Starting phenix.real_space_refine on Fri Feb 14 21:22:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8twm_41671/02_2025/8twm_41671.cif Found real_map, /net/cci-nas-00/data/ceres_data/8twm_41671/02_2025/8twm_41671.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/8twm_41671/02_2025/8twm_41671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8twm_41671/02_2025/8twm_41671.map" model { file = "/net/cci-nas-00/data/ceres_data/8twm_41671/02_2025/8twm_41671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8twm_41671/02_2025/8twm_41671.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= -0.001 sd= 0.075 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 26 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: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Time building chain proxies: 6.35, per 1000 atoms: 0.59 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: 2.48 Conformation dependent library (CDL) restraints added in 1.5 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: 58 helices and 8 sheets defined 54.4% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 35 through 45 removed outlier: 3.593A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.970A 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 226 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 339 Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 35 through 45 removed outlier: 3.598A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.902A 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 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 226 Processing helix chain 'B' and resid 244 through 260 Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 302 through 314 removed outlier: 6.546A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) 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 339 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 35 through 45 removed outlier: 3.581A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.925A 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 79 through 84 removed outlier: 3.914A pdb=" N TYR C 84 " --> pdb=" O HIS C 80 " (cutoff:3.500A) 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 226 Processing helix chain 'C' and resid 244 through 260 Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 302 through 314 removed outlier: 6.414A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) 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 339 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.836A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 4.079A 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 226 Processing helix chain 'D' and resid 244 through 260 Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 302 through 314 removed outlier: 6.424A pdb=" N SER D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) 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 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.550A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLY A 105 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL A 76 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LYS A 107 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU A 78 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL A 104 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ALA A 145 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE A 106 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N TRP A 147 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TRP A 147 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A 187 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL A 267 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER A 300 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.554A 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 32 removed outlier: 6.502A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA B 32 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY B 74 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLY B 105 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LYS B 107 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU B 78 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL B 104 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA B 145 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE B 106 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N TRP B 147 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP B 147 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 187 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL B 267 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER B 300 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 5.637A 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 32 removed outlier: 6.531A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ALA C 32 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLY C 74 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLY C 105 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL C 76 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LYS C 107 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU C 78 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL C 104 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ALA C 145 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ILE C 106 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TRP C 147 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP C 147 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 187 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL C 267 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER C 300 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 5.629A 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: 6.539A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA D 32 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY D 74 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLY D 105 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL D 76 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LYS D 107 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU D 78 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL D 104 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ALA D 145 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE D 106 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N TRP D 147 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP D 143 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE D 185 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA D 145 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU D 187 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TRP D 147 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU D 189 " --> pdb=" O TRP D 147 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N CYS D 149 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL D 267 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER D 300 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 5.590A 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 114 559 hydrogen bonds defined for protein. 1602 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: 3.71 Time building geometry restraints manager: 2.90 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: 3516 1.34 - 1.46: 1951 1.46 - 1.58: 5149 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 1.473 0.033 3.90e-02 6.57e+02 7.00e-01 bond pdb=" CB PRO B 158 " pdb=" CG PRO B 158 " ideal model delta sigma weight residual 1.506 1.474 0.032 3.90e-02 6.57e+02 6.93e-01 bond pdb=" CB PRO C 158 " pdb=" CG PRO C 158 " ideal model delta sigma weight residual 1.506 1.475 0.031 3.90e-02 6.57e+02 6.36e-01 bond pdb=" CB PRO A 158 " pdb=" CG PRO A 158 " ideal model delta sigma weight residual 1.506 1.475 0.031 3.90e-02 6.57e+02 6.33e-01 bond pdb=" CG1 ILE C 221 " pdb=" CD1 ILE C 221 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 6.05e-01 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 14135 1.49 - 2.99: 263 2.99 - 4.48: 49 4.48 - 5.98: 16 5.98 - 7.47: 1 Bond angle restraints: 14464 Sorted by residual: angle pdb=" N GLY C 74 " pdb=" CA GLY C 74 " pdb=" C GLY C 74 " ideal model delta sigma weight residual 115.66 112.26 3.40 1.56e+00 4.11e-01 4.76e+00 angle pdb=" CA LEU B 61 " pdb=" CB LEU B 61 " pdb=" CG LEU B 61 " ideal model delta sigma weight residual 116.30 123.77 -7.47 3.50e+00 8.16e-02 4.56e+00 angle pdb=" CA TYR C 213 " pdb=" CB TYR C 213 " pdb=" CG TYR C 213 " ideal model delta sigma weight residual 113.90 110.34 3.56 1.80e+00 3.09e-01 3.91e+00 angle pdb=" CA TYR A 213 " pdb=" CB TYR A 213 " pdb=" CG TYR A 213 " ideal model delta sigma weight residual 113.90 110.35 3.55 1.80e+00 3.09e-01 3.90e+00 angle pdb=" CA TYR D 213 " pdb=" CB TYR D 213 " pdb=" CG TYR D 213 " ideal model delta sigma weight residual 113.90 110.38 3.52 1.80e+00 3.09e-01 3.83e+00 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 5663 17.77 - 35.54: 592 35.54 - 53.30: 207 53.30 - 71.07: 29 71.07 - 88.84: 13 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 -134.95 44.95 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 -135.36 -44.64 2 1.50e+01 4.44e-03 1.05e+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 -135.49 -44.51 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 919 0.024 - 0.048: 395 0.048 - 0.072: 183 0.072 - 0.095: 94 0.095 - 0.119: 53 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 3.56e-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 -0.12 2.00e-01 2.50e+01 3.52e-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 -0.12 2.00e-01 2.50e+01 3.49e-01 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 289 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO C 290 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 290 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 290 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 289 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO B 290 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 290 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 290 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 289 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO A 290 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " 0.024 5.00e-02 4.00e+02 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 577 2.71 - 3.25: 11262 3.25 - 3.80: 21216 3.80 - 4.35: 27800 4.35 - 4.90: 43534 Nonbonded interactions: 104389 Sorted by model distance: nonbonded pdb=" O GLY D 154 " pdb=" NH2 ARG D 200 " model vdw 2.158 3.120 nonbonded pdb=" OD2 ASP D 143 " pdb=" O HOH D 401 " model vdw 2.180 3.040 nonbonded pdb=" O GLY C 154 " pdb=" NH2 ARG C 200 " model vdw 2.187 3.120 nonbonded pdb=" O GLY A 154 " pdb=" NH2 ARG A 200 " model vdw 2.191 3.120 nonbonded pdb=" O GLY B 154 " pdb=" NH2 ARG B 200 " model vdw 2.197 3.120 ... (remaining 104384 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.900 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 0.033 10672 Z= 0.219 Angle : 0.539 7.471 14464 Z= 0.274 Chirality : 0.039 0.119 1644 Planarity : 0.004 0.046 1880 Dihedral : 16.696 88.838 3984 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.89 % Allowed : 19.06 % Favored : 79.05 % 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: 1.47 (0.23), residues: 1364 helix: 2.14 (0.19), residues: 692 sheet: -1.34 (0.35), residues: 184 loop : 0.37 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 147 HIS 0.003 0.001 HIS C 4 PHE 0.012 0.002 PHE D 144 TYR 0.013 0.001 TYR C 213 ARG 0.006 0.001 ARG A 91 *********************** 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 75 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 1.324 Fit side-chains REVERT: A 152 LYS cc_start: 0.7608 (pttp) cc_final: 0.6385 (ptpt) REVERT: A 311 LYS cc_start: 0.6691 (mptt) cc_final: 0.6261 (ttpt) REVERT: B 152 LYS cc_start: 0.7661 (pttp) cc_final: 0.6452 (ptpt) REVERT: B 311 LYS cc_start: 0.6415 (ttmt) cc_final: 0.5296 (mptt) REVERT: D 311 LYS cc_start: 0.7295 (ttpt) cc_final: 0.7038 (tttt) outliers start: 21 outliers final: 18 residues processed: 73 average time/residue: 1.4663 time to fit residues: 115.5994 Evaluate side-chains 71 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE 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 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 271 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 C residue 326 GLU 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 320 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 106 optimal weight: 0.0470 chunk 41 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 ASN C 319 ASN D 166 ASN D 168 ASN D 319 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.139138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.110336 restraints weight = 10636.722| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.51 r_work: 0.3180 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.0713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10672 Z= 0.229 Angle : 0.546 7.465 14464 Z= 0.273 Chirality : 0.041 0.122 1644 Planarity : 0.004 0.040 1880 Dihedral : 5.713 50.036 1498 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.86 % Allowed : 14.57 % Favored : 80.58 % 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 (0.24), residues: 1364 helix: 2.33 (0.19), residues: 696 sheet: -1.54 (0.34), residues: 184 loop : 0.51 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 147 HIS 0.002 0.001 HIS C 2 PHE 0.013 0.002 PHE D 144 TYR 0.016 0.002 TYR C 213 ARG 0.003 0.000 ARG A 91 *********************** 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 115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 61 time to evaluate : 1.079 Fit side-chains REVERT: A 107 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8086 (ttmm) REVERT: A 326 GLU cc_start: 0.6302 (OUTLIER) cc_final: 0.5655 (mp0) REVERT: B 311 LYS cc_start: 0.6650 (ttmt) cc_final: 0.5518 (mptt) REVERT: B 326 GLU cc_start: 0.6475 (OUTLIER) cc_final: 0.5835 (mp0) outliers start: 54 outliers final: 24 residues processed: 104 average time/residue: 1.4053 time to fit residues: 157.7633 Evaluate side-chains 80 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 53 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 326 GLU 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 175 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 326 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 175 SER Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 7 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN D 168 ASN D 180 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.132520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.103518 restraints weight = 10818.057| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.49 r_work: 0.3068 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1059 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= 0.380 Angle : 0.614 7.234 14464 Z= 0.308 Chirality : 0.044 0.129 1644 Planarity : 0.005 0.040 1880 Dihedral : 6.078 56.518 1490 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.95 % Allowed : 13.85 % 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: 1.30 (0.23), residues: 1364 helix: 2.01 (0.19), residues: 696 sheet: -1.61 (0.36), residues: 184 loop : 0.32 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 147 HIS 0.003 0.001 HIS C 80 PHE 0.017 0.002 PHE D 144 TYR 0.024 0.002 TYR A 213 ARG 0.005 0.001 ARG A 91 *********************** 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 123 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 68 time to evaluate : 1.265 Fit side-chains REVERT: A 107 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8234 (ttmm) REVERT: B 107 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8150 (ttmm) REVERT: B 311 LYS cc_start: 0.6899 (ttmt) cc_final: 0.5622 (mptt) REVERT: B 326 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.5798 (mp0) REVERT: C 91 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6741 (ttp80) REVERT: D 86 LYS cc_start: 0.7782 (mttp) cc_final: 0.7533 (mtpp) outliers start: 55 outliers final: 30 residues processed: 108 average time/residue: 1.5221 time to fit residues: 176.3525 Evaluate side-chains 92 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 58 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 134 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 133 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.132017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.102876 restraints weight = 10618.999| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.51 r_work: 0.3082 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10672 Z= 0.293 Angle : 0.562 6.875 14464 Z= 0.282 Chirality : 0.042 0.117 1644 Planarity : 0.004 0.038 1880 Dihedral : 5.912 59.924 1487 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.95 % Allowed : 13.94 % 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: 1.43 (0.23), residues: 1364 helix: 2.14 (0.19), residues: 696 sheet: -1.62 (0.43), residues: 128 loop : 0.11 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 147 HIS 0.002 0.001 HIS C 4 PHE 0.015 0.002 PHE A 144 TYR 0.020 0.002 TYR B 213 ARG 0.003 0.000 ARG A 91 *********************** 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 122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 67 time to evaluate : 1.242 Fit side-chains REVERT: A 91 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6798 (ttp80) REVERT: A 107 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8178 (ttmm) REVERT: A 295 TRP cc_start: 0.8624 (OUTLIER) cc_final: 0.7129 (m-90) REVERT: A 311 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6700 (ttpt) REVERT: B 295 TRP cc_start: 0.8651 (OUTLIER) cc_final: 0.7184 (m-90) REVERT: B 311 LYS cc_start: 0.6806 (ttmt) cc_final: 0.5546 (mptt) REVERT: C 295 TRP cc_start: 0.8636 (OUTLIER) cc_final: 0.7149 (m-90) REVERT: D 86 LYS cc_start: 0.7803 (mttp) cc_final: 0.7553 (mtpp) REVERT: D 295 TRP cc_start: 0.8626 (OUTLIER) cc_final: 0.7020 (m-90) outliers start: 55 outliers final: 27 residues processed: 109 average time/residue: 1.6004 time to fit residues: 186.3744 Evaluate side-chains 99 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 65 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 212 VAL 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 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 212 VAL 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 D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 100 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.136674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.107796 restraints weight = 10542.462| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.49 r_work: 0.3138 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10672 Z= 0.222 Angle : 0.525 6.752 14464 Z= 0.262 Chirality : 0.040 0.114 1644 Planarity : 0.004 0.035 1880 Dihedral : 5.675 58.141 1487 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.50 % Allowed : 15.11 % 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: 1.60 (0.23), residues: 1364 helix: 2.37 (0.19), residues: 692 sheet: -1.68 (0.41), residues: 128 loop : 0.12 (0.29), residues: 544 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 0.014 0.002 PHE C 144 TYR 0.017 0.002 TYR C 213 ARG 0.003 0.000 ARG C 91 *********************** 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 113 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 63 time to evaluate : 1.249 Fit side-chains REVERT: A 91 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6749 (ttp80) REVERT: A 107 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8075 (ttmm) REVERT: A 295 TRP cc_start: 0.8598 (OUTLIER) cc_final: 0.6898 (m-90) REVERT: A 311 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.5772 (mptt) REVERT: B 295 TRP cc_start: 0.8642 (OUTLIER) cc_final: 0.6958 (m-90) REVERT: B 311 LYS cc_start: 0.6784 (ttmt) cc_final: 0.5527 (mptt) REVERT: C 295 TRP cc_start: 0.8612 (OUTLIER) cc_final: 0.6916 (m-90) REVERT: D 86 LYS cc_start: 0.7805 (mttp) cc_final: 0.7509 (mtpp) REVERT: D 295 TRP cc_start: 0.8593 (OUTLIER) cc_final: 0.6945 (m-90) outliers start: 50 outliers final: 23 residues processed: 100 average time/residue: 1.5556 time to fit residues: 166.6143 Evaluate side-chains 90 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 212 VAL 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 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 212 VAL 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 131 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 128 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.137212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.108339 restraints weight = 10685.173| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.50 r_work: 0.3157 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1366 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= 0.215 Angle : 0.518 6.716 14464 Z= 0.258 Chirality : 0.040 0.112 1644 Planarity : 0.004 0.034 1880 Dihedral : 5.470 54.291 1487 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.87 % Allowed : 16.28 % Favored : 79.86 % 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: 1.60 (0.23), residues: 1364 helix: 2.39 (0.19), residues: 696 sheet: -1.68 (0.41), residues: 128 loop : 0.07 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 295 HIS 0.001 0.001 HIS C 4 PHE 0.013 0.002 PHE C 144 TYR 0.018 0.002 TYR C 213 ARG 0.003 0.000 ARG C 91 *********************** 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 106 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 63 time to evaluate : 1.078 Fit side-chains REVERT: A 91 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.6703 (ttp80) REVERT: A 107 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8043 (ttmm) REVERT: A 295 TRP cc_start: 0.8667 (OUTLIER) cc_final: 0.6909 (m-90) REVERT: A 311 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.5746 (mptt) REVERT: B 53 GLU cc_start: 0.6955 (tp30) cc_final: 0.6631 (tp30) REVERT: B 295 TRP cc_start: 0.8687 (OUTLIER) cc_final: 0.6942 (m-90) REVERT: B 311 LYS cc_start: 0.6757 (ttmt) cc_final: 0.5494 (mptt) REVERT: C 91 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.5274 (mtp85) REVERT: C 295 TRP cc_start: 0.8676 (OUTLIER) cc_final: 0.6939 (m-90) REVERT: C 326 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5716 (mp0) REVERT: D 86 LYS cc_start: 0.7796 (mttp) cc_final: 0.7516 (mtpp) REVERT: D 295 TRP cc_start: 0.8663 (OUTLIER) cc_final: 0.6816 (m-90) outliers start: 43 outliers final: 27 residues processed: 94 average time/residue: 1.7192 time to fit residues: 172.9420 Evaluate side-chains 95 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 59 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 39 ILE 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 212 VAL Chi-restraints excluded: chain D residue 232 MET 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: 0.6980 chunk 59 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.139458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110680 restraints weight = 10688.172| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.51 r_work: 0.3146 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10672 Z= 0.197 Angle : 0.504 6.634 14464 Z= 0.250 Chirality : 0.040 0.111 1644 Planarity : 0.004 0.033 1880 Dihedral : 5.111 48.874 1484 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.87 % Allowed : 16.28 % Favored : 79.86 % 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: 1.69 (0.24), residues: 1364 helix: 2.50 (0.19), residues: 692 sheet: -1.71 (0.40), residues: 128 loop : 0.08 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 295 HIS 0.001 0.001 HIS A 220 PHE 0.013 0.002 PHE C 144 TYR 0.016 0.002 TYR C 213 ARG 0.001 0.000 ARG B 258 *********************** 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 109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 66 time to evaluate : 1.170 Fit side-chains REVERT: A 107 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.7992 (ttmm) REVERT: A 295 TRP cc_start: 0.8654 (OUTLIER) cc_final: 0.6840 (m-90) REVERT: A 311 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.5724 (mptt) REVERT: B 295 TRP cc_start: 0.8673 (OUTLIER) cc_final: 0.6835 (m-90) REVERT: B 311 LYS cc_start: 0.6695 (ttmt) cc_final: 0.5453 (mptt) REVERT: B 341 LYS cc_start: 0.8080 (mtmm) cc_final: 0.7805 (mtpp) REVERT: C 91 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.5069 (mtp85) REVERT: C 295 TRP cc_start: 0.8667 (OUTLIER) cc_final: 0.6869 (m-90) REVERT: C 326 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.5617 (mp0) REVERT: D 86 LYS cc_start: 0.7705 (mttp) cc_final: 0.7424 (mtpp) REVERT: D 295 TRP cc_start: 0.8632 (OUTLIER) cc_final: 0.6702 (m-90) outliers start: 43 outliers final: 24 residues processed: 97 average time/residue: 1.6723 time to fit residues: 173.3798 Evaluate side-chains 93 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 61 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 232 MET 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: 3.9990 chunk 13 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.137464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.108540 restraints weight = 10473.814| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.51 r_work: 0.3170 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1445 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= 0.211 Angle : 0.510 6.390 14464 Z= 0.253 Chirality : 0.040 0.112 1644 Planarity : 0.004 0.033 1880 Dihedral : 5.002 48.255 1483 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.69 % Allowed : 16.64 % Favored : 79.68 % 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 (0.24), residues: 1364 helix: 2.48 (0.19), residues: 696 sheet: -1.71 (0.40), residues: 128 loop : 0.06 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 295 HIS 0.002 0.001 HIS C 4 PHE 0.013 0.002 PHE A 144 TYR 0.018 0.002 TYR C 213 ARG 0.002 0.000 ARG C 91 *********************** 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 107 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 66 time to evaluate : 1.176 Fit side-chains REVERT: A 107 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8013 (ttmm) REVERT: A 295 TRP cc_start: 0.8692 (OUTLIER) cc_final: 0.6770 (m-90) REVERT: A 311 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.5739 (mptt) REVERT: B 295 TRP cc_start: 0.8706 (OUTLIER) cc_final: 0.6898 (m-90) REVERT: B 311 LYS cc_start: 0.6721 (ttmt) cc_final: 0.5468 (mptt) REVERT: B 329 LYS cc_start: 0.6939 (ptpp) cc_final: 0.6583 (pttt) REVERT: C 91 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.5244 (mtp85) REVERT: C 295 TRP cc_start: 0.8695 (OUTLIER) cc_final: 0.6800 (m-90) REVERT: C 326 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.5651 (mp0) REVERT: C 341 LYS cc_start: 0.8031 (mtmm) cc_final: 0.7757 (mtpp) REVERT: D 86 LYS cc_start: 0.7721 (mttp) cc_final: 0.7439 (mtpp) REVERT: D 295 TRP cc_start: 0.8699 (OUTLIER) cc_final: 0.6795 (m-90) outliers start: 41 outliers final: 26 residues processed: 96 average time/residue: 1.4342 time to fit residues: 148.0547 Evaluate side-chains 98 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 64 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 250 MET 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: 4.9990 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 GLN D 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.132896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.103814 restraints weight = 10600.678| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.51 r_work: 0.3108 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10672 Z= 0.293 Angle : 0.551 6.269 14464 Z= 0.276 Chirality : 0.042 0.118 1644 Planarity : 0.004 0.034 1880 Dihedral : 5.127 47.917 1483 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.42 % Allowed : 16.82 % Favored : 79.77 % 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: 1.52 (0.24), residues: 1364 helix: 2.30 (0.19), residues: 696 sheet: -1.69 (0.42), residues: 128 loop : 0.05 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 295 HIS 0.002 0.001 HIS C 4 PHE 0.016 0.002 PHE A 144 TYR 0.021 0.002 TYR A 213 ARG 0.003 0.000 ARG C 91 *********************** 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 107 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 69 time to evaluate : 1.133 Fit side-chains REVERT: A 107 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8181 (ttmm) REVERT: A 295 TRP cc_start: 0.8682 (OUTLIER) cc_final: 0.6871 (m-90) REVERT: B 53 GLU cc_start: 0.6991 (tp30) cc_final: 0.6722 (tp30) REVERT: B 295 TRP cc_start: 0.8732 (OUTLIER) cc_final: 0.6952 (m-90) REVERT: B 311 LYS cc_start: 0.6828 (ttmt) cc_final: 0.5555 (mptt) REVERT: B 329 LYS cc_start: 0.7004 (ptpp) cc_final: 0.6645 (pttt) REVERT: C 91 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.5368 (mtp85) REVERT: C 295 TRP cc_start: 0.8724 (OUTLIER) cc_final: 0.6932 (m-90) REVERT: C 326 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.5749 (mp0) REVERT: D 86 LYS cc_start: 0.7767 (mttp) cc_final: 0.7489 (mtpp) REVERT: D 295 TRP cc_start: 0.8711 (OUTLIER) cc_final: 0.6846 (m-90) outliers start: 38 outliers final: 19 residues processed: 96 average time/residue: 1.5717 time to fit residues: 161.4708 Evaluate side-chains 93 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 96 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.107005 restraints weight = 10519.436| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.40 r_work: 0.3077 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10672 Z= 0.347 Angle : 0.585 6.337 14464 Z= 0.294 Chirality : 0.043 0.123 1644 Planarity : 0.004 0.034 1880 Dihedral : 5.229 47.865 1483 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.88 % Allowed : 17.63 % Favored : 79.50 % 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: 1.38 (0.24), residues: 1364 helix: 2.14 (0.19), residues: 696 sheet: -1.79 (0.43), residues: 128 loop : 0.06 (0.30), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 147 HIS 0.003 0.001 HIS C 4 PHE 0.017 0.002 PHE B 144 TYR 0.024 0.002 TYR C 213 ARG 0.003 0.000 ARG C 91 ********************** 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 102 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 1.269 Fit side-chains REVERT: A 107 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7873 (ttmm) REVERT: A 295 TRP cc_start: 0.8327 (OUTLIER) cc_final: 0.6357 (m-90) REVERT: B 53 GLU cc_start: 0.6468 (tp30) cc_final: 0.6176 (tp30) REVERT: B 295 TRP cc_start: 0.8374 (OUTLIER) cc_final: 0.6418 (m-90) REVERT: B 311 LYS cc_start: 0.6370 (ttmt) cc_final: 0.5097 (mptt) REVERT: C 91 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.5056 (mtp85) REVERT: C 295 TRP cc_start: 0.8378 (OUTLIER) cc_final: 0.6443 (m-90) REVERT: C 326 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.5167 (mp0) REVERT: D 68 ARG cc_start: 0.7004 (ptm-80) cc_final: 0.6690 (ptm-80) REVERT: D 86 LYS cc_start: 0.7176 (mttp) cc_final: 0.6905 (mtpp) REVERT: D 295 TRP cc_start: 0.8362 (OUTLIER) cc_final: 0.6436 (m-90) outliers start: 32 outliers final: 19 residues processed: 96 average time/residue: 1.6086 time to fit residues: 165.0238 Evaluate side-chains 94 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 212 VAL 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 B residue 69 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 61 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 ASN D 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.106886 restraints weight = 10564.960| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.48 r_work: 0.3158 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10672 Z= 0.237 Angle : 0.530 6.473 14464 Z= 0.266 Chirality : 0.040 0.115 1644 Planarity : 0.004 0.033 1880 Dihedral : 5.036 48.573 1483 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.43 % Allowed : 18.08 % Favored : 79.50 % 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: 1.52 (0.24), residues: 1364 helix: 2.32 (0.19), residues: 696 sheet: -1.83 (0.41), residues: 128 loop : 0.07 (0.30), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 295 HIS 0.002 0.001 HIS C 4 PHE 0.014 0.002 PHE C 144 TYR 0.019 0.002 TYR C 213 ARG 0.002 0.000 ARG C 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6603.26 seconds wall clock time: 118 minutes 12.92 seconds (7092.92 seconds total)