Starting phenix.real_space_refine on Thu Feb 15 01:36:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kal_22774/02_2024/7kal_22774.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kal_22774/02_2024/7kal_22774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kal_22774/02_2024/7kal_22774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kal_22774/02_2024/7kal_22774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kal_22774/02_2024/7kal_22774.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kal_22774/02_2024/7kal_22774.pdb" } resolution = 4.0 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= 0.005 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 7021 2.51 5 N 1853 2.21 5 O 1868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 230": "NH1" <-> "NH2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "C ASP 30": "OD1" <-> "OD2" Residue "C ARG 31": "NH1" <-> "NH2" Residue "D ARG 230": "NH1" <-> "NH2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D ASP 307": "OD1" <-> "OD2" Residue "D ARG 311": "NH1" <-> "NH2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "E ARG 93": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 173": "NH1" <-> "NH2" Residue "F ARG 88": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 118": "NH1" <-> "NH2" Residue "F GLU 119": "OE1" <-> "OE2" Residue "F GLU 169": "OE1" <-> "OE2" Residue "F GLU 181": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10789 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3264 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 21, 'TRANS': 415} Chain breaks: 3 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "C" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 440 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 54} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 245 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3673 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 31, 'TRANS': 443} Chain breaks: 5 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 67 Chain: "E" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1359 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "F" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1454 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "G" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 354 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 3, 'TRANS': 58} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'TRP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 6.08, per 1000 atoms: 0.56 Number of scatterers: 10789 At special positions: 0 Unit cell: (109.44, 126.54, 137.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1868 8.00 N 1853 7.00 C 7021 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 - 3.50 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=0, symmetry=0 Time building additional restraints: 4.12 Conformation dependent library (CDL) restraints added in 2.0 seconds 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2662 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 7 sheets defined 69.2% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 28 through 48 removed outlier: 3.557A pdb=" N LEU A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 99 Processing helix chain 'A' and resid 107 through 137 removed outlier: 3.509A pdb=" N ARG A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY A 137 " --> pdb=" O HIS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 149 through 173 removed outlier: 3.644A pdb=" N LEU A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 198 Processing helix chain 'A' and resid 213 through 225 removed outlier: 3.540A pdb=" N LEU A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 243 through 262 removed outlier: 3.584A pdb=" N LEU A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 312 removed outlier: 3.601A pdb=" N MET A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 324 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 357 through 383 removed outlier: 4.330A pdb=" N GLU A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 382 " --> pdb=" O THR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 408 through 439 removed outlier: 3.778A pdb=" N GLU A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Proline residue: A 418 - end of helix removed outlier: 3.682A pdb=" N ALA A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 464 removed outlier: 3.503A pdb=" N ILE A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 30 through 68 removed outlier: 3.569A pdb=" N PHE C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Proline residue: C 61 - end of helix Processing helix chain 'B' and resid 95 through 123 removed outlier: 3.551A pdb=" N PHE B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 28 Processing helix chain 'D' and resid 30 through 35 removed outlier: 4.117A pdb=" N LEU D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 68 removed outlier: 3.964A pdb=" N LEU D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 98 removed outlier: 4.335A pdb=" N ILE D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ALA D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 231 removed outlier: 4.776A pdb=" N LYS D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TYR D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Proline residue: D 218 - end of helix removed outlier: 4.217A pdb=" N TYR D 231 " --> pdb=" O GLY D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 247 removed outlier: 3.671A pdb=" N ARG D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 removed outlier: 3.745A pdb=" N VAL D 258 " --> pdb=" O GLY D 254 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN D 259 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 3.884A pdb=" N GLU D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 291 removed outlier: 3.573A pdb=" N GLY D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ALA D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 4.084A pdb=" N VAL D 302 " --> pdb=" O LYS D 298 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 306 " --> pdb=" O VAL D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 322 Processing helix chain 'D' and resid 331 through 358 removed outlier: 4.186A pdb=" N GLU D 335 " --> pdb=" O VAL D 331 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER D 341 " --> pdb=" O TYR D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 376 removed outlier: 3.668A pdb=" N ARG D 368 " --> pdb=" O ILE D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.848A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 414 Processing helix chain 'D' and resid 419 through 424 Processing helix chain 'D' and resid 431 through 443 Processing helix chain 'E' and resid 4 through 37 Proline residue: E 9 - end of helix Processing helix chain 'E' and resid 46 through 61 Processing helix chain 'E' and resid 70 through 106 removed outlier: 3.968A pdb=" N LEU E 74 " --> pdb=" O PRO E 70 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLN E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY E 106 " --> pdb=" O LEU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 138 removed outlier: 3.907A pdb=" N TRP E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 168 removed outlier: 3.926A pdb=" N GLN E 147 " --> pdb=" O GLN E 143 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 removed outlier: 3.836A pdb=" N GLU E 172 " --> pdb=" O THR E 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 56 removed outlier: 3.823A pdb=" N ASP F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 89 removed outlier: 4.426A pdb=" N SER F 72 " --> pdb=" O ASN F 68 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY F 89 " --> pdb=" O ALA F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 107 Processing helix chain 'F' and resid 114 through 135 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 156 through 171 Processing helix chain 'F' and resid 172 through 187 Processing helix chain 'F' and resid 192 through 203 Processing helix chain 'G' and resid 245 through 266 removed outlier: 3.681A pdb=" N LEU G 266 " --> pdb=" O PHE G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 270 Processing helix chain 'G' and resid 274 through 305 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 7.022A pdb=" N GLU A 19 " --> pdb=" O VAL B 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA5, first strand: chain 'D' and resid 448 through 457 removed outlier: 5.564A pdb=" N ILE D 450 " --> pdb=" O ARG D 476 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG D 476 " --> pdb=" O ILE D 450 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS D 452 " --> pdb=" O LYS D 474 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 558 through 560 removed outlier: 3.623A pdb=" N VAL D 560 " --> pdb=" O LEU D 550 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU D 550 " --> pdb=" O VAL D 560 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 13 through 15 740 hydrogen bonds defined for protein. 2199 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: 3.12 Time building geometry restraints manager: 4.48 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: 3430 1.34 - 1.46: 2212 1.46 - 1.58: 5301 1.58 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 11024 Sorted by residual: bond pdb=" N GLY G 245 " pdb=" CA GLY G 245 " ideal model delta sigma weight residual 1.443 1.459 -0.017 1.37e-02 5.33e+03 1.46e+00 bond pdb=" CA VAL G 283 " pdb=" CB VAL G 283 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.25e-02 6.40e+03 9.43e-01 bond pdb=" C PRO F 57 " pdb=" N PRO F 58 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.42e-01 bond pdb=" N PRO G 246 " pdb=" CA PRO G 246 " ideal model delta sigma weight residual 1.472 1.459 0.013 1.32e-02 5.74e+03 9.18e-01 bond pdb=" CA ILE G 297 " pdb=" CB ILE G 297 " ideal model delta sigma weight residual 1.540 1.529 0.012 1.25e-02 6.40e+03 8.61e-01 ... (remaining 11019 not shown) Histogram of bond angle deviations from ideal: 100.25 - 107.00: 396 107.00 - 113.75: 6238 113.75 - 120.50: 4449 120.50 - 127.25: 3771 127.25 - 134.00: 134 Bond angle restraints: 14988 Sorted by residual: angle pdb=" N PRO G 246 " pdb=" CA PRO G 246 " pdb=" CB PRO G 246 " ideal model delta sigma weight residual 103.33 110.14 -6.81 1.10e+00 8.26e-01 3.83e+01 angle pdb=" C ILE A 417 " pdb=" CA ILE A 417 " pdb=" CB ILE A 417 " ideal model delta sigma weight residual 114.00 110.71 3.29 1.31e+00 5.83e-01 6.30e+00 angle pdb=" N ALA D 535 " pdb=" CA ALA D 535 " pdb=" CB ALA D 535 " ideal model delta sigma weight residual 111.66 109.08 2.58 1.11e+00 8.12e-01 5.41e+00 angle pdb=" C VAL A 416 " pdb=" N ILE A 417 " pdb=" CA ILE A 417 " ideal model delta sigma weight residual 120.33 122.17 -1.84 8.00e-01 1.56e+00 5.27e+00 angle pdb=" C ALA D 535 " pdb=" CA ALA D 535 " pdb=" CB ALA D 535 " ideal model delta sigma weight residual 111.20 109.64 1.56 7.10e-01 1.98e+00 4.82e+00 ... (remaining 14983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6123 17.76 - 35.52: 386 35.52 - 53.28: 53 53.28 - 71.04: 12 71.04 - 88.80: 6 Dihedral angle restraints: 6580 sinusoidal: 2457 harmonic: 4123 Sorted by residual: dihedral pdb=" CA GLY D 426 " pdb=" C GLY D 426 " pdb=" N PRO D 427 " pdb=" CA PRO D 427 " ideal model delta harmonic sigma weight residual 180.00 160.73 19.27 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA LEU D 327 " pdb=" C LEU D 327 " pdb=" N GLU D 328 " pdb=" CA GLU D 328 " ideal model delta harmonic sigma weight residual -180.00 -161.22 -18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA GLU D 328 " pdb=" C GLU D 328 " pdb=" N ASP D 329 " pdb=" CA ASP D 329 " ideal model delta harmonic sigma weight residual 180.00 163.18 16.82 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 6577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1414 0.045 - 0.089: 286 0.089 - 0.134: 48 0.134 - 0.178: 3 0.178 - 0.223: 1 Chirality restraints: 1752 Sorted by residual: chirality pdb=" CA PRO G 246 " pdb=" N PRO G 246 " pdb=" C PRO G 246 " pdb=" CB PRO G 246 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB ILE D 473 " pdb=" CA ILE D 473 " pdb=" CG1 ILE D 473 " pdb=" CG2 ILE D 473 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA THR A 14 " pdb=" N THR A 14 " pdb=" C THR A 14 " pdb=" CB THR A 14 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 1749 not shown) Planarity restraints: 1881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE G 267 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO G 268 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO G 268 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 268 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 57 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO F 58 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO F 58 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 58 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 56 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO F 57 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO F 57 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 57 " -0.018 5.00e-02 4.00e+02 ... (remaining 1878 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2512 2.79 - 3.32: 10874 3.32 - 3.84: 17415 3.84 - 4.37: 17492 4.37 - 4.90: 31120 Nonbonded interactions: 79413 Sorted by model distance: nonbonded pdb=" NE2 GLN D 63 " pdb=" OE2 GLU D 334 " model vdw 2.262 2.520 nonbonded pdb=" O THR D 464 " pdb=" OG SER D 467 " model vdw 2.267 2.440 nonbonded pdb=" NE2 GLN D 371 " pdb=" O TYR D 610 " model vdw 2.278 2.520 nonbonded pdb=" OG1 THR D 232 " pdb=" O GLY E 106 " model vdw 2.285 2.440 nonbonded pdb=" OD1 ASN A 243 " pdb=" ND2 ASN A 246 " model vdw 2.300 2.520 ... (remaining 79408 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.060 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: 4.070 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 30.910 Find NCS groups from input model: 0.340 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.002 0.029 11024 Z= 0.142 Angle : 0.511 6.810 14988 Z= 0.283 Chirality : 0.036 0.223 1752 Planarity : 0.003 0.033 1881 Dihedral : 11.874 88.798 3918 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.58 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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: -0.72 (0.22), residues: 1394 helix: 0.50 (0.16), residues: 940 sheet: -2.56 (0.52), residues: 88 loop : -2.39 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 141 HIS 0.002 0.000 HIS D 534 PHE 0.011 0.001 PHE D 15 TYR 0.013 0.001 TYR D 435 ARG 0.002 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 LEU cc_start: 0.9145 (tp) cc_final: 0.8805 (tt) REVERT: C 54 ILE cc_start: 0.9296 (tp) cc_final: 0.9049 (tp) REVERT: E 10 PHE cc_start: 0.7975 (m-10) cc_final: 0.7745 (m-80) REVERT: E 84 GLU cc_start: 0.9140 (tp30) cc_final: 0.8729 (tm-30) REVERT: E 104 GLN cc_start: 0.8546 (mp10) cc_final: 0.8191 (mp10) REVERT: E 121 LYS cc_start: 0.9453 (ttpt) cc_final: 0.9220 (pptt) REVERT: E 125 ASP cc_start: 0.8761 (t0) cc_final: 0.8530 (t0) REVERT: F 100 TYR cc_start: 0.9348 (t80) cc_final: 0.9008 (t80) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2458 time to fit residues: 46.6290 Evaluate side-chains 92 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 129 GLN A 133 HIS ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN D 386 GLN D 529 GLN D 534 HIS D 584 GLN D 595 GLN D 604 HIS ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 97 GLN F 10 HIS F 49 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11024 Z= 0.347 Angle : 0.641 7.402 14988 Z= 0.323 Chirality : 0.038 0.166 1752 Planarity : 0.004 0.032 1881 Dihedral : 3.584 18.773 1530 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.59 % Favored : 96.34 % Rotamer: Outliers : 2.23 % Allowed : 11.78 % Favored : 85.99 % 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: 0.71 (0.24), residues: 1394 helix: 1.63 (0.17), residues: 949 sheet: -2.25 (0.53), residues: 88 loop : -1.99 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 141 HIS 0.009 0.002 HIS A 336 PHE 0.033 0.002 PHE G 267 TYR 0.013 0.001 TYR D 435 ARG 0.007 0.000 ARG F 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9085 (mmm) cc_final: 0.8788 (mmm) REVERT: C 54 ILE cc_start: 0.9371 (tp) cc_final: 0.9131 (tp) REVERT: D 357 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8658 (t80) REVERT: D 471 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8642 (pt) REVERT: E 84 GLU cc_start: 0.9297 (tp30) cc_final: 0.8744 (tm-30) REVERT: E 85 ASP cc_start: 0.9095 (m-30) cc_final: 0.8595 (m-30) REVERT: E 94 GLU cc_start: 0.8287 (tp30) cc_final: 0.8003 (tp30) REVERT: E 121 LYS cc_start: 0.9469 (ttpt) cc_final: 0.9263 (pptt) REVERT: E 125 ASP cc_start: 0.8864 (t0) cc_final: 0.8653 (t0) REVERT: F 100 TYR cc_start: 0.9410 (t80) cc_final: 0.9045 (t80) REVERT: F 133 MET cc_start: 0.9229 (mtm) cc_final: 0.9025 (mtt) outliers start: 24 outliers final: 16 residues processed: 106 average time/residue: 0.1859 time to fit residues: 30.6007 Evaluate side-chains 101 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 186 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 113 optimal weight: 0.8980 chunk 126 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 HIS ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11024 Z= 0.273 Angle : 0.592 7.609 14988 Z= 0.294 Chirality : 0.037 0.139 1752 Planarity : 0.004 0.033 1881 Dihedral : 3.554 18.086 1530 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.44 % Favored : 96.48 % Rotamer: Outliers : 2.32 % Allowed : 15.49 % Favored : 82.19 % 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: 1.21 (0.24), residues: 1394 helix: 2.01 (0.17), residues: 951 sheet: -2.05 (0.55), residues: 88 loop : -1.85 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 141 HIS 0.006 0.001 HIS A 336 PHE 0.027 0.001 PHE E 10 TYR 0.020 0.001 TYR E 158 ARG 0.006 0.000 ARG F 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9096 (mmm) cc_final: 0.8779 (mmm) REVERT: C 54 ILE cc_start: 0.9364 (tp) cc_final: 0.9111 (tp) REVERT: D 357 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8745 (t80) REVERT: D 369 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9184 (tp) REVERT: E 84 GLU cc_start: 0.9259 (tp30) cc_final: 0.8730 (tm-30) REVERT: E 85 ASP cc_start: 0.9120 (m-30) cc_final: 0.8557 (m-30) REVERT: F 100 TYR cc_start: 0.9390 (t80) cc_final: 0.8870 (t80) outliers start: 25 outliers final: 15 residues processed: 106 average time/residue: 0.1844 time to fit residues: 30.6129 Evaluate side-chains 102 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 174 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 0.0670 chunk 14 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11024 Z= 0.253 Angle : 0.576 6.830 14988 Z= 0.288 Chirality : 0.037 0.143 1752 Planarity : 0.004 0.040 1881 Dihedral : 3.542 17.787 1530 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 2.97 % Allowed : 17.63 % Favored : 79.41 % 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 (0.24), residues: 1394 helix: 2.13 (0.17), residues: 950 sheet: -2.02 (0.54), residues: 88 loop : -1.79 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 141 HIS 0.005 0.001 HIS A 336 PHE 0.020 0.001 PHE C 45 TYR 0.013 0.001 TYR E 158 ARG 0.005 0.000 ARG F 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 89 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9109 (mmm) cc_final: 0.8783 (mmm) REVERT: C 54 ILE cc_start: 0.9367 (tp) cc_final: 0.9125 (tp) REVERT: D 357 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8649 (t80) REVERT: D 369 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9166 (tp) REVERT: D 471 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8589 (pt) REVERT: E 84 GLU cc_start: 0.9239 (tp30) cc_final: 0.8729 (tm-30) REVERT: E 85 ASP cc_start: 0.9069 (m-30) cc_final: 0.8534 (m-30) REVERT: E 94 GLU cc_start: 0.8411 (tp30) cc_final: 0.8147 (tp30) REVERT: F 100 TYR cc_start: 0.9377 (t80) cc_final: 0.8850 (t80) outliers start: 32 outliers final: 23 residues processed: 113 average time/residue: 0.1802 time to fit residues: 32.2850 Evaluate side-chains 111 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 85 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 174 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 93 optimal weight: 0.0670 chunk 0 optimal weight: 30.0000 chunk 69 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11024 Z= 0.143 Angle : 0.558 8.599 14988 Z= 0.268 Chirality : 0.037 0.148 1752 Planarity : 0.004 0.039 1881 Dihedral : 3.388 16.261 1530 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.01 % Favored : 96.92 % Rotamer: Outliers : 2.41 % Allowed : 19.02 % Favored : 78.57 % 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: 1.66 (0.24), residues: 1394 helix: 2.36 (0.17), residues: 942 sheet: -2.04 (0.53), residues: 90 loop : -1.56 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 141 HIS 0.006 0.001 HIS A 336 PHE 0.018 0.001 PHE C 45 TYR 0.013 0.001 TYR E 158 ARG 0.004 0.000 ARG F 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9121 (mmm) cc_final: 0.8540 (mmm) REVERT: C 54 ILE cc_start: 0.9305 (tp) cc_final: 0.9076 (tp) REVERT: D 94 ILE cc_start: 0.9265 (mm) cc_final: 0.8972 (mm) REVERT: D 369 ILE cc_start: 0.9447 (OUTLIER) cc_final: 0.9050 (tp) REVERT: E 84 GLU cc_start: 0.9183 (tp30) cc_final: 0.8689 (tm-30) REVERT: E 85 ASP cc_start: 0.9012 (m-30) cc_final: 0.8559 (m-30) REVERT: E 94 GLU cc_start: 0.8318 (tp30) cc_final: 0.8117 (tp30) REVERT: F 100 TYR cc_start: 0.9385 (t80) cc_final: 0.8902 (t80) outliers start: 26 outliers final: 13 residues processed: 113 average time/residue: 0.1758 time to fit residues: 31.1732 Evaluate side-chains 102 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 186 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11024 Z= 0.401 Angle : 0.703 12.043 14988 Z= 0.349 Chirality : 0.039 0.212 1752 Planarity : 0.004 0.044 1881 Dihedral : 3.755 18.366 1530 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.02 % Favored : 95.91 % Rotamer: Outliers : 3.71 % Allowed : 19.11 % Favored : 77.18 % 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 (0.24), residues: 1394 helix: 2.18 (0.17), residues: 952 sheet: -2.07 (0.53), residues: 88 loop : -1.70 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 141 HIS 0.005 0.001 HIS D 547 PHE 0.021 0.002 PHE E 23 TYR 0.014 0.002 TYR D 321 ARG 0.005 0.001 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 85 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 ILE cc_start: 0.9422 (tp) cc_final: 0.9194 (tp) REVERT: D 94 ILE cc_start: 0.9274 (mm) cc_final: 0.8993 (mm) REVERT: D 369 ILE cc_start: 0.9531 (OUTLIER) cc_final: 0.9264 (tp) REVERT: E 84 GLU cc_start: 0.9266 (tp30) cc_final: 0.8733 (tm-30) REVERT: E 85 ASP cc_start: 0.9095 (m-30) cc_final: 0.8786 (m-30) REVERT: F 100 TYR cc_start: 0.9408 (t80) cc_final: 0.8903 (t80) outliers start: 40 outliers final: 23 residues processed: 116 average time/residue: 0.1690 time to fit residues: 31.2526 Evaluate side-chains 107 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 174 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 134 optimal weight: 50.0000 chunk 84 optimal weight: 0.0970 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN F 136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11024 Z= 0.161 Angle : 0.609 11.123 14988 Z= 0.288 Chirality : 0.037 0.151 1752 Planarity : 0.004 0.045 1881 Dihedral : 3.570 21.609 1530 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.73 % Favored : 97.20 % Rotamer: Outliers : 2.13 % Allowed : 21.24 % Favored : 76.62 % 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: 1.66 (0.24), residues: 1394 helix: 2.34 (0.17), residues: 952 sheet: -2.29 (0.52), residues: 90 loop : -1.51 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 141 HIS 0.005 0.001 HIS A 336 PHE 0.018 0.001 PHE C 45 TYR 0.011 0.001 TYR E 158 ARG 0.003 0.000 ARG F 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: A 294 MET cc_start: 0.8850 (ttp) cc_final: 0.8516 (ptm) REVERT: C 54 ILE cc_start: 0.9339 (tp) cc_final: 0.9125 (tp) REVERT: D 94 ILE cc_start: 0.9267 (mm) cc_final: 0.8964 (mm) REVERT: D 369 ILE cc_start: 0.9465 (OUTLIER) cc_final: 0.9112 (tp) REVERT: E 84 GLU cc_start: 0.9207 (tp30) cc_final: 0.8709 (tm-30) REVERT: E 85 ASP cc_start: 0.9016 (m-30) cc_final: 0.8593 (m-30) REVERT: F 100 TYR cc_start: 0.9395 (t80) cc_final: 0.8926 (t80) outliers start: 23 outliers final: 18 residues processed: 104 average time/residue: 0.1740 time to fit residues: 28.8034 Evaluate side-chains 104 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain E residue 19 CYS Chi-restraints excluded: chain E residue 110 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11024 Z= 0.180 Angle : 0.592 11.208 14988 Z= 0.285 Chirality : 0.037 0.154 1752 Planarity : 0.004 0.044 1881 Dihedral : 3.513 24.648 1530 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.08 % Favored : 96.84 % Rotamer: Outliers : 2.13 % Allowed : 21.06 % Favored : 76.81 % 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: 1.80 (0.24), residues: 1394 helix: 2.44 (0.17), residues: 945 sheet: -2.31 (0.51), residues: 90 loop : -1.37 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 141 HIS 0.004 0.001 HIS A 336 PHE 0.019 0.001 PHE C 45 TYR 0.009 0.001 TYR D 435 ARG 0.003 0.000 ARG F 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: C 54 ILE cc_start: 0.9342 (tp) cc_final: 0.9138 (tp) REVERT: D 94 ILE cc_start: 0.9244 (mm) cc_final: 0.8944 (mm) REVERT: D 369 ILE cc_start: 0.9483 (OUTLIER) cc_final: 0.9138 (tp) REVERT: D 599 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8648 (p90) REVERT: E 84 GLU cc_start: 0.9214 (tp30) cc_final: 0.8701 (tm-30) REVERT: E 85 ASP cc_start: 0.9034 (m-30) cc_final: 0.8598 (m-30) REVERT: F 100 TYR cc_start: 0.9390 (t80) cc_final: 0.8915 (t80) REVERT: F 133 MET cc_start: 0.8982 (mmm) cc_final: 0.8770 (mmm) outliers start: 23 outliers final: 14 residues processed: 103 average time/residue: 0.1838 time to fit residues: 30.0026 Evaluate side-chains 101 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain E residue 110 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 98 optimal weight: 0.1980 chunk 38 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11024 Z= 0.235 Angle : 0.633 11.462 14988 Z= 0.306 Chirality : 0.037 0.174 1752 Planarity : 0.004 0.044 1881 Dihedral : 3.542 24.378 1530 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.16 % Favored : 96.77 % Rotamer: Outliers : 2.13 % Allowed : 20.87 % Favored : 76.99 % 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: 1.74 (0.24), residues: 1394 helix: 2.39 (0.17), residues: 952 sheet: -2.35 (0.51), residues: 90 loop : -1.41 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 176 HIS 0.004 0.001 HIS A 336 PHE 0.020 0.001 PHE C 45 TYR 0.010 0.001 TYR D 435 ARG 0.003 0.000 ARG F 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 1.486 Fit side-chains revert: symmetry clash REVERT: A 294 MET cc_start: 0.8893 (ttp) cc_final: 0.8539 (ptm) REVERT: C 54 ILE cc_start: 0.9377 (tp) cc_final: 0.9148 (tp) REVERT: D 94 ILE cc_start: 0.9244 (mm) cc_final: 0.8941 (mm) REVERT: D 369 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9110 (tp) REVERT: D 415 MET cc_start: 0.8405 (tpt) cc_final: 0.8008 (tmm) REVERT: D 599 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8693 (p90) REVERT: E 84 GLU cc_start: 0.9220 (tp30) cc_final: 0.8720 (tm-30) REVERT: E 85 ASP cc_start: 0.9041 (m-30) cc_final: 0.8611 (m-30) REVERT: F 100 TYR cc_start: 0.9397 (t80) cc_final: 0.8921 (t80) REVERT: F 133 MET cc_start: 0.8973 (mmm) cc_final: 0.8695 (mmm) outliers start: 23 outliers final: 18 residues processed: 102 average time/residue: 0.1755 time to fit residues: 28.5857 Evaluate side-chains 104 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 186 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.0000 chunk 63 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 139 optimal weight: 50.0000 chunk 128 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 0.4980 chunk 88 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11024 Z= 0.156 Angle : 0.612 12.299 14988 Z= 0.291 Chirality : 0.037 0.144 1752 Planarity : 0.004 0.046 1881 Dihedral : 3.461 22.261 1530 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.58 % Favored : 97.35 % Rotamer: Outliers : 1.67 % Allowed : 21.89 % Favored : 76.44 % 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: 1.90 (0.24), residues: 1394 helix: 2.53 (0.17), residues: 936 sheet: -2.19 (0.53), residues: 84 loop : -1.30 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 176 HIS 0.004 0.001 HIS A 336 PHE 0.018 0.001 PHE C 45 TYR 0.011 0.001 TYR E 158 ARG 0.004 0.000 ARG A 388 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: A 294 MET cc_start: 0.8791 (ttp) cc_final: 0.8496 (ptm) REVERT: C 54 ILE cc_start: 0.9311 (tp) cc_final: 0.9087 (tp) REVERT: D 94 ILE cc_start: 0.9199 (mm) cc_final: 0.8914 (mm) REVERT: D 369 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.8818 (tp) REVERT: D 588 MET cc_start: 0.7996 (ttp) cc_final: 0.7779 (ttt) REVERT: D 599 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8696 (p90) REVERT: E 84 GLU cc_start: 0.9186 (tp30) cc_final: 0.8660 (tm-30) REVERT: E 85 ASP cc_start: 0.9027 (m-30) cc_final: 0.8576 (m-30) REVERT: F 100 TYR cc_start: 0.9377 (t80) cc_final: 0.8912 (t80) outliers start: 18 outliers final: 13 residues processed: 99 average time/residue: 0.1775 time to fit residues: 27.8961 Evaluate side-chains 100 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain E residue 110 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.055721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.045679 restraints weight = 75898.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.046575 restraints weight = 38921.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.046911 restraints weight = 27035.361| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11024 Z= 0.160 Angle : 0.637 13.609 14988 Z= 0.297 Chirality : 0.037 0.154 1752 Planarity : 0.004 0.045 1881 Dihedral : 3.427 21.418 1530 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.58 % Favored : 97.35 % Rotamer: Outliers : 1.76 % Allowed : 21.61 % Favored : 76.62 % 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: 1.94 (0.24), residues: 1394 helix: 2.55 (0.17), residues: 936 sheet: -2.13 (0.53), residues: 84 loop : -1.28 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 176 HIS 0.004 0.001 HIS A 336 PHE 0.025 0.001 PHE C 45 TYR 0.010 0.001 TYR E 158 ARG 0.003 0.000 ARG F 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1717.19 seconds wall clock time: 33 minutes 38.14 seconds (2018.14 seconds total)