Starting phenix.real_space_refine on Tue Aug 6 06:18:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn3_27553/08_2024/8dn3_27553_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn3_27553/08_2024/8dn3_27553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn3_27553/08_2024/8dn3_27553.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn3_27553/08_2024/8dn3_27553.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn3_27553/08_2024/8dn3_27553_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn3_27553/08_2024/8dn3_27553_trim.cif" } resolution = 3.55 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= 0.008 sd= 0.086 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 S 102 5.16 5 Cl 2 4.86 5 C 9467 2.51 5 N 2270 2.21 5 O 2474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14315 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 2762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2762 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Chain: "A" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2796 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 15, 'TRANS': 327} Chain breaks: 1 Chain: "B" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2768 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 15, 'TRANS': 324} Chain breaks: 1 Chain: "C" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2785 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2707 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 107 Unusual residues: {'DD9': 1, 'HEX': 3, 'HP6': 2, 'NAG': 1, 'NBU': 2, 'UND': 4} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Unusual residues: {'DD9': 2, 'HEX': 4, 'HP6': 2, 'NAG': 1, 'UND': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 81 Unusual residues: {'DD9': 5, 'HEX': 3, 'NAG': 1, 'NBU': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 116 Unusual residues: {'D10': 1, 'DD9': 3, 'HEX': 3, 'HP6': 2, 'NAG': 1, 'UND': 3} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 90 Unusual residues: {' CL': 2, 'DD9': 2, 'HEX': 2, 'HP6': 2, 'NAG': 1, 'NBU': 2, 'UND': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.65, per 1000 atoms: 0.60 Number of scatterers: 14315 At special positions: 0 Unit cell: (103.75, 127.82, 132.8, 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) Cl 2 17.00 S 102 16.00 O 2474 8.00 N 2270 7.00 C 9467 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=5, symmetry=0 Links applied NAG-ASN " NAG C 503 " - " ASN C 38 " " NAG D 501 " - " ASN D 38 " " NAG E 504 " - " ASN E 220 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.16 Conformation dependent library (CDL) restraints added in 2.6 seconds 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3252 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 13 sheets defined 38.9% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'D' and resid 9 through 18 removed outlier: 3.536A pdb=" N LEU D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 220 through 243 Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 248 through 274 removed outlier: 4.049A pdb=" N ALA D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 311 removed outlier: 3.962A pdb=" N TRP D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N HIS D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 419 removed outlier: 4.280A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE D 402 " --> pdb=" O SER D 398 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.617A pdb=" N LEU A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 228 through 243 Processing helix chain 'A' and resid 248 through 271 removed outlier: 3.620A pdb=" N ARG A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 311 removed outlier: 3.798A pdb=" N HIS A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 419 removed outlier: 3.961A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 9 through 18 Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 221 through 243 Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 248 through 274 removed outlier: 3.602A pdb=" N ARG B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 310 Processing helix chain 'B' and resid 385 through 419 removed outlier: 3.789A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Proline residue: B 403 - end of helix removed outlier: 3.625A pdb=" N TRP B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 18 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 220 through 241 Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 248 through 274 Processing helix chain 'C' and resid 283 through 313 removed outlier: 3.919A pdb=" N HIS C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS C 312 " --> pdb=" O SER C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 417 removed outlier: 3.748A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'E' and resid 34 through 43 removed outlier: 3.614A pdb=" N LEU E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 95 Processing helix chain 'E' and resid 112 through 116 removed outlier: 3.520A pdb=" N LEU E 116 " --> pdb=" O TYR E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 170 Processing helix chain 'E' and resid 244 through 251 Processing helix chain 'E' and resid 251 through 265 removed outlier: 3.820A pdb=" N SER E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 268 No H-bonds generated for 'chain 'E' and resid 266 through 268' Processing helix chain 'E' and resid 272 through 295 Proline residue: E 278 - end of helix Processing helix chain 'E' and resid 305 through 333 Processing helix chain 'E' and resid 448 through 475 removed outlier: 3.805A pdb=" N ALA E 457 " --> pdb=" O LEU E 453 " (cutoff:3.500A) Proline residue: E 460 - end of helix Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 45 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 37 through 45 current: chain 'D' and resid 57 through 68 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 57 through 68 current: chain 'D' and resid 126 through 134 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 98 through 100 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 149 through 158 current: chain 'D' and resid 205 through 217 Processing sheet with id=AA3, first strand: chain 'A' and resid 37 through 44 removed outlier: 6.533A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 65 through 69 current: chain 'A' and resid 116 through 121 removed outlier: 4.523A pdb=" N ASN A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 49 through 52 removed outlier: 5.181A pdb=" N SER A 50 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG A 59 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 57 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS A 107 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 100 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 151 through 158 current: chain 'A' and resid 205 through 217 Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 44 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 37 through 44 current: chain 'B' and resid 57 through 69 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 57 through 69 current: chain 'B' and resid 125 through 137 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 99 through 100 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 149 through 157 current: chain 'B' and resid 205 through 217 Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 52 removed outlier: 7.071A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE C 44 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 69 current: chain 'C' and resid 125 through 134 Processing sheet with id=AA9, first strand: chain 'C' and resid 98 through 100 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 149 through 158 current: chain 'C' and resid 206 through 217 Processing sheet with id=AB1, first strand: chain 'E' and resid 105 through 106 removed outlier: 4.464A pdb=" N ASP E 148 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASP E 78 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER E 71 " --> pdb=" O ASP E 78 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARG E 80 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N PHE E 69 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL E 58 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ILE E 192 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL E 60 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 121 through 123 Processing sheet with id=AB3, first strand: chain 'E' and resid 172 through 176 Processing sheet with id=AB4, first strand: chain 'E' and resid 223 through 225 removed outlier: 3.540A pdb=" N LYS E 223 " --> pdb=" O TYR E 231 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR E 225 " --> pdb=" O GLY E 229 " (cutoff:3.500A) 529 hydrogen bonds defined for protein. 1551 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: 3.78 Time building geometry restraints manager: 5.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4181 1.34 - 1.46: 2289 1.46 - 1.57: 7965 1.57 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 14607 Sorted by residual: bond pdb=" N GLN D 310 " pdb=" CA GLN D 310 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.87e+00 bond pdb=" N VAL C 37 " pdb=" CA VAL C 37 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.18e+00 bond pdb=" N VAL D 37 " pdb=" CA VAL D 37 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.23e-02 6.61e+03 7.41e+00 bond pdb=" N ILE A 257 " pdb=" CA ILE A 257 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.35e+00 bond pdb=" N LYS A 312 " pdb=" CA LYS A 312 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.45e+00 ... (remaining 14602 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.62: 436 106.62 - 113.46: 7631 113.46 - 120.31: 5441 120.31 - 127.15: 5935 127.15 - 134.00: 169 Bond angle restraints: 19612 Sorted by residual: angle pdb=" N ARG B 309 " pdb=" CA ARG B 309 " pdb=" C ARG B 309 " ideal model delta sigma weight residual 112.89 107.11 5.78 1.24e+00 6.50e-01 2.17e+01 angle pdb=" CA HIS A 311 " pdb=" C HIS A 311 " pdb=" O HIS A 311 " ideal model delta sigma weight residual 121.19 117.38 3.81 1.10e+00 8.26e-01 1.20e+01 angle pdb=" CA THR A 258 " pdb=" C THR A 258 " pdb=" O THR A 258 " ideal model delta sigma weight residual 120.82 117.49 3.33 1.05e+00 9.07e-01 1.01e+01 angle pdb=" N GLN A 310 " pdb=" CA GLN A 310 " pdb=" C GLN A 310 " ideal model delta sigma weight residual 111.71 108.07 3.64 1.15e+00 7.56e-01 1.00e+01 angle pdb=" N PHE D 412 " pdb=" CA PHE D 412 " pdb=" C PHE D 412 " ideal model delta sigma weight residual 112.89 109.00 3.89 1.24e+00 6.50e-01 9.85e+00 ... (remaining 19607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 8530 24.23 - 48.47: 273 48.47 - 72.70: 18 72.70 - 96.93: 11 96.93 - 121.16: 6 Dihedral angle restraints: 8838 sinusoidal: 3821 harmonic: 5017 Sorted by residual: dihedral pdb=" C3 DD9 A 508 " pdb=" C4 DD9 A 508 " pdb=" C5 DD9 A 508 " pdb=" C6 DD9 A 508 " ideal model delta sinusoidal sigma weight residual 179.92 58.76 121.16 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" C1 DD9 A 508 " pdb=" C2 DD9 A 508 " pdb=" C3 DD9 A 508 " pdb=" C4 DD9 A 508 " ideal model delta sinusoidal sigma weight residual 179.94 -67.82 -112.24 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C2 NAG E 504 " pdb=" C3 NAG E 504 " pdb=" C4 NAG E 504 " pdb=" C5 NAG E 504 " ideal model delta sinusoidal sigma weight residual 53.78 -48.09 101.87 1 3.00e+01 1.11e-03 1.29e+01 ... (remaining 8835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 2154 0.173 - 0.346: 1 0.346 - 0.519: 0 0.519 - 0.692: 0 0.692 - 0.865: 1 Chirality restraints: 2156 Sorted by residual: chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 38 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.87e+01 chirality pdb=" C1 NAG E 504 " pdb=" ND2 ASN E 220 " pdb=" C2 NAG E 504 " pdb=" O5 NAG E 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA VAL C 37 " pdb=" N VAL C 37 " pdb=" C VAL C 37 " pdb=" CB VAL C 37 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 2153 not shown) Planarity restraints: 2415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 501 " 0.321 2.00e-02 2.50e+03 2.74e-01 9.37e+02 pdb=" C7 NAG A 501 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG A 501 " -0.003 2.00e-02 2.50e+03 pdb=" N2 NAG A 501 " -0.466 2.00e-02 2.50e+03 pdb=" O7 NAG A 501 " 0.221 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " -0.292 2.00e-02 2.50e+03 2.48e-01 7.68e+02 pdb=" C7 NAG D 501 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " 0.429 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 503 " -0.281 2.00e-02 2.50e+03 2.35e-01 6.90e+02 pdb=" C7 NAG C 503 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG C 503 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG C 503 " 0.396 2.00e-02 2.50e+03 pdb=" O7 NAG C 503 " -0.008 2.00e-02 2.50e+03 ... (remaining 2412 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 661 2.73 - 3.27: 14154 3.27 - 3.81: 22580 3.81 - 4.36: 26996 4.36 - 4.90: 46970 Nonbonded interactions: 111361 Sorted by model distance: nonbonded pdb=" O LEU A 98 " pdb=" OG1 THR B 112 " model vdw 2.181 3.040 nonbonded pdb=" O ALA D 282 " pdb=" OH TYR D 413 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR A 112 " pdb=" O LEU E 121 " model vdw 2.234 3.040 nonbonded pdb=" O LEU B 98 " pdb=" OG1 THR C 112 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR B 162 " pdb=" OD1 ASN B 164 " model vdw 2.238 3.040 ... (remaining 111356 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' and (resid 9 through 310 or resid 384 through 386 or (resid 387 and ( \ name N or name CA or name C or name O or name CB )) or resid 388 through 419)) selection = (chain 'B' and (resid 9 through 310 or resid 384 through 386 or (resid 387 and ( \ name N or name CA or name C or name O or name CB )) or resid 388 through 419)) selection = (chain 'C' and (resid 9 through 310 or resid 384 through 419)) selection = (chain 'D' and (resid 9 through 310 or resid 384 through 386 or (resid 387 and ( \ name N or name CA or name C or name O or name CB )) or resid 388 through 419)) } 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: 0.010 Normalize map: mean=0, sd=1: 1.030 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: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 39.390 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 0.038 14607 Z= 0.219 Angle : 0.565 8.288 19612 Z= 0.287 Chirality : 0.046 0.865 2156 Planarity : 0.009 0.274 2412 Dihedral : 11.886 121.162 5559 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.87 % Favored : 96.01 % Rotamer: Outliers : 1.97 % Allowed : 5.51 % Favored : 92.52 % 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: 0.56 (0.22), residues: 1679 helix: 2.25 (0.22), residues: 583 sheet: -0.40 (0.30), residues: 359 loop : -0.75 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 243 HIS 0.002 0.000 HIS A 311 PHE 0.010 0.001 PHE D 242 TYR 0.017 0.001 TYR E 325 ARG 0.002 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 332 time to evaluate : 1.676 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: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8081 (t70) cc_final: 0.7671 (p0) REVERT: D 246 MET cc_start: 0.7313 (mtm) cc_final: 0.7076 (mtt) REVERT: A 91 ASP cc_start: 0.8812 (t0) cc_final: 0.8612 (t0) REVERT: A 169 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7849 (mt-10) REVERT: A 173 GLN cc_start: 0.8343 (pp30) cc_final: 0.8086 (pp30) REVERT: A 203 ASN cc_start: 0.8690 (m-40) cc_final: 0.8006 (p0) REVERT: A 396 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7571 (mtmm) REVERT: A 400 ILE cc_start: 0.8271 (tp) cc_final: 0.7582 (pt) REVERT: B 18 MET cc_start: 0.8467 (ppp) cc_final: 0.8112 (ptt) REVERT: B 83 LEU cc_start: 0.7978 (tt) cc_final: 0.7710 (tt) REVERT: B 397 ILE cc_start: 0.8516 (mm) cc_final: 0.8249 (mt) REVERT: B 411 MET cc_start: 0.7501 (mmp) cc_final: 0.6547 (ttp) REVERT: C 191 GLU cc_start: 0.8209 (tp30) cc_final: 0.7933 (tp30) REVERT: E 176 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8196 (mmtt) REVERT: E 187 ASP cc_start: 0.8308 (t0) cc_final: 0.7799 (t0) REVERT: E 329 GLN cc_start: 0.8469 (tp40) cc_final: 0.8204 (tp40) outliers start: 30 outliers final: 12 residues processed: 357 average time/residue: 0.2509 time to fit residues: 131.5172 Evaluate side-chains 261 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 249 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain E residue 167 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 152 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 HIS D 125 ASN D 201 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14607 Z= 0.254 Angle : 0.602 9.599 19612 Z= 0.298 Chirality : 0.044 0.350 2156 Planarity : 0.004 0.038 2412 Dihedral : 6.965 68.166 2242 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.41 % Favored : 95.53 % Rotamer: Outliers : 2.69 % Allowed : 10.89 % Favored : 86.43 % 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: 0.41 (0.21), residues: 1679 helix: 2.08 (0.21), residues: 593 sheet: -0.57 (0.29), residues: 379 loop : -0.78 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 243 HIS 0.004 0.001 HIS A 311 PHE 0.012 0.001 PHE E 84 TYR 0.020 0.002 TYR A 301 ARG 0.007 0.000 ARG C 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 263 time to evaluate : 1.563 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: symmetry clash REVERT: D 141 ASP cc_start: 0.8125 (t70) cc_final: 0.7751 (p0) REVERT: D 246 MET cc_start: 0.7421 (mtm) cc_final: 0.7142 (mtt) REVERT: D 263 MET cc_start: 0.8562 (mmm) cc_final: 0.8121 (tmm) REVERT: D 298 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7800 (tt) REVERT: A 169 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7777 (mt-10) REVERT: A 173 GLN cc_start: 0.8431 (pp30) cc_final: 0.8122 (pp30) REVERT: A 203 ASN cc_start: 0.8702 (m-40) cc_final: 0.8044 (p0) REVERT: A 396 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7521 (mtmm) REVERT: A 400 ILE cc_start: 0.8270 (tp) cc_final: 0.7613 (pt) REVERT: A 411 MET cc_start: 0.6758 (mmp) cc_final: 0.6336 (mmp) REVERT: B 18 MET cc_start: 0.8459 (ppp) cc_final: 0.8219 (ptt) REVERT: B 83 LEU cc_start: 0.8117 (tt) cc_final: 0.7801 (tt) REVERT: B 397 ILE cc_start: 0.8488 (mm) cc_final: 0.8225 (mt) REVERT: B 411 MET cc_start: 0.7572 (mmp) cc_final: 0.6498 (ttp) REVERT: C 206 LYS cc_start: 0.7343 (mptt) cc_final: 0.6772 (ttpt) REVERT: E 88 LYS cc_start: 0.8158 (ttmt) cc_final: 0.7685 (tttp) REVERT: E 176 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8150 (mmtt) REVERT: E 187 ASP cc_start: 0.8342 (t0) cc_final: 0.7793 (t0) REVERT: E 329 GLN cc_start: 0.8742 (tp40) cc_final: 0.8537 (tp40) REVERT: E 331 MET cc_start: 0.8031 (mmp) cc_final: 0.7796 (mmm) outliers start: 41 outliers final: 31 residues processed: 289 average time/residue: 0.2398 time to fit residues: 103.9778 Evaluate side-chains 270 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 238 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 103 optimal weight: 0.0870 chunk 42 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 165 optimal weight: 20.0000 chunk 136 optimal weight: 10.0000 chunk 151 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 201 HIS C 46 ASN E 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14607 Z= 0.238 Angle : 0.570 10.074 19612 Z= 0.285 Chirality : 0.044 0.294 2156 Planarity : 0.004 0.039 2412 Dihedral : 6.037 57.086 2229 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.11 % Favored : 95.83 % Rotamer: Outliers : 2.82 % Allowed : 11.93 % Favored : 85.25 % 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: 0.45 (0.21), residues: 1679 helix: 2.17 (0.21), residues: 594 sheet: -0.56 (0.29), residues: 379 loop : -0.81 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 243 HIS 0.003 0.001 HIS A 311 PHE 0.012 0.001 PHE C 13 TYR 0.021 0.002 TYR A 301 ARG 0.007 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 248 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8145 (t70) cc_final: 0.7698 (p0) REVERT: D 246 MET cc_start: 0.7471 (mtm) cc_final: 0.7184 (mtt) REVERT: D 263 MET cc_start: 0.8538 (mmm) cc_final: 0.8091 (tmm) REVERT: D 298 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7825 (tt) REVERT: A 169 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7767 (mt-10) REVERT: A 173 GLN cc_start: 0.8453 (pp30) cc_final: 0.8124 (pp30) REVERT: A 203 ASN cc_start: 0.8698 (m-40) cc_final: 0.8064 (p0) REVERT: A 220 MET cc_start: 0.7697 (mmm) cc_final: 0.7351 (mmm) REVERT: A 396 LYS cc_start: 0.8053 (mmtt) cc_final: 0.7495 (mtmm) REVERT: A 400 ILE cc_start: 0.8287 (tp) cc_final: 0.7665 (pt) REVERT: A 411 MET cc_start: 0.6701 (mmp) cc_final: 0.6313 (mmp) REVERT: B 18 MET cc_start: 0.8495 (ppp) cc_final: 0.8245 (ptt) REVERT: B 83 LEU cc_start: 0.8119 (tt) cc_final: 0.7735 (tt) REVERT: B 397 ILE cc_start: 0.8412 (mm) cc_final: 0.8076 (mt) REVERT: B 411 MET cc_start: 0.7578 (mmp) cc_final: 0.6500 (ttp) REVERT: E 77 MET cc_start: 0.8558 (mmt) cc_final: 0.8222 (mmt) REVERT: E 176 LYS cc_start: 0.8655 (mmtt) cc_final: 0.8049 (mmtt) REVERT: E 187 ASP cc_start: 0.8379 (t0) cc_final: 0.7851 (t0) REVERT: E 248 MET cc_start: 0.8700 (tpp) cc_final: 0.8274 (tpp) outliers start: 43 outliers final: 31 residues processed: 276 average time/residue: 0.2506 time to fit residues: 105.8067 Evaluate side-chains 270 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 238 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 80 optimal weight: 0.0470 chunk 145 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 243 GLN E 333 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14607 Z= 0.221 Angle : 0.563 9.963 19612 Z= 0.281 Chirality : 0.043 0.247 2156 Planarity : 0.004 0.039 2412 Dihedral : 5.904 55.946 2229 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.11 % Favored : 95.83 % Rotamer: Outliers : 3.54 % Allowed : 12.92 % Favored : 83.54 % 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: 0.45 (0.21), residues: 1679 helix: 2.22 (0.21), residues: 594 sheet: -0.64 (0.29), residues: 385 loop : -0.81 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 243 HIS 0.003 0.001 HIS D 311 PHE 0.013 0.001 PHE A 402 TYR 0.024 0.001 TYR E 224 ARG 0.009 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 249 time to evaluate : 1.715 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: D 141 ASP cc_start: 0.8165 (t70) cc_final: 0.7684 (p0) REVERT: D 246 MET cc_start: 0.7420 (mtm) cc_final: 0.7139 (mtt) REVERT: D 263 MET cc_start: 0.8539 (mmm) cc_final: 0.8086 (tmm) REVERT: D 298 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7801 (tt) REVERT: A 169 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7749 (mt-10) REVERT: A 173 GLN cc_start: 0.8456 (pp30) cc_final: 0.8118 (pp30) REVERT: A 203 ASN cc_start: 0.8705 (m-40) cc_final: 0.8069 (p0) REVERT: A 220 MET cc_start: 0.7721 (mmm) cc_final: 0.7375 (mmm) REVERT: A 396 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7502 (mtmm) REVERT: A 400 ILE cc_start: 0.8286 (tp) cc_final: 0.7628 (pt) REVERT: A 411 MET cc_start: 0.6760 (mmt) cc_final: 0.6346 (mmp) REVERT: B 83 LEU cc_start: 0.8151 (tt) cc_final: 0.7748 (tt) REVERT: E 77 MET cc_start: 0.8585 (mmt) cc_final: 0.8239 (mmt) REVERT: E 141 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8152 (tt) REVERT: E 176 LYS cc_start: 0.8691 (mmtt) cc_final: 0.8168 (mmtt) REVERT: E 187 ASP cc_start: 0.8390 (t0) cc_final: 0.7856 (t0) REVERT: E 248 MET cc_start: 0.8626 (tpp) cc_final: 0.8251 (tpp) outliers start: 54 outliers final: 37 residues processed: 287 average time/residue: 0.2434 time to fit residues: 104.8682 Evaluate side-chains 269 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 230 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN D 46 ASN D 186 GLN D 201 HIS A 125 ASN C 155 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN E 467 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 14607 Z= 0.514 Angle : 0.713 11.154 19612 Z= 0.362 Chirality : 0.048 0.217 2156 Planarity : 0.005 0.040 2412 Dihedral : 7.207 53.784 2229 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.72 % Allowed : 14.56 % Favored : 80.72 % 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: -0.11 (0.21), residues: 1679 helix: 1.78 (0.21), residues: 593 sheet: -1.13 (0.28), residues: 391 loop : -1.01 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 243 HIS 0.010 0.002 HIS D 311 PHE 0.021 0.002 PHE B 48 TYR 0.029 0.002 TYR E 224 ARG 0.009 0.001 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 217 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 97 ASP cc_start: 0.8191 (t0) cc_final: 0.7886 (t0) REVERT: D 141 ASP cc_start: 0.8172 (t70) cc_final: 0.7855 (p0) REVERT: A 173 GLN cc_start: 0.8510 (pp30) cc_final: 0.8140 (pp30) REVERT: A 203 ASN cc_start: 0.8759 (m-40) cc_final: 0.8121 (p0) REVERT: A 220 MET cc_start: 0.7892 (mmm) cc_final: 0.7575 (mmm) REVERT: A 396 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7639 (mtmm) REVERT: A 411 MET cc_start: 0.6749 (mmt) cc_final: 0.6368 (mmp) REVERT: B 83 LEU cc_start: 0.8197 (tt) cc_final: 0.7939 (tt) REVERT: E 88 LYS cc_start: 0.8317 (ttmt) cc_final: 0.7692 (tttt) REVERT: E 141 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8313 (tt) REVERT: E 176 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8235 (mmtt) REVERT: E 187 ASP cc_start: 0.8504 (t0) cc_final: 0.7953 (t0) REVERT: E 316 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8506 (mp) REVERT: E 329 GLN cc_start: 0.8672 (tp40) cc_final: 0.8263 (tp40) outliers start: 72 outliers final: 54 residues processed: 265 average time/residue: 0.2421 time to fit residues: 96.7413 Evaluate side-chains 265 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 209 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 213 LYS Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14607 Z= 0.176 Angle : 0.571 9.513 19612 Z= 0.284 Chirality : 0.043 0.187 2156 Planarity : 0.004 0.041 2412 Dihedral : 6.548 57.913 2229 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.87 % Allowed : 16.59 % Favored : 79.54 % 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: 0.30 (0.21), residues: 1679 helix: 2.17 (0.21), residues: 592 sheet: -0.88 (0.28), residues: 395 loop : -0.85 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 243 HIS 0.004 0.001 HIS D 311 PHE 0.014 0.001 PHE A 402 TYR 0.028 0.001 TYR E 224 ARG 0.009 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 246 time to evaluate : 1.628 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: D 141 ASP cc_start: 0.8165 (t70) cc_final: 0.7693 (p0) REVERT: D 191 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7641 (tm-30) REVERT: D 246 MET cc_start: 0.7410 (mtm) cc_final: 0.7111 (mtt) REVERT: D 298 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7729 (tt) REVERT: A 173 GLN cc_start: 0.8536 (pp30) cc_final: 0.8164 (pp30) REVERT: A 203 ASN cc_start: 0.8703 (m-40) cc_final: 0.8075 (p0) REVERT: A 220 MET cc_start: 0.7784 (mmm) cc_final: 0.7536 (mmm) REVERT: A 396 LYS cc_start: 0.8073 (mmtt) cc_final: 0.7548 (mtmm) REVERT: A 411 MET cc_start: 0.6699 (mmt) cc_final: 0.6410 (mmp) REVERT: E 141 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8233 (tt) REVERT: E 176 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8212 (mmtt) REVERT: E 187 ASP cc_start: 0.8423 (t0) cc_final: 0.7885 (t0) REVERT: E 316 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8281 (mp) REVERT: E 329 GLN cc_start: 0.8597 (tp40) cc_final: 0.8204 (tp40) outliers start: 59 outliers final: 43 residues processed: 287 average time/residue: 0.2338 time to fit residues: 101.0270 Evaluate side-chains 267 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 221 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 0.0570 chunk 90 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 GLN E 243 GLN E 333 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14607 Z= 0.162 Angle : 0.565 11.416 19612 Z= 0.277 Chirality : 0.043 0.183 2156 Planarity : 0.004 0.044 2412 Dihedral : 6.164 58.940 2229 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.21 % Allowed : 17.51 % Favored : 79.28 % 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: 0.44 (0.21), residues: 1679 helix: 2.26 (0.21), residues: 594 sheet: -0.77 (0.28), residues: 397 loop : -0.76 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 243 HIS 0.003 0.000 HIS D 311 PHE 0.021 0.001 PHE C 13 TYR 0.029 0.001 TYR E 224 ARG 0.003 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 246 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8199 (t70) cc_final: 0.7685 (p0) REVERT: D 246 MET cc_start: 0.7367 (mtm) cc_final: 0.7067 (mtt) REVERT: D 400 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8110 (tp) REVERT: A 173 GLN cc_start: 0.8530 (pp30) cc_final: 0.8149 (pp30) REVERT: A 203 ASN cc_start: 0.8686 (m-40) cc_final: 0.8055 (p0) REVERT: A 220 MET cc_start: 0.7752 (mmm) cc_final: 0.7463 (mmm) REVERT: A 263 MET cc_start: 0.8704 (mmm) cc_final: 0.8492 (tpp) REVERT: A 271 ARG cc_start: 0.8012 (tpt90) cc_final: 0.7673 (tpp80) REVERT: A 396 LYS cc_start: 0.7973 (mmtt) cc_final: 0.7485 (mtmm) REVERT: A 411 MET cc_start: 0.6724 (mmt) cc_final: 0.6420 (mmp) REVERT: B 83 LEU cc_start: 0.8112 (tt) cc_final: 0.7675 (tt) REVERT: E 141 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8177 (tt) REVERT: E 176 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8149 (mmtt) REVERT: E 187 ASP cc_start: 0.8412 (t0) cc_final: 0.7887 (t0) REVERT: E 329 GLN cc_start: 0.8594 (tp40) cc_final: 0.8159 (tp40) outliers start: 49 outliers final: 41 residues processed: 276 average time/residue: 0.2350 time to fit residues: 97.2997 Evaluate side-chains 279 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 236 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 73.1935 > 50: distance: 68 - 85: 34.755 distance: 72 - 91: 35.701 distance: 77 - 97: 35.052 distance: 81 - 85: 33.459 distance: 82 - 101: 33.969 distance: 85 - 86: 21.190 distance: 86 - 87: 58.637 distance: 86 - 89: 43.659 distance: 87 - 88: 39.297 distance: 87 - 91: 69.971 distance: 88 - 107: 47.494 distance: 89 - 90: 27.672 distance: 91 - 92: 52.047 distance: 92 - 93: 21.409 distance: 92 - 95: 21.614 distance: 93 - 94: 13.530 distance: 93 - 97: 59.248 distance: 94 - 118: 36.088 distance: 95 - 96: 40.905 distance: 97 - 98: 6.229 distance: 98 - 99: 32.024 distance: 99 - 100: 67.892 distance: 99 - 101: 57.782 distance: 100 - 123: 39.906 distance: 101 - 102: 17.013 distance: 102 - 103: 59.650 distance: 102 - 105: 44.578 distance: 103 - 104: 24.530 distance: 103 - 107: 30.950 distance: 104 - 129: 23.675 distance: 105 - 106: 40.852 distance: 107 - 108: 32.696 distance: 108 - 109: 38.723 distance: 108 - 111: 40.709 distance: 109 - 110: 45.397 distance: 109 - 118: 36.859 distance: 111 - 112: 43.983 distance: 112 - 113: 42.490 distance: 113 - 114: 4.713 distance: 114 - 115: 28.603 distance: 115 - 116: 43.609 distance: 115 - 117: 48.988 distance: 118 - 119: 52.174 distance: 119 - 120: 42.294 distance: 119 - 122: 40.221 distance: 120 - 121: 28.194 distance: 120 - 123: 38.822 distance: 123 - 124: 39.510 distance: 124 - 125: 45.732 distance: 124 - 127: 11.525 distance: 125 - 126: 57.910 distance: 125 - 129: 44.040 distance: 127 - 128: 48.906 distance: 129 - 130: 24.592 distance: 130 - 131: 24.098 distance: 130 - 133: 53.465 distance: 131 - 132: 48.436 distance: 131 - 137: 41.157 distance: 133 - 134: 41.877 distance: 134 - 135: 53.511 distance: 134 - 136: 40.729 distance: 137 - 138: 27.261 distance: 137 - 143: 52.489 distance: 138 - 139: 27.206 distance: 138 - 141: 10.933 distance: 139 - 140: 43.424 distance: 139 - 144: 18.464 distance: 141 - 142: 15.270 distance: 142 - 143: 47.861 distance: 144 - 145: 14.237 distance: 145 - 146: 14.770 distance: 145 - 148: 31.744 distance: 146 - 147: 31.087 distance: 146 - 153: 29.702 distance: 148 - 149: 36.263 distance: 149 - 150: 40.408 distance: 150 - 151: 39.709 distance: 151 - 152: 56.857