Starting phenix.real_space_refine on Fri Feb 14 21:25:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8twk_41669/02_2025/8twk_41669.cif Found real_map, /net/cci-nas-00/data/ceres_data/8twk_41669/02_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_41669/02_2025/8twk_41669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8twk_41669/02_2025/8twk_41669.map" model { file = "/net/cci-nas-00/data/ceres_data/8twk_41669/02_2025/8twk_41669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8twk_41669/02_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-5592/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: 6.26, per 1000 atoms: 0.58 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: 2.47 Conformation dependent library (CDL) restraints added in 1.4 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: 3.49 Time building geometry restraints manager: 2.87 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: 1.020 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.080 Find NCS groups from input model: 0.360 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:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.980 ------------------------------------------------------------------------------- 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= 0.184 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 *********************** 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 : 1.279 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: 1.4132 time to fit residues: 169.0257 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 : 1.180 ------------------------------------------------------------------------------- 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 = 53)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116063 restraints weight = 10763.204| |-----------------------------------------------------------------------------| 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: 0.3202 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- 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= 0.291 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 *********************** 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 : 1.236 Fit side-chains REVERT: A 169 VAL cc_start: 0.8705 (t) cc_final: 0.8481 (p) REVERT: A 295 TRP cc_start: 0.8730 (OUTLIER) cc_final: 0.7083 (m-90) REVERT: A 341 LYS cc_start: 0.7619 (pttt) cc_final: 0.7365 (pttt) REVERT: B 295 TRP cc_start: 0.8730 (OUTLIER) cc_final: 0.7111 (m-90) REVERT: B 303 ARG cc_start: 0.6261 (OUTLIER) cc_final: 0.5368 (ttp80) REVERT: C 295 TRP cc_start: 0.8696 (OUTLIER) cc_final: 0.7126 (m-90) REVERT: D 169 VAL cc_start: 0.8715 (t) cc_final: 0.8493 (p) REVERT: D 276 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7742 (mt-10) REVERT: D 295 TRP cc_start: 0.8722 (OUTLIER) cc_final: 0.7047 (m-90) REVERT: D 303 ARG cc_start: 0.6224 (mtp-110) cc_final: 0.5253 (ttp80) outliers start: 46 outliers final: 14 residues processed: 125 average time/residue: 1.6198 time to fit residues: 216.0583 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 : 1.230 ------------------------------------------------------------------------------- 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: 0.0270 chunk 86 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.141687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117357 restraints weight = 10848.392| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.48 r_work: 0.3331 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10672 Z= 0.234 Angle : 0.537 7.176 14464 Z= 0.267 Chirality : 0.041 0.136 1644 Planarity : 0.004 0.029 1880 Dihedral : 5.182 47.315 1488 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.15 % Allowed : 14.57 % Favored : 82.28 % 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: 1.35 (0.23), residues: 1364 helix: 2.26 (0.19), residues: 720 sheet: -1.92 (0.29), residues: 216 loop : 0.21 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 147 HIS 0.003 0.001 HIS D 80 PHE 0.013 0.002 PHE C 144 TYR 0.017 0.002 TYR A 213 ARG 0.002 0.000 ARG A 42 *********************** 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 125 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 1.212 Fit side-chains REVERT: A 169 VAL cc_start: 0.8708 (t) cc_final: 0.8498 (p) REVERT: A 295 TRP cc_start: 0.8772 (OUTLIER) cc_final: 0.6989 (m-90) REVERT: A 326 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6453 (tp30) REVERT: A 329 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6553 (ptpt) REVERT: A 341 LYS cc_start: 0.7597 (pttt) cc_final: 0.7374 (pttt) REVERT: B 98 LYS cc_start: 0.7959 (mttp) cc_final: 0.7720 (mttp) REVERT: B 295 TRP cc_start: 0.8759 (OUTLIER) cc_final: 0.7007 (m-90) REVERT: B 303 ARG cc_start: 0.6366 (mtp-110) cc_final: 0.5432 (tmm160) REVERT: C 295 TRP cc_start: 0.8735 (OUTLIER) cc_final: 0.7027 (m-90) REVERT: D 295 TRP cc_start: 0.8762 (OUTLIER) cc_final: 0.6941 (m-90) REVERT: D 303 ARG cc_start: 0.6329 (mtp-110) cc_final: 0.5381 (ttp80) outliers start: 35 outliers final: 12 residues processed: 117 average time/residue: 1.5429 time to fit residues: 193.1096 Evaluate side-chains 105 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 320 LEU 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 Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 134 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 117 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 102 optimal weight: 0.0270 chunk 64 optimal weight: 0.0020 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 overall best weight: 0.7248 ------------------------------------------------------------------------------- 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** ** B 339 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 = 0.3647 r_free = 0.3647 target = 0.142800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118508 restraints weight = 10740.446| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.48 r_work: 0.3340 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10672 Z= 0.210 Angle : 0.520 7.271 14464 Z= 0.257 Chirality : 0.041 0.143 1644 Planarity : 0.003 0.029 1880 Dihedral : 4.839 46.942 1482 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.70 % Allowed : 15.29 % Favored : 82.01 % 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: 1.40 (0.23), residues: 1364 helix: 2.32 (0.19), residues: 720 sheet: -1.94 (0.29), residues: 216 loop : 0.22 (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 0.013 0.002 PHE C 144 TYR 0.017 0.002 TYR A 213 ARG 0.002 0.000 ARG B 42 *********************** 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 120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 1.205 Fit side-chains REVERT: A 295 TRP cc_start: 0.8742 (OUTLIER) cc_final: 0.6926 (m-90) REVERT: A 341 LYS cc_start: 0.7646 (pttt) cc_final: 0.7445 (pttt) REVERT: B 42 ARG cc_start: 0.6165 (OUTLIER) cc_final: 0.5714 (mtt180) REVERT: B 98 LYS cc_start: 0.7908 (mttp) cc_final: 0.7691 (mttp) REVERT: B 295 TRP cc_start: 0.8716 (OUTLIER) cc_final: 0.6932 (m-90) REVERT: B 303 ARG cc_start: 0.6359 (mtp-110) cc_final: 0.5442 (ttp80) REVERT: C 295 TRP cc_start: 0.8741 (OUTLIER) cc_final: 0.6980 (m-90) REVERT: D 295 TRP cc_start: 0.8735 (OUTLIER) cc_final: 0.6898 (m-90) REVERT: D 303 ARG cc_start: 0.6253 (mtp-110) cc_final: 0.5207 (tmm160) outliers start: 30 outliers final: 14 residues processed: 114 average time/residue: 1.4525 time to fit residues: 177.6361 Evaluate side-chains 98 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 320 LEU Chi-restraints excluded: chain B residue 42 ARG 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 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: 7.9990 chunk 120 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.140970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116483 restraints weight = 10691.481| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.47 r_work: 0.3332 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10672 Z= 0.217 Angle : 0.523 7.270 14464 Z= 0.259 Chirality : 0.041 0.142 1644 Planarity : 0.003 0.029 1880 Dihedral : 4.860 46.737 1482 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.24 % Allowed : 15.56 % 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: 1.39 (0.23), residues: 1364 helix: 2.32 (0.19), residues: 720 sheet: -1.95 (0.28), residues: 216 loop : 0.21 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 147 HIS 0.002 0.001 HIS A 80 PHE 0.013 0.002 PHE B 144 TYR 0.018 0.002 TYR B 213 ARG 0.002 0.000 ARG B 42 *********************** 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 116 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 80 time to evaluate : 1.169 Fit side-chains REVERT: A 295 TRP cc_start: 0.8765 (OUTLIER) cc_final: 0.6840 (m-90) REVERT: A 329 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6978 (pttm) REVERT: B 42 ARG cc_start: 0.6024 (OUTLIER) cc_final: 0.5709 (mtt180) REVERT: B 295 TRP cc_start: 0.8734 (OUTLIER) cc_final: 0.6847 (m-90) REVERT: B 303 ARG cc_start: 0.6312 (mtp-110) cc_final: 0.5420 (ttp80) REVERT: C 295 TRP cc_start: 0.8731 (OUTLIER) cc_final: 0.6876 (m-90) REVERT: D 295 TRP cc_start: 0.8754 (OUTLIER) cc_final: 0.6814 (m-90) REVERT: D 303 ARG cc_start: 0.6252 (mtp-110) cc_final: 0.5195 (tmm160) outliers start: 36 outliers final: 17 residues processed: 106 average time/residue: 1.4787 time to fit residues: 168.3264 Evaluate side-chains 95 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 329 LYS Chi-restraints excluded: chain B residue 42 ARG 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 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 182 ILE 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: 0.7980 chunk 31 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 33 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 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 = 0.3655 r_free = 0.3655 target = 0.143468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.119003 restraints weight = 10774.147| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.49 r_work: 0.3349 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1444 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= 0.196 Angle : 0.509 7.280 14464 Z= 0.252 Chirality : 0.041 0.140 1644 Planarity : 0.003 0.029 1880 Dihedral : 4.795 46.522 1482 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.79 % Allowed : 16.01 % 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: 1.46 (0.23), residues: 1364 helix: 2.39 (0.19), residues: 720 sheet: -1.95 (0.29), residues: 216 loop : 0.22 (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 B 80 PHE 0.012 0.002 PHE C 144 TYR 0.016 0.002 TYR B 213 ARG 0.003 0.000 ARG B 42 *********************** 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 103 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 1.378 Fit side-chains REVERT: A 295 TRP cc_start: 0.8750 (OUTLIER) cc_final: 0.6837 (m-90) REVERT: A 325 GLU cc_start: 0.6073 (OUTLIER) cc_final: 0.5684 (tp30) REVERT: A 329 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.7052 (pttm) REVERT: B 295 TRP cc_start: 0.8734 (OUTLIER) cc_final: 0.6740 (m-90) REVERT: B 303 ARG cc_start: 0.6256 (OUTLIER) cc_final: 0.5411 (ttp80) REVERT: C 42 ARG cc_start: 0.6259 (mmm160) cc_final: 0.5944 (mtp180) REVERT: C 295 TRP cc_start: 0.8729 (OUTLIER) cc_final: 0.6783 (m-90) REVERT: D 295 TRP cc_start: 0.8746 (OUTLIER) cc_final: 0.6831 (m-90) REVERT: D 303 ARG cc_start: 0.6203 (mtp-110) cc_final: 0.5142 (tmm160) outliers start: 31 outliers final: 18 residues processed: 99 average time/residue: 1.4885 time to fit residues: 158.7876 Evaluate side-chains 95 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 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 303 ARG 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 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 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: 0.0270 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 67 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 57 optimal weight: 0.0870 chunk 124 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 overall best weight: 0.4416 ------------------------------------------------------------------------------- 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 324 GLN A 339 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.144664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120088 restraints weight = 10849.973| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.50 r_work: 0.3374 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10672 Z= 0.166 Angle : 0.491 7.378 14464 Z= 0.242 Chirality : 0.040 0.139 1644 Planarity : 0.003 0.029 1880 Dihedral : 4.697 46.724 1482 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.24 % Allowed : 15.56 % 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: 1.57 (0.24), residues: 1364 helix: 2.47 (0.20), residues: 716 sheet: -1.92 (0.29), residues: 216 loop : 0.33 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 147 HIS 0.001 0.000 HIS C 4 PHE 0.012 0.002 PHE D 144 TYR 0.014 0.002 TYR C 213 ARG 0.002 0.000 ARG B 42 *********************** 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 113 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 77 time to evaluate : 1.218 Fit side-chains REVERT: A 193 ASP cc_start: 0.8687 (m-30) cc_final: 0.8433 (m-30) REVERT: A 295 TRP cc_start: 0.8709 (OUTLIER) cc_final: 0.6809 (m-90) REVERT: B 295 TRP cc_start: 0.8688 (OUTLIER) cc_final: 0.6715 (m-90) REVERT: B 303 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.5367 (ttp80) REVERT: C 42 ARG cc_start: 0.6175 (mmm160) cc_final: 0.5880 (mtp180) REVERT: C 295 TRP cc_start: 0.8695 (OUTLIER) cc_final: 0.6774 (m-90) REVERT: D 295 TRP cc_start: 0.8725 (OUTLIER) cc_final: 0.6701 (m-90) REVERT: D 303 ARG cc_start: 0.6099 (mtp-110) cc_final: 0.5178 (ttp-170) outliers start: 36 outliers final: 11 residues processed: 106 average time/residue: 1.4822 time to fit residues: 168.7330 Evaluate side-chains 86 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 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 303 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 125 optimal weight: 0.0470 chunk 30 optimal weight: 0.0770 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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** ** B 339 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 = 0.3687 r_free = 0.3687 target = 0.146458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122052 restraints weight = 10672.163| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.49 r_work: 0.3382 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1578 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= 0.168 Angle : 0.498 7.397 14464 Z= 0.244 Chirality : 0.040 0.140 1644 Planarity : 0.003 0.029 1880 Dihedral : 4.646 45.664 1482 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.25 % Allowed : 16.64 % Favored : 81.12 % 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: 1.66 (0.23), residues: 1364 helix: 2.51 (0.20), residues: 716 sheet: -2.26 (0.30), residues: 176 loop : 0.36 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 147 HIS 0.001 0.000 HIS B 80 PHE 0.012 0.002 PHE D 144 TYR 0.016 0.001 TYR C 213 ARG 0.002 0.000 ARG A 303 *********************** 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 102 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 1.269 Fit side-chains REVERT: A 91 ARG cc_start: 0.7906 (mtp85) cc_final: 0.7703 (mtm110) REVERT: A 295 TRP cc_start: 0.8726 (OUTLIER) cc_final: 0.6716 (m-90) REVERT: B 295 TRP cc_start: 0.8688 (OUTLIER) cc_final: 0.6715 (m-90) REVERT: B 303 ARG cc_start: 0.6169 (OUTLIER) cc_final: 0.5337 (ttt180) REVERT: C 42 ARG cc_start: 0.6094 (mmm160) cc_final: 0.5857 (mtp180) REVERT: C 295 TRP cc_start: 0.8710 (OUTLIER) cc_final: 0.6798 (m-90) REVERT: D 295 TRP cc_start: 0.8729 (OUTLIER) cc_final: 0.6709 (m-90) REVERT: D 303 ARG cc_start: 0.6158 (mtp-110) cc_final: 0.5148 (ttp-170) outliers start: 25 outliers final: 12 residues processed: 96 average time/residue: 1.4936 time to fit residues: 154.2954 Evaluate side-chains 90 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 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 295 TRP Chi-restraints excluded: chain B residue 303 ARG 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 182 ILE 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: 0.7980 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 57 optimal weight: 0.0670 chunk 96 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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** ** B 339 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 168 ASN ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119757 restraints weight = 10776.747| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.50 r_work: 0.3372 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10672 Z= 0.181 Angle : 0.501 7.502 14464 Z= 0.246 Chirality : 0.041 0.142 1644 Planarity : 0.003 0.029 1880 Dihedral : 4.662 45.364 1482 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.16 % Allowed : 16.82 % 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: 1.59 (0.24), residues: 1364 helix: 2.46 (0.19), residues: 720 sheet: -1.85 (0.29), residues: 216 loop : 0.33 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 147 HIS 0.002 0.000 HIS B 80 PHE 0.012 0.002 PHE C 144 TYR 0.017 0.002 TYR C 213 ARG 0.002 0.000 ARG B 42 *********************** 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 103 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 295 TRP cc_start: 0.8761 (OUTLIER) cc_final: 0.6861 (m-90) REVERT: B 295 TRP cc_start: 0.8729 (OUTLIER) cc_final: 0.6756 (m-90) REVERT: B 303 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.5318 (ttt180) REVERT: C 295 TRP cc_start: 0.8739 (OUTLIER) cc_final: 0.6824 (m-90) REVERT: D 295 TRP cc_start: 0.8750 (OUTLIER) cc_final: 0.6724 (m-90) REVERT: D 303 ARG cc_start: 0.6191 (mtp-110) cc_final: 0.5175 (ttp-170) outliers start: 24 outliers final: 14 residues processed: 96 average time/residue: 1.5141 time to fit residues: 156.0574 Evaluate side-chains 95 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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 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 B residue 303 ARG 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 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 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: 0.5980 chunk 133 optimal weight: 0.0270 chunk 124 optimal weight: 3.9990 chunk 125 optimal weight: 0.0010 chunk 9 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.7248 ------------------------------------------------------------------------------- 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** ** B 339 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 168 ASN ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.142974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118243 restraints weight = 10736.856| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.49 r_work: 0.3354 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1601 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= 0.198 Angle : 0.512 7.435 14464 Z= 0.252 Chirality : 0.041 0.141 1644 Planarity : 0.003 0.029 1880 Dihedral : 4.733 45.613 1482 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.16 % Allowed : 17.00 % Favored : 80.85 % 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: 1.56 (0.23), residues: 1364 helix: 2.44 (0.19), residues: 720 sheet: -1.85 (0.29), residues: 216 loop : 0.32 (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 D 80 PHE 0.013 0.002 PHE C 144 TYR 0.018 0.002 TYR C 213 ARG 0.002 0.000 ARG B 42 ********************** 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 104 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 1.187 Fit side-chains REVERT: A 91 ARG cc_start: 0.7942 (mtp85) cc_final: 0.7685 (mtm110) REVERT: A 295 TRP cc_start: 0.8794 (OUTLIER) cc_final: 0.6885 (m-90) REVERT: A 325 GLU cc_start: 0.6023 (OUTLIER) cc_final: 0.5668 (tp30) REVERT: B 295 TRP cc_start: 0.8749 (OUTLIER) cc_final: 0.6764 (m-90) REVERT: B 303 ARG cc_start: 0.6235 (OUTLIER) cc_final: 0.5366 (ttt180) REVERT: C 42 ARG cc_start: 0.6118 (mmm160) cc_final: 0.5887 (mtp180) REVERT: C 295 TRP cc_start: 0.8769 (OUTLIER) cc_final: 0.6844 (m-90) REVERT: D 295 TRP cc_start: 0.8778 (OUTLIER) cc_final: 0.6749 (m-90) REVERT: D 303 ARG cc_start: 0.6221 (mtp-110) cc_final: 0.5277 (ttp-170) outliers start: 24 outliers final: 14 residues processed: 98 average time/residue: 1.5764 time to fit residues: 165.2003 Evaluate side-chains 94 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 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 303 ARG 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 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 295 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 61 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 31 optimal weight: 0.1980 chunk 88 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** B 339 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 = 0.3646 r_free = 0.3646 target = 0.143173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118486 restraints weight = 10653.193| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.49 r_work: 0.3357 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.003 0.025 10672 Z= 0.193 Angle : 0.508 7.476 14464 Z= 0.250 Chirality : 0.041 0.141 1644 Planarity : 0.003 0.029 1880 Dihedral : 4.728 45.818 1482 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.98 % Allowed : 17.18 % Favored : 80.85 % 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: 1.56 (0.24), residues: 1364 helix: 2.43 (0.19), residues: 720 sheet: -1.84 (0.29), residues: 216 loop : 0.33 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 C 213 ARG 0.002 0.000 ARG B 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6381.10 seconds wall clock time: 114 minutes 0.73 seconds (6840.73 seconds total)