Starting phenix.real_space_refine on Sun Nov 17 16:54:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcf_6551/11_2024/3jcf_6551.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcf_6551/11_2024/3jcf_6551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcf_6551/11_2024/3jcf_6551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcf_6551/11_2024/3jcf_6551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcf_6551/11_2024/3jcf_6551.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcf_6551/11_2024/3jcf_6551.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians Mg 13 5.21 5 S 40 5.16 5 C 9250 2.51 5 N 2305 2.21 5 O 2620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14228 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2843 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 333} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2843 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 333} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2843 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 333} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2843 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 333} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2843 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 333} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 8.99, per 1000 atoms: 0.63 Number of scatterers: 14228 At special positions: 0 Unit cell: (116.025, 113.475, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 Mg 13 11.99 O 2620 8.00 N 2305 7.00 C 9250 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: 3.49 Conformation dependent library (CDL) restraints added in 1.9 seconds 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 57.6% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 50 through 56 removed outlier: 3.576A pdb=" N PHE A 53 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A 55 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 80 removed outlier: 3.527A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 159 through 163 removed outlier: 4.106A pdb=" N ARG A 162 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 201 removed outlier: 3.596A pdb=" N TYR A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 237 Proline residue: A 227 - end of helix removed outlier: 4.170A pdb=" N GLU A 230 " --> pdb=" O TRP A 226 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 299 removed outlier: 3.929A pdb=" N TYR A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 325 through 345 removed outlier: 3.566A pdb=" N VAL A 329 " --> pdb=" O TRP A 325 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 removed outlier: 3.575A pdb=" N PHE B 53 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP B 55 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 80 removed outlier: 3.527A pdb=" N VAL B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 159 through 163 removed outlier: 4.105A pdb=" N ARG B 162 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 201 removed outlier: 3.598A pdb=" N TYR B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 237 Proline residue: B 227 - end of helix removed outlier: 4.169A pdb=" N GLU B 230 " --> pdb=" O TRP B 226 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 235 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 299 removed outlier: 3.928A pdb=" N TYR B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 253 " --> pdb=" O PRO B 249 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 259 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 313 Processing helix chain 'B' and resid 325 through 345 removed outlier: 3.568A pdb=" N VAL B 329 " --> pdb=" O TRP B 325 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 56 removed outlier: 3.576A pdb=" N PHE C 53 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP C 55 " --> pdb=" O PRO C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.527A pdb=" N VAL C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 92 Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 159 through 163 removed outlier: 4.104A pdb=" N ARG C 162 " --> pdb=" O GLY C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 201 removed outlier: 3.596A pdb=" N TYR C 181 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE C 182 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 237 Proline residue: C 227 - end of helix removed outlier: 4.170A pdb=" N GLU C 230 " --> pdb=" O TRP C 226 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 299 removed outlier: 3.928A pdb=" N TYR C 250 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP C 253 " --> pdb=" O PRO C 249 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 259 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 313 Processing helix chain 'C' and resid 325 through 345 removed outlier: 3.563A pdb=" N VAL C 329 " --> pdb=" O TRP C 325 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 56 removed outlier: 3.575A pdb=" N PHE D 53 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP D 55 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 80 removed outlier: 3.526A pdb=" N VAL D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 159 through 163 removed outlier: 4.106A pdb=" N ARG D 162 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 201 removed outlier: 3.597A pdb=" N TYR D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE D 182 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL D 183 " --> pdb=" O ASP D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 237 Proline residue: D 227 - end of helix removed outlier: 4.169A pdb=" N GLU D 230 " --> pdb=" O TRP D 226 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 299 removed outlier: 3.928A pdb=" N TYR D 250 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP D 253 " --> pdb=" O PRO D 249 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 259 " --> pdb=" O TYR D 255 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 313 Processing helix chain 'D' and resid 325 through 345 removed outlier: 3.567A pdb=" N VAL D 329 " --> pdb=" O TRP D 325 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 56 removed outlier: 3.574A pdb=" N PHE E 53 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP E 55 " --> pdb=" O PRO E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 80 removed outlier: 3.526A pdb=" N VAL E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 159 through 163 removed outlier: 4.105A pdb=" N ARG E 162 " --> pdb=" O GLY E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 201 removed outlier: 3.597A pdb=" N TYR E 181 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE E 182 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL E 183 " --> pdb=" O ASP E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 237 Proline residue: E 227 - end of helix removed outlier: 4.170A pdb=" N GLU E 230 " --> pdb=" O TRP E 226 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU E 235 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 299 removed outlier: 3.927A pdb=" N TYR E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP E 253 " --> pdb=" O PRO E 249 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 259 " --> pdb=" O TYR E 255 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY E 274 " --> pdb=" O ASP E 270 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 313 Processing helix chain 'E' and resid 325 through 345 removed outlier: 3.566A pdb=" N VAL E 329 " --> pdb=" O TRP E 325 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 39 through 44 Processing sheet with id=B, first strand: chain 'B' and resid 39 through 44 Processing sheet with id=C, first strand: chain 'C' and resid 39 through 44 Processing sheet with id=D, first strand: chain 'D' and resid 39 through 44 Processing sheet with id=E, first strand: chain 'E' and resid 39 through 44 880 hydrogen bonds defined for protein. 2565 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: 4.25 Time building geometry restraints manager: 4.07 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: 4471 1.34 - 1.46: 1966 1.46 - 1.57: 8013 1.57 - 1.69: 0 1.69 - 1.80: 75 Bond restraints: 14525 Sorted by residual: bond pdb=" CA PRO C 240 " pdb=" C PRO C 240 " ideal model delta sigma weight residual 1.517 1.546 -0.028 9.30e-03 1.16e+04 9.35e+00 bond pdb=" CA PRO E 240 " pdb=" C PRO E 240 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 9.11e+00 bond pdb=" CA PRO A 240 " pdb=" C PRO A 240 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 8.95e+00 bond pdb=" CA PRO B 240 " pdb=" C PRO B 240 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 8.92e+00 bond pdb=" CA PRO D 240 " pdb=" C PRO D 240 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 8.78e+00 ... (remaining 14520 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 18688 2.03 - 4.06: 941 4.06 - 6.08: 55 6.08 - 8.11: 41 8.11 - 10.14: 5 Bond angle restraints: 19730 Sorted by residual: angle pdb=" C PRO C 240 " pdb=" N PRO C 241 " pdb=" CA PRO C 241 " ideal model delta sigma weight residual 119.84 113.54 6.30 1.25e+00 6.40e-01 2.54e+01 angle pdb=" C PRO B 240 " pdb=" N PRO B 241 " pdb=" CA PRO B 241 " ideal model delta sigma weight residual 119.84 113.59 6.25 1.25e+00 6.40e-01 2.50e+01 angle pdb=" C PRO D 240 " pdb=" N PRO D 241 " pdb=" CA PRO D 241 " ideal model delta sigma weight residual 119.84 113.59 6.25 1.25e+00 6.40e-01 2.50e+01 angle pdb=" C PRO E 240 " pdb=" N PRO E 241 " pdb=" CA PRO E 241 " ideal model delta sigma weight residual 119.84 113.60 6.24 1.25e+00 6.40e-01 2.49e+01 angle pdb=" C PRO A 240 " pdb=" N PRO A 241 " pdb=" CA PRO A 241 " ideal model delta sigma weight residual 119.84 113.62 6.22 1.25e+00 6.40e-01 2.48e+01 ... (remaining 19725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.97: 7974 7.97 - 15.93: 576 15.93 - 23.90: 118 23.90 - 31.86: 59 31.86 - 39.83: 28 Dihedral angle restraints: 8755 sinusoidal: 3570 harmonic: 5185 Sorted by residual: dihedral pdb=" CA LEU C 131 " pdb=" CB LEU C 131 " pdb=" CG LEU C 131 " pdb=" CD1 LEU C 131 " ideal model delta sinusoidal sigma weight residual 180.00 140.17 39.83 3 1.50e+01 4.44e-03 7.07e+00 dihedral pdb=" CA LEU A 131 " pdb=" CB LEU A 131 " pdb=" CG LEU A 131 " pdb=" CD1 LEU A 131 " ideal model delta sinusoidal sigma weight residual 180.00 140.19 39.81 3 1.50e+01 4.44e-03 7.07e+00 dihedral pdb=" CA LEU B 131 " pdb=" CB LEU B 131 " pdb=" CG LEU B 131 " pdb=" CD1 LEU B 131 " ideal model delta sinusoidal sigma weight residual 180.00 140.22 39.78 3 1.50e+01 4.44e-03 7.06e+00 ... (remaining 8752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1630 0.024 - 0.047: 245 0.047 - 0.071: 109 0.071 - 0.095: 178 0.095 - 0.119: 128 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CA ILE C 160 " pdb=" N ILE C 160 " pdb=" C ILE C 160 " pdb=" CB ILE C 160 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA ILE B 160 " pdb=" N ILE B 160 " pdb=" C ILE B 160 " pdb=" CB ILE B 160 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA ILE B 143 " pdb=" N ILE B 143 " pdb=" C ILE B 143 " pdb=" CB ILE B 143 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.37e-01 ... (remaining 2287 not shown) Planarity restraints: 2490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 239 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO E 240 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 240 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 240 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 239 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO C 240 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 240 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 240 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 239 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO B 240 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 240 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 240 " 0.021 5.00e-02 4.00e+02 ... (remaining 2487 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 181 2.63 - 3.19: 13699 3.19 - 3.76: 22099 3.76 - 4.33: 30360 4.33 - 4.90: 49384 Nonbonded interactions: 115723 Sorted by model distance: nonbonded pdb=" OD1 ASP C 253 " pdb="MG MG D 402 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP B 253 " pdb="MG MG C 402 " model vdw 2.058 2.170 nonbonded pdb=" OD1 ASP D 253 " pdb="MG MG E 402 " model vdw 2.059 2.170 nonbonded pdb=" OD1 ASP A 253 " pdb="MG MG B 402 " model vdw 2.059 2.170 nonbonded pdb=" OD1 ASP E 253 " pdb="MG MG A 402 " model vdw 2.062 2.170 ... (remaining 115718 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' selection = (chain 'E' and (resid 3 through 351 or resid 402 through 501)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 33.110 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 : 0.004 0.028 14525 Z= 0.247 Angle : 1.028 10.141 19730 Z= 0.718 Chirality : 0.039 0.119 2290 Planarity : 0.003 0.036 2490 Dihedral : 6.812 39.830 5395 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.18), residues: 1735 helix: -0.43 (0.14), residues: 910 sheet: -1.06 (0.32), residues: 240 loop : -1.96 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 61 HIS 0.001 0.000 HIS A 83 PHE 0.005 0.001 PHE A 345 TYR 0.007 0.001 TYR D 317 ARG 0.001 0.000 ARG C 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8092 (mtp) cc_final: 0.7527 (mtm) REVERT: A 74 GLN cc_start: 0.8920 (tt0) cc_final: 0.8652 (tp-100) REVERT: A 140 GLN cc_start: 0.8565 (mt0) cc_final: 0.8356 (mt0) REVERT: A 152 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8752 (mt-10) REVERT: A 209 GLN cc_start: 0.9136 (tt0) cc_final: 0.8909 (tm-30) REVERT: A 288 ASN cc_start: 0.8986 (t0) cc_final: 0.8757 (t0) REVERT: B 28 GLU cc_start: 0.7954 (tt0) cc_final: 0.7633 (tm-30) REVERT: B 32 MET cc_start: 0.8429 (mtp) cc_final: 0.7998 (mtt) REVERT: B 74 GLN cc_start: 0.9130 (tt0) cc_final: 0.8741 (tp-100) REVERT: B 138 MET cc_start: 0.8479 (ttp) cc_final: 0.8007 (tmm) REVERT: B 140 GLN cc_start: 0.8738 (mt0) cc_final: 0.8530 (mt0) REVERT: B 152 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8755 (mt-10) REVERT: B 213 GLN cc_start: 0.9103 (mm-40) cc_final: 0.8648 (tp40) REVERT: C 32 MET cc_start: 0.8150 (mtp) cc_final: 0.7678 (mtt) REVERT: C 74 GLN cc_start: 0.9003 (tt0) cc_final: 0.8561 (tp-100) REVERT: D 32 MET cc_start: 0.8199 (mtp) cc_final: 0.7330 (mtm) REVERT: D 61 TRP cc_start: 0.8533 (t60) cc_final: 0.8278 (t60) REVERT: D 74 GLN cc_start: 0.9032 (tt0) cc_final: 0.8549 (tp-100) REVERT: D 112 MET cc_start: 0.8932 (mtm) cc_final: 0.8599 (mtt) REVERT: D 209 GLN cc_start: 0.9249 (tt0) cc_final: 0.9044 (tm-30) REVERT: D 213 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8537 (tp40) REVERT: D 217 ASN cc_start: 0.8839 (m-40) cc_final: 0.8573 (m110) REVERT: D 296 ILE cc_start: 0.7743 (pt) cc_final: 0.7499 (pt) REVERT: E 32 MET cc_start: 0.7933 (mtp) cc_final: 0.7266 (mtt) REVERT: E 61 TRP cc_start: 0.8523 (t60) cc_final: 0.8143 (t60) REVERT: E 74 GLN cc_start: 0.8885 (tt0) cc_final: 0.8505 (tp-100) REVERT: E 152 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8655 (mt-10) REVERT: E 209 GLN cc_start: 0.9252 (tt0) cc_final: 0.8987 (tm-30) REVERT: E 213 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8635 (tp40) REVERT: E 277 ASP cc_start: 0.9019 (m-30) cc_final: 0.8755 (t70) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.2863 time to fit residues: 137.4720 Evaluate side-chains 164 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 133 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 140 GLN A 314 ASN B 94 HIS B 95 GLN B 140 GLN B 260 GLN B 314 ASN C 95 GLN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 GLN C 314 ASN D 94 HIS D 126 GLN D 314 ASN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 HIS E 95 GLN E 140 GLN E 314 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14525 Z= 0.288 Angle : 0.679 7.510 19730 Z= 0.357 Chirality : 0.043 0.185 2290 Planarity : 0.004 0.047 2490 Dihedral : 4.084 14.334 1925 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.17 % Allowed : 6.82 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.20), residues: 1735 helix: 1.67 (0.17), residues: 940 sheet: -0.85 (0.28), residues: 285 loop : -1.83 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 61 HIS 0.005 0.001 HIS D 83 PHE 0.014 0.002 PHE D 306 TYR 0.016 0.002 TYR A 327 ARG 0.007 0.001 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8587 (tmm) cc_final: 0.7320 (tmm) REVERT: B 74 GLN cc_start: 0.9259 (tt0) cc_final: 0.8922 (tp-100) REVERT: B 100 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8276 (mm-30) REVERT: B 134 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8163 (m-40) REVERT: B 138 MET cc_start: 0.8761 (ttp) cc_final: 0.8102 (tmm) REVERT: B 140 GLN cc_start: 0.8795 (mt0) cc_final: 0.8532 (mt0) REVERT: C 74 GLN cc_start: 0.8989 (tt0) cc_final: 0.8627 (tp-100) REVERT: C 138 MET cc_start: 0.8410 (ttp) cc_final: 0.8103 (tmm) REVERT: D 32 MET cc_start: 0.8264 (mtp) cc_final: 0.7949 (mtm) REVERT: D 74 GLN cc_start: 0.9109 (tt0) cc_final: 0.8748 (tp-100) REVERT: D 112 MET cc_start: 0.8752 (mtm) cc_final: 0.8492 (mtp) REVERT: D 152 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8705 (tt0) REVERT: D 173 LEU cc_start: 0.9420 (mt) cc_final: 0.9099 (mp) REVERT: D 213 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8779 (tp40) REVERT: E 32 MET cc_start: 0.8095 (mtp) cc_final: 0.7624 (mtt) REVERT: E 61 TRP cc_start: 0.8605 (t60) cc_final: 0.8351 (t60) REVERT: E 209 GLN cc_start: 0.9323 (tt0) cc_final: 0.9042 (tm-30) outliers start: 34 outliers final: 24 residues processed: 210 average time/residue: 0.1974 time to fit residues: 68.2539 Evaluate side-chains 163 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 343 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN C 95 GLN C 126 GLN C 314 ASN D 314 ASN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN E 213 GLN E 314 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14525 Z= 0.240 Angle : 0.619 7.465 19730 Z= 0.320 Chirality : 0.042 0.137 2290 Planarity : 0.004 0.050 2490 Dihedral : 4.001 14.821 1925 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.42 % Allowed : 8.98 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.85 (0.20), residues: 1735 helix: 2.07 (0.17), residues: 940 sheet: -0.54 (0.29), residues: 285 loop : -1.68 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 61 HIS 0.004 0.001 HIS E 83 PHE 0.019 0.001 PHE D 306 TYR 0.017 0.001 TYR A 327 ARG 0.004 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 1.885 Fit side-chains REVERT: A 138 MET cc_start: 0.8554 (tmm) cc_final: 0.7341 (tmm) REVERT: A 175 ASP cc_start: 0.8765 (t0) cc_final: 0.8546 (t0) REVERT: A 300 ILE cc_start: 0.7858 (pt) cc_final: 0.7640 (pt) REVERT: B 74 GLN cc_start: 0.9259 (tt0) cc_final: 0.8926 (tp-100) REVERT: B 100 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8280 (mm-30) REVERT: B 134 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8199 (m-40) REVERT: B 138 MET cc_start: 0.8775 (ttp) cc_final: 0.8145 (tmm) REVERT: B 140 GLN cc_start: 0.8770 (mt0) cc_final: 0.8471 (mt0) REVERT: B 295 THR cc_start: 0.8698 (t) cc_final: 0.8378 (t) REVERT: C 74 GLN cc_start: 0.8982 (tt0) cc_final: 0.8629 (tp-100) REVERT: C 306 PHE cc_start: 0.7018 (t80) cc_final: 0.6775 (t80) REVERT: D 32 MET cc_start: 0.8308 (mtp) cc_final: 0.7943 (mtm) REVERT: D 74 GLN cc_start: 0.9071 (tt0) cc_final: 0.8692 (tp-100) REVERT: D 152 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8738 (tt0) REVERT: E 138 MET cc_start: 0.8645 (ttp) cc_final: 0.7009 (tmm) REVERT: E 209 GLN cc_start: 0.9357 (tt0) cc_final: 0.9011 (tm-30) outliers start: 38 outliers final: 23 residues processed: 170 average time/residue: 0.1925 time to fit residues: 55.1881 Evaluate side-chains 137 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 334 MET Chi-restraints excluded: chain E residue 343 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN B 314 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN C 213 GLN C 314 ASN ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN E 314 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14525 Z= 0.236 Angle : 0.618 12.000 19730 Z= 0.316 Chirality : 0.042 0.173 2290 Planarity : 0.004 0.048 2490 Dihedral : 3.926 15.291 1925 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.17 % Allowed : 10.38 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.21), residues: 1735 helix: 2.28 (0.17), residues: 935 sheet: -0.21 (0.30), residues: 280 loop : -1.50 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 61 HIS 0.003 0.001 HIS E 83 PHE 0.017 0.001 PHE C 306 TYR 0.016 0.001 TYR A 327 ARG 0.003 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 1.666 Fit side-chains REVERT: A 138 MET cc_start: 0.8435 (tmm) cc_final: 0.7175 (tmm) REVERT: A 291 MET cc_start: 0.8765 (mmp) cc_final: 0.7377 (mmp) REVERT: B 74 GLN cc_start: 0.9241 (tt0) cc_final: 0.8916 (tp-100) REVERT: B 100 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8284 (mm-30) REVERT: B 134 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8237 (m-40) REVERT: B 138 MET cc_start: 0.8782 (ttp) cc_final: 0.8161 (tmm) REVERT: B 140 GLN cc_start: 0.8816 (mt0) cc_final: 0.8525 (mt0) REVERT: B 295 THR cc_start: 0.8664 (t) cc_final: 0.8345 (t) REVERT: C 74 GLN cc_start: 0.9006 (tt0) cc_final: 0.8772 (tp-100) REVERT: D 32 MET cc_start: 0.8335 (mtp) cc_final: 0.7977 (mtm) REVERT: D 74 GLN cc_start: 0.9117 (tt0) cc_final: 0.8748 (tp-100) REVERT: D 152 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8698 (tt0) REVERT: D 295 THR cc_start: 0.8481 (t) cc_final: 0.8279 (t) REVERT: E 138 MET cc_start: 0.8634 (ttp) cc_final: 0.6926 (tmm) REVERT: E 209 GLN cc_start: 0.9360 (tt0) cc_final: 0.9017 (tm-30) REVERT: E 291 MET cc_start: 0.7688 (mmm) cc_final: 0.7308 (mmt) REVERT: E 300 ILE cc_start: 0.8208 (pt) cc_final: 0.8007 (pt) outliers start: 34 outliers final: 21 residues processed: 160 average time/residue: 0.1963 time to fit residues: 52.5961 Evaluate side-chains 138 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 334 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 122 optimal weight: 0.1980 chunk 67 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN C 83 HIS C 95 GLN C 314 ASN ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN E 314 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 14525 Z= 0.427 Angle : 0.716 10.583 19730 Z= 0.362 Chirality : 0.045 0.197 2290 Planarity : 0.005 0.051 2490 Dihedral : 4.197 17.899 1925 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.63 % Allowed : 10.13 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.21), residues: 1735 helix: 2.23 (0.17), residues: 945 sheet: -0.44 (0.31), residues: 270 loop : -1.32 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 325 HIS 0.008 0.002 HIS C 83 PHE 0.021 0.002 PHE B 306 TYR 0.016 0.002 TYR E 327 ARG 0.004 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 123 time to evaluate : 1.944 Fit side-chains REVERT: A 138 MET cc_start: 0.8777 (tmm) cc_final: 0.7515 (tmm) REVERT: B 74 GLN cc_start: 0.9242 (tt0) cc_final: 0.8958 (tp-100) REVERT: B 129 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8961 (pp) REVERT: B 138 MET cc_start: 0.8966 (ttp) cc_final: 0.8438 (tmm) REVERT: B 140 GLN cc_start: 0.8927 (mt0) cc_final: 0.8665 (mt0) REVERT: B 291 MET cc_start: 0.8911 (mmp) cc_final: 0.8559 (mmp) REVERT: B 341 MET cc_start: 0.8222 (mmp) cc_final: 0.7934 (mmp) REVERT: C 74 GLN cc_start: 0.9042 (tt0) cc_final: 0.8695 (tp-100) REVERT: C 129 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9090 (pp) REVERT: C 341 MET cc_start: 0.8348 (mmp) cc_final: 0.8105 (mmp) REVERT: D 32 MET cc_start: 0.8458 (mtp) cc_final: 0.8068 (mtm) REVERT: D 74 GLN cc_start: 0.9122 (tt0) cc_final: 0.8796 (tp-100) REVERT: E 100 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7898 (mm-30) REVERT: E 138 MET cc_start: 0.8879 (ttp) cc_final: 0.8176 (tmm) REVERT: E 209 GLN cc_start: 0.9372 (tt0) cc_final: 0.9041 (tm-30) REVERT: E 300 ILE cc_start: 0.8409 (pt) cc_final: 0.8184 (pt) outliers start: 57 outliers final: 37 residues processed: 165 average time/residue: 0.1890 time to fit residues: 52.8874 Evaluate side-chains 143 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 334 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN C 95 GLN C 314 ASN ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14525 Z= 0.272 Angle : 0.642 7.955 19730 Z= 0.326 Chirality : 0.043 0.231 2290 Planarity : 0.004 0.048 2490 Dihedral : 4.063 17.543 1925 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.68 % Allowed : 11.46 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.21), residues: 1735 helix: 2.35 (0.17), residues: 945 sheet: -0.19 (0.32), residues: 265 loop : -1.27 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 325 HIS 0.002 0.001 HIS A 120 PHE 0.012 0.001 PHE D 306 TYR 0.019 0.001 TYR C 327 ARG 0.006 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 1.865 Fit side-chains REVERT: A 138 MET cc_start: 0.8727 (tmm) cc_final: 0.7525 (tmm) REVERT: B 74 GLN cc_start: 0.9225 (tt0) cc_final: 0.8929 (tp-100) REVERT: B 129 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8804 (pp) REVERT: B 134 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8285 (m-40) REVERT: B 138 MET cc_start: 0.8892 (ttp) cc_final: 0.8394 (tmm) REVERT: B 140 GLN cc_start: 0.8845 (mt0) cc_final: 0.8579 (mt0) REVERT: C 74 GLN cc_start: 0.9010 (tt0) cc_final: 0.8799 (tp-100) REVERT: C 129 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9089 (pp) REVERT: D 32 MET cc_start: 0.8411 (mtp) cc_final: 0.8019 (mtm) REVERT: D 74 GLN cc_start: 0.9132 (tt0) cc_final: 0.8773 (tp-100) REVERT: D 291 MET cc_start: 0.8729 (mmp) cc_final: 0.8418 (tpp) REVERT: E 129 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8812 (pp) REVERT: E 138 MET cc_start: 0.8806 (ttp) cc_final: 0.7122 (tmm) REVERT: E 209 GLN cc_start: 0.9341 (tt0) cc_final: 0.9044 (tm-30) outliers start: 42 outliers final: 27 residues processed: 150 average time/residue: 0.1981 time to fit residues: 50.7582 Evaluate side-chains 139 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 334 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 91 optimal weight: 0.1980 chunk 163 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN B 314 ASN C 95 GLN C 314 ASN ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14525 Z= 0.378 Angle : 0.682 8.270 19730 Z= 0.344 Chirality : 0.044 0.156 2290 Planarity : 0.004 0.051 2490 Dihedral : 4.164 18.927 1925 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.80 % Allowed : 11.91 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.34 (0.21), residues: 1735 helix: 2.38 (0.17), residues: 940 sheet: -0.19 (0.32), residues: 265 loop : -1.35 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 325 HIS 0.004 0.001 HIS D 83 PHE 0.018 0.002 PHE B 306 TYR 0.015 0.002 TYR A 327 ARG 0.002 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 110 time to evaluate : 1.944 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.8809 (tmm) cc_final: 0.7583 (tmm) REVERT: B 74 GLN cc_start: 0.9226 (tt0) cc_final: 0.8938 (tp-100) REVERT: B 129 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8813 (pp) REVERT: B 138 MET cc_start: 0.8973 (ttp) cc_final: 0.8486 (tmm) REVERT: C 74 GLN cc_start: 0.9007 (tt0) cc_final: 0.8688 (tp-100) REVERT: C 129 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9105 (pp) REVERT: D 32 MET cc_start: 0.8407 (mtp) cc_final: 0.8027 (mtm) REVERT: D 74 GLN cc_start: 0.9118 (tt0) cc_final: 0.8813 (tp-100) REVERT: D 291 MET cc_start: 0.8809 (mmp) cc_final: 0.8484 (tpp) REVERT: E 100 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7925 (mm-30) REVERT: E 138 MET cc_start: 0.8833 (ttp) cc_final: 0.8179 (tmm) REVERT: E 209 GLN cc_start: 0.9350 (tt0) cc_final: 0.9045 (tm-30) REVERT: E 291 MET cc_start: 0.8635 (mmm) cc_final: 0.8398 (mmt) outliers start: 44 outliers final: 35 residues processed: 144 average time/residue: 0.1954 time to fit residues: 47.8529 Evaluate side-chains 143 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 334 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN B 314 ASN C 95 GLN C 314 ASN ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14525 Z= 0.300 Angle : 0.650 8.955 19730 Z= 0.328 Chirality : 0.043 0.164 2290 Planarity : 0.004 0.049 2490 Dihedral : 4.070 18.201 1925 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.55 % Allowed : 12.68 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.44 (0.21), residues: 1735 helix: 2.39 (0.17), residues: 945 sheet: 0.13 (0.34), residues: 255 loop : -1.32 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 325 HIS 0.003 0.001 HIS D 83 PHE 0.015 0.001 PHE A 301 TYR 0.015 0.001 TYR A 327 ARG 0.002 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 1.891 Fit side-chains REVERT: A 138 MET cc_start: 0.8820 (tmm) cc_final: 0.7687 (tmm) REVERT: B 74 GLN cc_start: 0.9211 (tt0) cc_final: 0.8925 (tp-100) REVERT: B 129 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8820 (pp) REVERT: B 138 MET cc_start: 0.8932 (ttp) cc_final: 0.8464 (tmm) REVERT: C 74 GLN cc_start: 0.8987 (tt0) cc_final: 0.8665 (tp-100) REVERT: C 112 MET cc_start: 0.7782 (mtt) cc_final: 0.7509 (mtm) REVERT: C 129 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9117 (pp) REVERT: D 32 MET cc_start: 0.8396 (mtp) cc_final: 0.8011 (mtm) REVERT: D 74 GLN cc_start: 0.9128 (tt0) cc_final: 0.8815 (tp-100) REVERT: D 126 GLN cc_start: 0.9055 (tt0) cc_final: 0.8823 (tt0) REVERT: D 291 MET cc_start: 0.8832 (mmp) cc_final: 0.8524 (mmp) REVERT: E 129 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8802 (pp) REVERT: E 138 MET cc_start: 0.8828 (ttp) cc_final: 0.7166 (tmm) REVERT: E 209 GLN cc_start: 0.9344 (tt0) cc_final: 0.9035 (tm-30) outliers start: 40 outliers final: 34 residues processed: 143 average time/residue: 0.2165 time to fit residues: 52.9847 Evaluate side-chains 143 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 334 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 3.9990 chunk 143 optimal weight: 0.2980 chunk 152 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN B 140 GLN B 314 ASN C 314 ASN ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14525 Z= 0.188 Angle : 0.624 13.794 19730 Z= 0.312 Chirality : 0.042 0.184 2290 Planarity : 0.004 0.048 2490 Dihedral : 3.945 17.581 1925 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.10 % Allowed : 12.99 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.21), residues: 1735 helix: 2.53 (0.17), residues: 940 sheet: 0.38 (0.34), residues: 255 loop : -1.34 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 325 HIS 0.003 0.000 HIS B 83 PHE 0.018 0.001 PHE B 306 TYR 0.015 0.001 TYR C 327 ARG 0.002 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 1.771 Fit side-chains REVERT: A 138 MET cc_start: 0.8740 (tmm) cc_final: 0.7617 (tmm) REVERT: B 74 GLN cc_start: 0.9202 (tt0) cc_final: 0.8928 (tp-100) REVERT: B 129 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8706 (pp) REVERT: B 138 MET cc_start: 0.8831 (ttp) cc_final: 0.8256 (tmm) REVERT: C 302 MET cc_start: 0.6068 (mmp) cc_final: 0.5844 (mmp) REVERT: D 32 MET cc_start: 0.8421 (mtp) cc_final: 0.8049 (mtm) REVERT: D 74 GLN cc_start: 0.9121 (tt0) cc_final: 0.8812 (tp-100) REVERT: D 295 THR cc_start: 0.8574 (t) cc_final: 0.8359 (t) REVERT: E 138 MET cc_start: 0.8713 (ttp) cc_final: 0.8466 (tmm) REVERT: E 209 GLN cc_start: 0.9330 (tt0) cc_final: 0.8999 (tm-30) outliers start: 33 outliers final: 24 residues processed: 143 average time/residue: 0.2027 time to fit residues: 49.0058 Evaluate side-chains 133 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 334 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 14 optimal weight: 0.0470 chunk 104 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN B 314 ASN C 314 ASN ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4101 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: