Starting phenix.real_space_refine on Fri Oct 11 20:32:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twl_41670/10_2024/8twl_41670.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twl_41670/10_2024/8twl_41670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twl_41670/10_2024/8twl_41670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twl_41670/10_2024/8twl_41670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twl_41670/10_2024/8twl_41670.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twl_41670/10_2024/8twl_41670.cif" } resolution = 2.7 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= 0.066 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 39 residue(s): 0.05s 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: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Time building chain proxies: 6.88, per 1000 atoms: 0.64 Number of scatterers: 10800 At special positions: 0 Unit cell: (103.53, 79.17, 96.57, 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: 2.35 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: 60 helices and 8 sheets defined 54.3% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.641A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 180 Processing helix chain 'A' and resid 197 through 219 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 244 through 260 Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.655A pdb=" N GLN A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) 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 37 through 45 removed outlier: 3.630A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 180 Processing helix chain 'B' and resid 197 through 219 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 244 through 260 Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 306 through 314 Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 319 through 339 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 37 through 45 removed outlier: 3.611A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 180 Processing helix chain 'C' and resid 197 through 219 Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 244 through 260 Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.614A pdb=" N GLN C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.056A 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 37 through 45 removed outlier: 3.780A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 4.104A 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 71 Proline residue: D 71 - end of helix Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 180 Processing helix chain 'D' and resid 197 through 219 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 244 through 260 Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 302 through 314 removed outlier: 3.538A pdb=" N GLN D 306 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N SER D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 5.197A 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: 6.451A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N GLY A 105 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 76 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LYS A 107 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU A 78 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 104 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N LYS A 146 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE A 106 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ARG A 148 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP A 147 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL A 267 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER A 300 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE A 269 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.432A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY B 74 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N GLY B 105 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LYS B 107 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU B 78 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 104 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LYS B 146 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 106 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N ARG B 148 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP B 147 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 187 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL B 267 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N SER B 300 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE B 269 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.464A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY C 74 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLY C 105 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL C 76 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LYS C 107 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU C 78 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL C 104 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N LYS C 146 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE C 106 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ARG C 148 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP C 147 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL C 267 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N SER C 300 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 5.513A 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: 6.445A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA D 32 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY D 74 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLY D 105 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL D 76 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS D 107 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU D 78 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL D 104 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N LYS D 146 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE D 106 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ARG D 148 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP D 147 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL D 267 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER D 300 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 5.546A 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 114 554 hydrogen bonds defined for protein. 1590 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: 3.26 Time building geometry restraints manager: 2.73 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: 2029 1.46 - 1.58: 5071 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" CB PRO A 5 " pdb=" CG PRO A 5 " ideal model delta sigma weight residual 1.492 1.534 -0.042 5.00e-02 4.00e+02 6.99e-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 6.94e-01 bond pdb=" CB PRO A 158 " pdb=" CG PRO A 158 " ideal model delta sigma weight residual 1.506 1.474 0.032 3.90e-02 6.57e+02 6.74e-01 bond pdb=" CB PRO D 158 " pdb=" CG PRO D 158 " ideal model delta sigma weight residual 1.506 1.474 0.032 3.90e-02 6.57e+02 6.59e-01 bond pdb=" CB PRO B 5 " pdb=" CG PRO B 5 " ideal model delta sigma weight residual 1.492 1.532 -0.040 5.00e-02 4.00e+02 6.54e-01 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 14120 1.31 - 2.62: 265 2.62 - 3.93: 58 3.93 - 5.24: 13 5.24 - 6.55: 8 Bond angle restraints: 14464 Sorted by residual: angle pdb=" CA LEU C 320 " pdb=" CB LEU C 320 " pdb=" CG LEU C 320 " ideal model delta sigma weight residual 116.30 122.85 -6.55 3.50e+00 8.16e-02 3.50e+00 angle pdb=" CA LEU B 61 " pdb=" CB LEU B 61 " pdb=" CG LEU B 61 " ideal model delta sigma weight residual 116.30 122.82 -6.52 3.50e+00 8.16e-02 3.47e+00 angle pdb=" CA LEU D 320 " pdb=" CB LEU D 320 " pdb=" CG LEU D 320 " ideal model delta sigma weight residual 116.30 122.54 -6.24 3.50e+00 8.16e-02 3.18e+00 angle pdb=" CA LEU D 61 " pdb=" CB LEU D 61 " pdb=" CG LEU D 61 " ideal model delta sigma weight residual 116.30 122.47 -6.17 3.50e+00 8.16e-02 3.11e+00 angle pdb=" CA TYR B 213 " pdb=" CB TYR B 213 " pdb=" CG TYR B 213 " ideal model delta sigma weight residual 113.90 110.74 3.16 1.80e+00 3.09e-01 3.07e+00 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 5655 16.89 - 33.79: 577 33.79 - 50.68: 191 50.68 - 67.58: 60 67.58 - 84.47: 21 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 -134.99 44.99 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG B 59 " pdb=" CD ARG B 59 " pdb=" NE ARG B 59 " pdb=" CZ ARG B 59 " ideal model delta sinusoidal sigma weight residual -90.00 -134.96 44.96 2 1.50e+01 4.44e-03 1.07e+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 -135.61 -44.39 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 933 0.024 - 0.047: 387 0.047 - 0.071: 167 0.071 - 0.094: 102 0.094 - 0.118: 55 Chirality restraints: 1644 Sorted by residual: 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 3.47e-01 chirality pdb=" CA ILE A 77 " pdb=" N ILE A 77 " pdb=" C ILE A 77 " pdb=" CB ILE A 77 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.37e-01 chirality pdb=" CA ILE B 77 " pdb=" N ILE B 77 " pdb=" C ILE B 77 " pdb=" CB ILE B 77 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.26e-01 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 4 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 5 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 5 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 5 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 4 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO B 5 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 5 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 5 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 4 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO D 5 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 5 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 5 " -0.022 5.00e-02 4.00e+02 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 539 2.70 - 3.25: 11198 3.25 - 3.80: 21253 3.80 - 4.35: 27620 4.35 - 4.90: 43526 Nonbonded interactions: 104136 Sorted by model distance: nonbonded pdb=" OG SER D 308 " pdb=" OE1 GLU D 326 " model vdw 2.155 3.040 nonbonded pdb=" NZ LYS C 207 " pdb=" O SER D 217 " model vdw 2.204 3.120 nonbonded pdb=" NZ LYS A 207 " pdb=" O SER B 217 " model vdw 2.204 3.120 nonbonded pdb=" O MET C 250 " pdb=" OG1 THR C 254 " model vdw 2.206 3.040 nonbonded pdb=" O SER A 217 " pdb=" NZ LYS B 207 " model vdw 2.209 3.120 ... (remaining 104131 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: 1.150 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.630 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 0.042 10672 Z= 0.205 Angle : 0.502 6.551 14464 Z= 0.254 Chirality : 0.038 0.118 1644 Planarity : 0.004 0.044 1880 Dihedral : 16.845 84.469 3984 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.34 % Allowed : 18.26 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.23), residues: 1364 helix: 2.12 (0.19), residues: 716 sheet: -1.53 (0.35), residues: 184 loop : 0.29 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 147 HIS 0.002 0.001 HIS D 80 PHE 0.011 0.001 PHE A 144 TYR 0.011 0.001 TYR B 213 ARG 0.004 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 102 time to evaluate : 1.074 Fit side-chains REVERT: C 321 LYS cc_start: 0.7425 (tttm) cc_final: 0.7163 (tptt) outliers start: 26 outliers final: 22 residues processed: 125 average time/residue: 1.4777 time to fit residues: 197.8534 Evaluate side-chains 118 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 81 GLU 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 270 LEU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 270 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.0170 chunk 35 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 241 GLN B 166 ASN B 241 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 ASN C 241 GLN D 166 ASN D 241 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.0763 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= 0.234 Angle : 0.537 7.550 14464 Z= 0.270 Chirality : 0.041 0.148 1644 Planarity : 0.004 0.029 1880 Dihedral : 5.676 47.163 1508 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.15 % Allowed : 15.11 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.23), residues: 1364 helix: 2.25 (0.19), residues: 720 sheet: -1.81 (0.30), residues: 216 loop : 0.43 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 147 HIS 0.003 0.001 HIS A 80 PHE 0.013 0.002 PHE D 144 TYR 0.015 0.002 TYR B 213 ARG 0.003 0.000 ARG A 200 *********************** 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 141 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 106 time to evaluate : 1.129 Fit side-chains REVERT: B 199 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7872 (mtmm) REVERT: C 277 GLU cc_start: 0.7998 (tp30) cc_final: 0.7797 (mm-30) REVERT: D 55 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7277 (mtm110) REVERT: D 199 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7878 (mtmm) outliers start: 35 outliers final: 25 residues processed: 124 average time/residue: 1.6687 time to fit residues: 219.8044 Evaluate side-chains 119 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 270 LEU 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 270 LEU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 55 ARG 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 199 LYS Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 341 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN B 241 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 324 GLN C 136 GLN C 241 GLN C 319 ASN D 241 GLN D 319 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1039 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= 0.241 Angle : 0.523 7.301 14464 Z= 0.262 Chirality : 0.041 0.137 1644 Planarity : 0.004 0.031 1880 Dihedral : 5.220 49.201 1488 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.78 % Allowed : 13.58 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.23), residues: 1364 helix: 2.25 (0.19), residues: 720 sheet: -1.91 (0.30), residues: 216 loop : 0.42 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 147 HIS 0.003 0.001 HIS D 80 PHE 0.014 0.002 PHE C 144 TYR 0.014 0.001 TYR C 213 ARG 0.002 0.000 ARG A 200 *********************** 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 144 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 102 time to evaluate : 1.307 Fit side-chains REVERT: A 107 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7950 (ttmm) REVERT: A 321 LYS cc_start: 0.6636 (mmtm) cc_final: 0.5695 (tptt) REVERT: A 326 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6829 (mm-30) REVERT: D 86 LYS cc_start: 0.7616 (mtpt) cc_final: 0.7047 (mttp) outliers start: 42 outliers final: 32 residues processed: 129 average time/residue: 1.5680 time to fit residues: 216.5017 Evaluate side-chains 119 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 85 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR 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 212 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 241 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1169 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= 0.225 Angle : 0.510 6.995 14464 Z= 0.255 Chirality : 0.040 0.136 1644 Planarity : 0.004 0.031 1880 Dihedral : 5.218 53.751 1488 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.87 % Allowed : 13.58 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.23), residues: 1364 helix: 2.30 (0.19), residues: 720 sheet: -1.95 (0.30), residues: 216 loop : 0.41 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 147 HIS 0.002 0.001 HIS D 80 PHE 0.013 0.002 PHE C 144 TYR 0.014 0.001 TYR C 213 ARG 0.002 0.000 ARG C 68 *********************** 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 147 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 104 time to evaluate : 1.141 Fit side-chains REVERT: A 107 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7958 (ttmm) REVERT: A 321 LYS cc_start: 0.6625 (mmtm) cc_final: 0.5691 (tptt) REVERT: A 326 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6825 (mm-30) REVERT: B 325 GLU cc_start: 0.6963 (tp30) cc_final: 0.6675 (mm-30) REVERT: C 325 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6846 (mm-30) REVERT: D 86 LYS cc_start: 0.7622 (mtpt) cc_final: 0.7005 (mttp) outliers start: 43 outliers final: 32 residues processed: 133 average time/residue: 1.4954 time to fit residues: 211.9851 Evaluate side-chains 124 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 89 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR 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 270 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 8 THR 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 270 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 341 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 241 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1243 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= 0.231 Angle : 0.511 6.863 14464 Z= 0.255 Chirality : 0.040 0.135 1644 Planarity : 0.004 0.031 1880 Dihedral : 5.190 58.214 1486 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.14 % Allowed : 13.49 % Favored : 82.37 % 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: 2.31 (0.19), residues: 720 sheet: -1.95 (0.30), residues: 216 loop : 0.42 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 147 HIS 0.003 0.001 HIS D 80 PHE 0.013 0.002 PHE C 144 TYR 0.014 0.001 TYR C 213 ARG 0.002 0.000 ARG A 200 *********************** 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 149 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 103 time to evaluate : 1.210 Fit side-chains REVERT: A 107 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7961 (ttmm) REVERT: A 321 LYS cc_start: 0.6643 (mmtm) cc_final: 0.5698 (tptt) REVERT: A 326 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6856 (mm-30) REVERT: B 325 GLU cc_start: 0.6999 (tp30) cc_final: 0.6713 (mm-30) REVERT: C 325 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6730 (mm-30) REVERT: D 86 LYS cc_start: 0.7655 (mtpt) cc_final: 0.7038 (mttp) outliers start: 46 outliers final: 35 residues processed: 138 average time/residue: 1.3088 time to fit residues: 194.3686 Evaluate side-chains 128 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 90 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR 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 212 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 8 THR 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 182 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 341 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 109 optimal weight: 0.0470 chunk 60 optimal weight: 0.6980 chunk 10 optimal weight: 0.0870 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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: