513 7.267 14464 Z= 0.254 Chirality : 0.041 0.140 1644 Planarity : 0.003 0.028 1880 Dihedral : 4.849 46.125 1482 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.06 % Allowed : 16.28 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.37 (0.23), residues: 1364 helix: 2.31 (0.20), residues: 720 sheet: -1.99 (0.28), residues: 216 loop : 0.20 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 147 HIS 0.002 0.001 HIS B 80 PHE 0.012 0.002 PHE A 144 TYR 0.016 0.002 TYR C 213 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 560) hydrogen bonds : angle 4.27262 ( 1596) covalent geometry : bond 0.00294 (10672) covalent geometry : angle 0.51273 (14464) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 76 time to evaluate : 1.275 Fit side-chains REVERT: A 242 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8472 (mmtt) REVERT: A 295 TRP cc_start: 0.8798 (OUTLIER) cc_final: 0.6821 (m-90) REVERT: B 295 TRP cc_start: 0.8765 (OUTLIER) cc_final: 0.6765 (m-90) REVERT: B 303 ARG cc_start: 0.6269 (OUTLIER) cc_final: 0.5290 (ttp-170) REVERT: C 34 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: C 42 ARG cc_start: 0.6219 (mmm160) cc_final: 0.5864 (mtt180) REVERT: C 295 TRP cc_start: 0.8758 (OUTLIER) cc_final: 0.6830 (m-90) REVERT: D 295 TRP cc_start: 0.8795 (OUTLIER) cc_final: 0.6805 (m-90) REVERT: D 303 ARG cc_start: 0.6234 (mtp-110) cc_final: 0.5185 (tmm160) outliers start: 34 outliers final: 21 residues processed: 102 average time/residue: 1.4984 time to fit residues: 164.8217 Evaluate side-chains 103 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 96 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 125 optimal weight: 0.0770 chunk 9 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.142407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.117967 restraints weight = 10712.716| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.47 r_work: 0.3326 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10672 Z= 0.132 Angle : 0.518 7.266 14464 Z= 0.257 Chirality : 0.041 0.139 1644 Planarity : 0.003 0.028 1880 Dihedral : 4.863 45.934 1482 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.52 % Allowed : 16.82 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.37 (0.24), residues: 1364 helix: 2.31 (0.20), residues: 720 sheet: -1.99 (0.28), residues: 216 loop : 0.21 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 147 HIS 0.002 0.001 HIS A 80 PHE 0.012 0.002 PHE C 144 TYR 0.017 0.002 TYR A 213 ARG 0.004 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 560) hydrogen bonds : angle 4.26375 ( 1596) covalent geometry : bond 0.00311 (10672) covalent geometry : angle 0.51797 (14464) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 1.241 Fit side-chains REVERT: A 242 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8485 (mmtt) REVERT: A 295 TRP cc_start: 0.8821 (OUTLIER) cc_final: 0.6828 (m-90) REVERT: B 295 TRP cc_start: 0.8776 (OUTLIER) cc_final: 0.6779 (m-90) REVERT: B 303 ARG cc_start: 0.6295 (mtp-110) cc_final: 0.5405 (ttp-170) REVERT: C 295 TRP cc_start: 0.8793 (OUTLIER) cc_final: 0.6875 (m-90) REVERT: D 295 TRP cc_start: 0.8830 (OUTLIER) cc_final: 0.6833 (m-90) REVERT: D 303 ARG cc_start: 0.6268 (mtp-110) cc_final: 0.5221 (tmm160) outliers start: 28 outliers final: 21 residues processed: 101 average time/residue: 1.6797 time to fit residues: 181.4671 Evaluate side-chains 102 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 61 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 83 optimal weight: 0.0030 chunk 64 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.143305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.118953 restraints weight = 10637.473| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.47 r_work: 0.3345 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10672 Z= 0.124 Angle : 0.511 7.265 14464 Z= 0.253 Chirality : 0.041 0.139 1644 Planarity : 0.003 0.028 1880 Dihedral : 4.823 45.965 1482 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.52 % Allowed : 16.73 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.39 (0.24), residues: 1364 helix: 2.33 (0.20), residues: 720 sheet: -1.99 (0.28), residues: 216 loop : 0.22 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 147 HIS 0.002 0.001 HIS B 80 PHE 0.012 0.002 PHE A 144 TYR 0.016 0.002 TYR C 213 ARG 0.004 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 560) hydrogen bonds : angle 4.23348 ( 1596) covalent geometry : bond 0.00293 (10672) covalent geometry : angle 0.51143 (14464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7163.59 seconds wall clock time: 129 minutes 12.28 seconds (7752.28 seconds total)