Starting phenix.real_space_refine on Sat Aug 23 07:48:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8twm_41671/08_2025/8twm_41671.cif Found real_map, /net/cci-nas-00/data/ceres_data/8twm_41671/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8twm_41671/08_2025/8twm_41671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8twm_41671/08_2025/8twm_41671.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8twm_41671/08_2025/8twm_41671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8twm_41671/08_2025/8twm_41671.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.80, per 1000 atoms: 0.26 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: 1.03 Conformation dependent library (CDL) restraints added in 647.1 milliseconds Enol-peptide restraints added in 1.7 microseconds 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: 0.45 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: 1.55 Time building geometry restraints manager: 1.33 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: 0.01 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: 0.960 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.180 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:5.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.330 ------------------------------------------------------------------------------- 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= 0.141 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG A 91 TYR 0.013 0.001 TYR C 213 PHE 0.012 0.002 PHE D 144 TRP 0.014 0.002 TRP C 147 HIS 0.003 0.001 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.00333 (10672) covalent geometry : angle 0.53939 (14464) hydrogen bonds : bond 0.13428 ( 559) hydrogen bonds : angle 5.15020 ( 1602) *********************** 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 : 0.265 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: 0.5897 time to fit residues: 46.1300 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 : 0.257 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.137977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.109132 restraints weight = 10575.900| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.52 r_work: 0.3157 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10672 Z= 0.146 Angle : 0.544 7.338 14464 Z= 0.272 Chirality : 0.040 0.123 1644 Planarity : 0.004 0.040 1880 Dihedral : 5.716 49.985 1498 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.77 % Allowed : 14.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.24), residues: 1364 helix: 2.33 (0.19), residues: 696 sheet: -1.55 (0.34), residues: 184 loop : 0.51 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 91 TYR 0.015 0.002 TYR C 213 PHE 0.013 0.002 PHE D 144 TRP 0.013 0.002 TRP C 147 HIS 0.002 0.001 HIS C 2 Details of bonding type rmsd covalent geometry : bond 0.00344 (10672) covalent geometry : angle 0.54373 (14464) hydrogen bonds : bond 0.03821 ( 559) hydrogen bonds : angle 4.35200 ( 1602) *********************** 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 113 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 60 time to evaluate : 0.271 Fit side-chains REVERT: A 107 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8085 (ttmm) REVERT: A 326 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.5638 (mp0) REVERT: B 311 LYS cc_start: 0.6652 (ttmt) cc_final: 0.5520 (mptt) REVERT: B 326 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.5829 (mp0) outliers start: 53 outliers final: 24 residues processed: 102 average time/residue: 0.5980 time to fit residues: 65.4209 Evaluate side-chains 81 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 54 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 74 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3553 r_free = 0.3553 target = 0.138328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.109411 restraints weight = 10761.198| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.52 r_work: 0.3140 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10672 Z= 0.154 Angle : 0.540 7.127 14464 Z= 0.269 Chirality : 0.041 0.117 1644 Planarity : 0.004 0.037 1880 Dihedral : 5.629 53.722 1490 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.96 % Allowed : 14.48 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.23), residues: 1364 helix: 2.32 (0.19), residues: 696 sheet: -1.58 (0.35), residues: 184 loop : 0.41 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 91 TYR 0.018 0.002 TYR C 213 PHE 0.014 0.002 PHE A 144 TRP 0.016 0.002 TRP C 147 HIS 0.002 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00370 (10672) covalent geometry : angle 0.54012 (14464) hydrogen bonds : bond 0.03653 ( 559) hydrogen bonds : angle 4.16726 ( 1602) *********************** 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 108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 64 time to evaluate : 0.279 Fit side-chains REVERT: A 107 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8093 (ttmm) REVERT: A 326 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.5680 (mp0) REVERT: B 311 LYS cc_start: 0.6818 (ttmt) cc_final: 0.5595 (mptt) REVERT: B 326 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.5792 (mp0) REVERT: D 86 LYS cc_start: 0.7733 (mttp) cc_final: 0.7447 (mtpp) outliers start: 44 outliers final: 19 residues processed: 97 average time/residue: 0.7137 time to fit residues: 73.6583 Evaluate side-chains 76 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 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 326 GLU Chi-restraints excluded: chain C residue 69 VAL 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 173 TYR Chi-restraints excluded: chain D residue 175 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 99 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.136868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.107839 restraints weight = 10653.321| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.53 r_work: 0.3140 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10672 Z= 0.143 Angle : 0.524 6.920 14464 Z= 0.261 Chirality : 0.041 0.115 1644 Planarity : 0.004 0.035 1880 Dihedral : 5.213 56.434 1483 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.23 % Allowed : 14.39 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.23), residues: 1364 helix: 2.40 (0.19), residues: 696 sheet: -1.62 (0.35), residues: 184 loop : 0.34 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 200 TYR 0.018 0.002 TYR B 213 PHE 0.014 0.002 PHE C 144 TRP 0.015 0.002 TRP B 147 HIS 0.002 0.001 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.00344 (10672) covalent geometry : angle 0.52446 (14464) hydrogen bonds : bond 0.03463 ( 559) hydrogen bonds : angle 4.10049 ( 1602) *********************** 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 103 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 56 time to evaluate : 0.434 Fit side-chains REVERT: A 107 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8088 (ttmm) REVERT: A 295 TRP cc_start: 0.8569 (OUTLIER) cc_final: 0.6887 (m-90) REVERT: B 295 TRP cc_start: 0.8586 (OUTLIER) cc_final: 0.6895 (m-90) REVERT: B 311 LYS cc_start: 0.6744 (ttmt) cc_final: 0.5501 (mptt) REVERT: D 86 LYS cc_start: 0.7756 (mttp) cc_final: 0.7487 (mtpp) outliers start: 47 outliers final: 24 residues processed: 93 average time/residue: 0.6875 time to fit residues: 68.4273 Evaluate side-chains 84 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 250 MET Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 35 SER 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 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 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 212 VAL Chi-restraints excluded: chain D residue 250 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 109 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 72 optimal weight: 0.5980 chunk 82 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 11 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.138950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.110058 restraints weight = 10546.586| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.52 r_work: 0.3184 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1211 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= 0.121 Angle : 0.503 6.761 14464 Z= 0.249 Chirality : 0.040 0.114 1644 Planarity : 0.004 0.033 1880 Dihedral : 5.174 59.246 1483 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.05 % Allowed : 14.66 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.23), residues: 1364 helix: 2.55 (0.19), residues: 692 sheet: -1.53 (0.41), residues: 128 loop : 0.18 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 91 TYR 0.015 0.001 TYR B 213 PHE 0.012 0.002 PHE C 144 TRP 0.013 0.002 TRP A 295 HIS 0.001 0.000 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.00289 (10672) covalent geometry : angle 0.50254 (14464) hydrogen bonds : bond 0.03232 ( 559) hydrogen bonds : angle 4.03546 ( 1602) *********************** 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 110 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 65 time to evaluate : 0.347 Fit side-chains REVERT: A 107 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8002 (ttmm) REVERT: A 164 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8306 (tmm) REVERT: A 295 TRP cc_start: 0.8551 (OUTLIER) cc_final: 0.6832 (m-90) REVERT: A 311 LYS cc_start: 0.7226 (ttpt) cc_final: 0.5767 (mptt) REVERT: B 91 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.7106 (ttp80) REVERT: B 295 TRP cc_start: 0.8560 (OUTLIER) cc_final: 0.6824 (m-90) REVERT: B 311 LYS cc_start: 0.6669 (ttmt) cc_final: 0.5432 (mptt) REVERT: D 86 LYS cc_start: 0.7741 (mttp) cc_final: 0.7481 (mtpp) outliers start: 45 outliers final: 28 residues processed: 100 average time/residue: 0.6592 time to fit residues: 70.5232 Evaluate side-chains 93 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 295 TRP 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 91 ARG 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 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 250 MET 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 250 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 5.9990 chunk 131 optimal weight: 0.1980 chunk 80 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 GLN ** B 306 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 = 0.3559 r_free = 0.3559 target = 0.138617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.109742 restraints weight = 10554.478| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.52 r_work: 0.3173 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1261 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= 0.132 Angle : 0.508 6.402 14464 Z= 0.252 Chirality : 0.040 0.111 1644 Planarity : 0.004 0.033 1880 Dihedral : 5.166 58.492 1483 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.14 % Allowed : 15.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.23), residues: 1364 helix: 2.51 (0.19), residues: 696 sheet: -1.54 (0.41), residues: 128 loop : 0.11 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 91 TYR 0.017 0.001 TYR A 213 PHE 0.013 0.002 PHE C 144 TRP 0.015 0.002 TRP A 295 HIS 0.001 0.000 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.00315 (10672) covalent geometry : angle 0.50763 (14464) hydrogen bonds : bond 0.03278 ( 559) hydrogen bonds : angle 4.01519 ( 1602) *********************** 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 110 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 64 time to evaluate : 0.395 Fit side-chains REVERT: A 107 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8008 (ttmm) REVERT: A 295 TRP cc_start: 0.8648 (OUTLIER) cc_final: 0.6809 (m-90) REVERT: A 311 LYS cc_start: 0.7299 (ttpt) cc_final: 0.5785 (mptt) REVERT: B 91 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.7107 (ttp80) REVERT: B 295 TRP cc_start: 0.8662 (OUTLIER) cc_final: 0.6929 (m-90) REVERT: B 311 LYS cc_start: 0.6712 (ttmt) cc_final: 0.5464 (mptt) REVERT: C 91 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.5296 (mtp85) REVERT: C 326 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.5676 (mp0) REVERT: D 86 LYS cc_start: 0.7801 (mttp) cc_final: 0.7517 (mtpp) outliers start: 46 outliers final: 26 residues processed: 100 average time/residue: 0.6565 time to fit residues: 70.2071 Evaluate side-chains 92 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 250 MET Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 91 ARG 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 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 250 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 67 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.138931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.109989 restraints weight = 10599.722| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.51 r_work: 0.3131 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1328 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= 0.141 Angle : 0.515 6.331 14464 Z= 0.256 Chirality : 0.040 0.114 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.141 54.842 1483 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.87 % Allowed : 15.92 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.23), residues: 1364 helix: 2.47 (0.19), residues: 696 sheet: -1.55 (0.41), residues: 128 loop : 0.09 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 91 TYR 0.018 0.002 TYR A 213 PHE 0.014 0.002 PHE C 144 TRP 0.021 0.002 TRP C 295 HIS 0.002 0.001 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.00338 (10672) covalent geometry : angle 0.51495 (14464) hydrogen bonds : bond 0.03349 ( 559) hydrogen bonds : angle 4.01913 ( 1602) *********************** 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 105 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 62 time to evaluate : 0.413 Fit side-chains REVERT: A 107 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8024 (ttmm) REVERT: A 295 TRP cc_start: 0.8658 (OUTLIER) cc_final: 0.6841 (m-90) REVERT: A 311 LYS cc_start: 0.7261 (ttpt) cc_final: 0.5748 (mptt) REVERT: B 91 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.7054 (ttp80) REVERT: B 295 TRP cc_start: 0.8675 (OUTLIER) cc_final: 0.6863 (m-90) REVERT: B 311 LYS cc_start: 0.6732 (ttmt) cc_final: 0.5468 (mptt) REVERT: B 341 LYS cc_start: 0.8038 (mtmm) cc_final: 0.7745 (mtpp) REVERT: C 91 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.5230 (mtp85) REVERT: C 326 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.5645 (mp0) REVERT: D 86 LYS cc_start: 0.7775 (mttp) cc_final: 0.7493 (mtpp) REVERT: D 91 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.5473 (mtp85) outliers start: 43 outliers final: 27 residues processed: 95 average time/residue: 0.6507 time to fit residues: 66.0969 Evaluate side-chains 95 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 61 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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 91 ARG 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 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 326 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 91 ARG 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 320 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 61 optimal weight: 5.9990 chunk 109 optimal weight: 0.0030 chunk 32 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111523 restraints weight = 10598.079| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.50 r_work: 0.3175 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1384 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= 0.125 Angle : 0.501 6.337 14464 Z= 0.249 Chirality : 0.040 0.122 1644 Planarity : 0.004 0.031 1880 Dihedral : 5.027 51.248 1483 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.42 % Allowed : 16.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.23), residues: 1364 helix: 2.53 (0.19), residues: 696 sheet: -1.55 (0.41), residues: 128 loop : 0.08 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 91 TYR 0.016 0.001 TYR A 213 PHE 0.013 0.002 PHE C 144 TRP 0.015 0.002 TRP A 295 HIS 0.001 0.000 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.00300 (10672) covalent geometry : angle 0.50083 (14464) hydrogen bonds : bond 0.03220 ( 559) hydrogen bonds : angle 3.98601 ( 1602) *********************** 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 100 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 62 time to evaluate : 0.372 Fit side-chains REVERT: A 107 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8020 (ttmm) REVERT: A 295 TRP cc_start: 0.8663 (OUTLIER) cc_final: 0.6760 (m-90) REVERT: A 311 LYS cc_start: 0.7251 (ttpt) cc_final: 0.5790 (mptt) REVERT: B 91 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.7072 (ttp80) REVERT: B 295 TRP cc_start: 0.8677 (OUTLIER) cc_final: 0.6749 (m-90) REVERT: B 311 LYS cc_start: 0.6746 (ttmt) cc_final: 0.5500 (mptt) REVERT: C 91 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.4982 (mtp85) REVERT: C 295 TRP cc_start: 0.8551 (OUTLIER) cc_final: 0.6671 (m-90) REVERT: C 326 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.5663 (mp0) REVERT: C 341 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7779 (mtpp) REVERT: D 86 LYS cc_start: 0.7738 (mttp) cc_final: 0.7451 (mtpp) REVERT: D 91 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.5420 (mtp85) outliers start: 38 outliers final: 27 residues processed: 93 average time/residue: 0.6568 time to fit residues: 65.0745 Evaluate side-chains 95 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 60 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 295 TRP Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 91 ARG 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 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 295 TRP Chi-restraints excluded: chain C residue 320 LEU 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 91 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.135663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.106732 restraints weight = 10636.876| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.50 r_work: 0.3137 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10672 Z= 0.175 Angle : 0.542 6.165 14464 Z= 0.270 Chirality : 0.042 0.116 1644 Planarity : 0.004 0.033 1880 Dihedral : 5.120 47.975 1483 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.60 % Allowed : 16.46 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.23), residues: 1364 helix: 2.38 (0.19), residues: 696 sheet: -1.56 (0.42), residues: 128 loop : 0.07 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 91 TYR 0.020 0.002 TYR A 213 PHE 0.016 0.002 PHE C 144 TRP 0.016 0.003 TRP B 147 HIS 0.002 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00422 (10672) covalent geometry : angle 0.54193 (14464) hydrogen bonds : bond 0.03580 ( 559) hydrogen bonds : angle 4.07537 ( 1602) *********************** 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 108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 68 time to evaluate : 0.385 Fit side-chains REVERT: A 86 LYS cc_start: 0.7745 (mttp) cc_final: 0.7472 (mtpp) REVERT: A 107 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8143 (ttmm) REVERT: A 295 TRP cc_start: 0.8673 (OUTLIER) cc_final: 0.6876 (m-90) REVERT: A 311 LYS cc_start: 0.7335 (ttpt) cc_final: 0.5827 (mptt) REVERT: B 91 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.7086 (ttp80) REVERT: B 295 TRP cc_start: 0.8705 (OUTLIER) cc_final: 0.6920 (m-90) REVERT: B 311 LYS cc_start: 0.6859 (ttmt) cc_final: 0.5570 (mptt) REVERT: C 91 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.5256 (mtp85) REVERT: C 295 TRP cc_start: 0.8666 (OUTLIER) cc_final: 0.6764 (m-90) REVERT: C 326 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.5653 (mp0) REVERT: D 86 LYS cc_start: 0.7761 (mttp) cc_final: 0.7481 (mtpp) REVERT: D 91 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.5417 (mtp85) outliers start: 40 outliers final: 26 residues processed: 98 average time/residue: 0.6428 time to fit residues: 67.5350 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 : 0.256 ------------------------------------------------------------------------------- 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 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 A residue 326 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 91 ARG 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 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 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 91 ARG 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 212 VAL 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 58 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.136670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107915 restraints weight = 10600.502| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.49 r_work: 0.3152 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 : 0.004 0.033 10672 Z= 0.148 Angle : 0.524 6.229 14464 Z= 0.262 Chirality : 0.041 0.113 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.026 48.390 1483 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.24), residues: 1364 helix: 2.42 (0.19), residues: 696 sheet: -1.64 (0.41), residues: 128 loop : 0.07 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 91 TYR 0.019 0.002 TYR B 213 PHE 0.014 0.002 PHE C 144 TRP 0.024 0.003 TRP D 295 HIS 0.002 0.001 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.00357 (10672) covalent geometry : angle 0.52392 (14464) hydrogen bonds : bond 0.03438 ( 559) hydrogen bonds : angle 4.04985 ( 1602) ********************** 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 101 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 63 time to evaluate : 0.349 Fit side-chains REVERT: A 107 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8081 (ttmm) REVERT: A 295 TRP cc_start: 0.8637 (OUTLIER) cc_final: 0.6729 (m-90) REVERT: A 311 LYS cc_start: 0.7335 (ttpt) cc_final: 0.5838 (mptt) REVERT: B 91 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.7055 (ttp80) REVERT: B 295 TRP cc_start: 0.8653 (OUTLIER) cc_final: 0.6766 (m-90) REVERT: B 311 LYS cc_start: 0.6864 (ttmt) cc_final: 0.5582 (mptt) REVERT: C 91 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.5171 (mtp85) REVERT: C 295 TRP cc_start: 0.8666 (OUTLIER) cc_final: 0.6723 (m-90) REVERT: C 326 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.5713 (mp0) REVERT: D 86 LYS cc_start: 0.7703 (mttp) cc_final: 0.7443 (mtpp) outliers start: 38 outliers final: 27 residues processed: 94 average time/residue: 0.6361 time to fit residues: 63.7455 Evaluate side-chains 96 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 62 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 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 277 GLU 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 91 ARG 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 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 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 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 212 VAL 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 70 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 11 optimal weight: 0.0000 chunk 3 optimal weight: 0.8980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.138174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.109378 restraints weight = 10573.234| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.51 r_work: 0.3175 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1491 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= 0.121 Angle : 0.502 6.217 14464 Z= 0.249 Chirality : 0.040 0.113 1644 Planarity : 0.004 0.031 1880 Dihedral : 4.845 48.534 1483 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.42 % Allowed : 16.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.23), residues: 1364 helix: 2.55 (0.19), residues: 692 sheet: -2.21 (0.44), residues: 88 loop : 0.15 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 91 TYR 0.016 0.002 TYR B 213 PHE 0.012 0.002 PHE C 144 TRP 0.018 0.002 TRP D 295 HIS 0.001 0.001 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.00290 (10672) covalent geometry : angle 0.50188 (14464) hydrogen bonds : bond 0.03194 ( 559) hydrogen bonds : angle 3.99968 ( 1602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3021.94 seconds wall clock time: 52 minutes 39.24 seconds (3159.24 seconds total)