Starting phenix.real_space_refine on Fri Oct 11 20:30:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twm_41671/10_2024/8twm_41671.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twm_41671/10_2024/8twm_41671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twm_41671/10_2024/8twm_41671.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twm_41671/10_2024/8twm_41671.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twm_41671/10_2024/8twm_41671.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twm_41671/10_2024/8twm_41671.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6588 2.51 5 N 1860 2.21 5 O 2308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 10800 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "D" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Time building chain proxies: 7.27, per 1000 atoms: 0.67 Number of scatterers: 10800 At special positions: 0 Unit cell: (103.53, 79.17, 94.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 2308 8.00 N 1860 7.00 C 6588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.5 seconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 8 sheets defined 54.4% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 35 through 45 removed outlier: 3.593A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 180 Processing helix chain 'A' and resid 197 through 219 Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 244 through 260 Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 319 through 339 Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 35 through 45 removed outlier: 3.598A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 180 Processing helix chain 'B' and resid 197 through 219 Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'B' and resid 244 through 260 Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 302 through 314 removed outlier: 6.546A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 319 through 339 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 35 through 45 removed outlier: 3.581A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.914A pdb=" N TYR C 84 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 180 Processing helix chain 'C' and resid 197 through 219 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 244 through 260 Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 302 through 314 removed outlier: 6.414A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 319 through 339 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.836A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 180 Processing helix chain 'D' and resid 197 through 219 Processing helix chain 'D' and resid 222 through 226 Processing helix chain 'D' and resid 244 through 260 Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 302 through 314 removed outlier: 6.424A pdb=" N SER D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 319 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.550A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLY A 105 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL A 76 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LYS A 107 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU A 78 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL A 104 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ALA A 145 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE A 106 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N TRP A 147 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TRP A 147 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A 187 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL A 267 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER A 300 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N PHE A 269 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 32 removed outlier: 6.502A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA B 32 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY B 74 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLY B 105 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LYS B 107 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU B 78 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL B 104 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA B 145 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE B 106 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N TRP B 147 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP B 147 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 187 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL B 267 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER B 300 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N PHE B 269 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 32 removed outlier: 6.531A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ALA C 32 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLY C 74 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLY C 105 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL C 76 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LYS C 107 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU C 78 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL C 104 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ALA C 145 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ILE C 106 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TRP C 147 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP C 147 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 187 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL C 267 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER C 300 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N PHE C 269 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32 removed outlier: 6.539A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA D 32 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY D 74 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLY D 105 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL D 76 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LYS D 107 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU D 78 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL D 104 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ALA D 145 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE D 106 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N TRP D 147 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP D 143 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE D 185 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA D 145 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU D 187 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TRP D 147 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU D 189 " --> pdb=" O TRP D 147 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N CYS D 149 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL D 267 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER D 300 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N PHE D 269 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 559 hydrogen bonds defined for protein. 1602 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.70 Time building geometry restraints manager: 3.03 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.620 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 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:13.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10672 Z= 0.219 Angle : 0.539 7.471 14464 Z= 0.274 Chirality : 0.039 0.119 1644 Planarity : 0.004 0.046 1880 Dihedral : 16.696 88.838 3984 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.89 % Allowed : 19.06 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.23), residues: 1364 helix: 2.14 (0.19), residues: 692 sheet: -1.34 (0.35), residues: 184 loop : 0.37 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 147 HIS 0.003 0.001 HIS C 4 PHE 0.012 0.002 PHE D 144 TYR 0.013 0.001 TYR C 213 ARG 0.006 0.001 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 54 time to evaluate : 1.219 Fit side-chains REVERT: A 152 LYS cc_start: 0.7608 (pttp) cc_final: 0.6385 (ptpt) REVERT: A 311 LYS cc_start: 0.6691 (mptt) cc_final: 0.6261 (ttpt) REVERT: B 152 LYS cc_start: 0.7661 (pttp) cc_final: 0.6452 (ptpt) REVERT: B 311 LYS cc_start: 0.6415 (ttmt) cc_final: 0.5296 (mptt) REVERT: D 311 LYS cc_start: 0.7295 (ttpt) cc_final: 0.7038 (tttt) outliers start: 21 outliers final: 18 residues processed: 73 average time/residue: 1.5007 time to fit residues: 117.9951 Evaluate side-chains 71 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 53 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 106 optimal weight: 0.0470 chunk 41 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 ASN C 319 ASN D 166 ASN D 168 ASN D 319 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.0713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10672 Z= 0.229 Angle : 0.546 7.465 14464 Z= 0.273 Chirality : 0.041 0.122 1644 Planarity : 0.004 0.040 1880 Dihedral : 5.713 50.036 1498 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.86 % Allowed : 14.57 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.24), residues: 1364 helix: 2.33 (0.19), residues: 696 sheet: -1.54 (0.34), residues: 184 loop : 0.51 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 147 HIS 0.002 0.001 HIS C 2 PHE 0.013 0.002 PHE D 144 TYR 0.016 0.002 TYR C 213 ARG 0.003 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 61 time to evaluate : 1.325 Fit side-chains REVERT: A 107 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7672 (ttmm) REVERT: A 326 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.5390 (mp0) REVERT: B 311 LYS cc_start: 0.6533 (ttmt) cc_final: 0.5434 (mptt) REVERT: B 326 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5484 (mp0) outliers start: 54 outliers final: 24 residues processed: 104 average time/residue: 1.4809 time to fit residues: 165.9760 Evaluate side-chains 80 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 53 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 68 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 10672 Z= 0.540 Angle : 0.693 7.320 14464 Z= 0.350 Chirality : 0.048 0.142 1644 Planarity : 0.005 0.042 1880 Dihedral : 6.525 59.975 1490 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.68 % Allowed : 13.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.23), residues: 1364 helix: 1.71 (0.18), residues: 696 sheet: -1.62 (0.44), residues: 128 loop : 0.03 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP D 147 HIS 0.003 0.001 HIS C 4 PHE 0.020 0.003 PHE D 144 TYR 0.029 0.003 TYR A 213 ARG 0.008 0.001 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 75 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: A 146 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8214 (tttm) REVERT: A 311 LYS cc_start: 0.6367 (mptt) cc_final: 0.6101 (ttpt) REVERT: B 107 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.7784 (ttmm) REVERT: B 311 LYS cc_start: 0.6935 (ttmt) cc_final: 0.5688 (mptt) REVERT: C 91 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6645 (ttp80) REVERT: D 68 ARG cc_start: 0.7201 (ptm-80) cc_final: 0.6944 (ptm-80) REVERT: D 86 LYS cc_start: 0.7512 (mttp) cc_final: 0.7260 (mtpp) outliers start: 52 outliers final: 30 residues processed: 116 average time/residue: 1.6183 time to fit residues: 200.4938 Evaluate side-chains 95 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 62 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 146 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 320 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1322 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= 0.245 Angle : 0.551 6.865 14464 Z= 0.278 Chirality : 0.041 0.118 1644 Planarity : 0.004 0.038 1880 Dihedral : 6.122 58.760 1490 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.77 % Allowed : 14.84 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.23), residues: 1364 helix: 2.09 (0.19), residues: 696 sheet: -1.69 (0.42), residues: 128 loop : 0.08 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 147 HIS 0.003 0.001 HIS B 4 PHE 0.014 0.002 PHE A 144 TYR 0.017 0.002 TYR C 213 ARG 0.003 0.000 ARG C 56 *********************** 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 123 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 70 time to evaluate : 1.143 Fit side-chains REVERT: A 91 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6601 (ttp80) REVERT: A 107 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7724 (ttmm) REVERT: A 295 TRP cc_start: 0.8148 (OUTLIER) cc_final: 0.6798 (m-90) REVERT: A 326 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5494 (mp0) REVERT: B 165 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7374 (mm-30) REVERT: B 295 TRP cc_start: 0.8167 (OUTLIER) cc_final: 0.6811 (m-90) REVERT: B 311 LYS cc_start: 0.6720 (ttmt) cc_final: 0.5479 (mptt) REVERT: C 295 TRP cc_start: 0.8163 (OUTLIER) cc_final: 0.6818 (m-90) REVERT: D 86 LYS cc_start: 0.7478 (mttp) cc_final: 0.7227 (mtpp) REVERT: D 295 TRP cc_start: 0.8123 (OUTLIER) cc_final: 0.6788 (m-90) outliers start: 53 outliers final: 28 residues processed: 113 average time/residue: 1.6080 time to fit residues: 193.8890 Evaluate side-chains 95 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 59 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 GLN C 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10672 Z= 0.233 Angle : 0.533 6.758 14464 Z= 0.266 Chirality : 0.040 0.124 1644 Planarity : 0.004 0.035 1880 Dihedral : 5.717 55.787 1487 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.95 % Allowed : 15.20 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.23), residues: 1364 helix: 2.27 (0.19), residues: 692 sheet: -1.73 (0.41), residues: 128 loop : 0.11 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 147 HIS 0.002 0.001 HIS D 80 PHE 0.014 0.002 PHE C 144 TYR 0.019 0.002 TYR B 213 ARG 0.002 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 64 time to evaluate : 1.216 Fit side-chains REVERT: A 91 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6543 (ttp80) REVERT: A 107 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7690 (ttmm) REVERT: A 165 GLU cc_start: 0.7508 (tp30) cc_final: 0.7233 (mm-30) REVERT: A 295 TRP cc_start: 0.8245 (OUTLIER) cc_final: 0.6593 (m-90) REVERT: A 311 LYS cc_start: 0.7173 (ttpt) cc_final: 0.5638 (mptt) REVERT: A 326 GLU cc_start: 0.6163 (OUTLIER) cc_final: 0.5432 (mp0) REVERT: B 91 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6812 (ttp80) REVERT: B 165 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7362 (mm-30) REVERT: B 295 TRP cc_start: 0.8255 (OUTLIER) cc_final: 0.6621 (m-90) REVERT: B 311 LYS cc_start: 0.6692 (ttmt) cc_final: 0.5434 (mptt) REVERT: C 295 TRP cc_start: 0.8263 (OUTLIER) cc_final: 0.6644 (m-90) REVERT: D 86 LYS cc_start: 0.7427 (mttp) cc_final: 0.7158 (mtpp) REVERT: D 91 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6701 (ttp80) REVERT: D 295 TRP cc_start: 0.8224 (OUTLIER) cc_final: 0.6597 (m-90) outliers start: 55 outliers final: 26 residues processed: 108 average time/residue: 1.5044 time to fit residues: 173.6187 Evaluate side-chains 98 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 62 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 3 SER 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 165 GLU Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 3 SER 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 295 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1447 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= 0.196 Angle : 0.508 6.738 14464 Z= 0.253 Chirality : 0.040 0.113 1644 Planarity : 0.004 0.033 1880 Dihedral : 5.448 52.269 1487 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.32 % Allowed : 16.01 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.23), residues: 1364 helix: 2.41 (0.19), residues: 692 sheet: -2.37 (0.43), residues: 88 loop : 0.08 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 295 HIS 0.001 0.000 HIS C 4 PHE 0.013 0.001 PHE C 144 TYR 0.016 0.002 TYR B 213 ARG 0.003 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 64 time to evaluate : 1.369 Fit side-chains REVERT: A 107 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7638 (ttmm) REVERT: A 295 TRP cc_start: 0.8248 (OUTLIER) cc_final: 0.6587 (m-90) REVERT: A 311 LYS cc_start: 0.7179 (ttpt) cc_final: 0.5662 (mptt) REVERT: A 326 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5468 (mp0) REVERT: B 53 GLU cc_start: 0.6800 (tp30) cc_final: 0.6542 (tp30) REVERT: B 91 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6626 (ttp80) REVERT: B 295 TRP cc_start: 0.8258 (OUTLIER) cc_final: 0.6597 (m-90) REVERT: B 311 LYS cc_start: 0.6609 (ttmt) cc_final: 0.5392 (mptt) REVERT: C 91 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.5035 (mtp85) REVERT: C 295 TRP cc_start: 0.8265 (OUTLIER) cc_final: 0.6609 (m-90) REVERT: D 86 LYS cc_start: 0.7405 (mttp) cc_final: 0.7145 (mtpp) REVERT: D 91 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6692 (ttp80) REVERT: D 295 TRP cc_start: 0.8214 (OUTLIER) cc_final: 0.6440 (m-90) outliers start: 48 outliers final: 34 residues processed: 101 average time/residue: 1.6446 time to fit residues: 177.2162 Evaluate side-chains 106 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 63 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER 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 A residue 320 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 3 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 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 295 TRP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 3 SER 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 Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: