Starting phenix.real_space_refine on Fri Sep 27 05:40:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spr_40682/09_2024/8spr_40682.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spr_40682/09_2024/8spr_40682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spr_40682/09_2024/8spr_40682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spr_40682/09_2024/8spr_40682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spr_40682/09_2024/8spr_40682.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spr_40682/09_2024/8spr_40682.cif" } resolution = 3.9 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= 0.004 sd= 0.064 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 40 5.16 5 C 9458 2.51 5 N 2575 2.21 5 O 2959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15032 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6226 Classifications: {'peptide': 787} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 756} Chain: "B" Number of atoms: 2795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2795 Classifications: {'peptide': 371} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 357} Chain: "C" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1231 Classifications: {'peptide': 161} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 149} Chain: "D" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1761 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 721 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain: "F" Number of atoms: 2298 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 302, 2286 Classifications: {'peptide': 302} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 299} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 302, 2286 Classifications: {'peptide': 302} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 299} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 2322 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR F1150 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR F1150 " occ=0.50 Time building chain proxies: 10.08, per 1000 atoms: 0.67 Number of scatterers: 15032 At special positions: 0 Unit cell: (138.24, 140.4, 137.16, 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 40 16.00 O 2959 8.00 N 2575 7.00 C 9458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS F1041 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 2.3 seconds 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3508 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 26 sheets defined 20.5% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 55 through 70 Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.666A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 297 through 313 Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.023A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 4.300A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.563A pdb=" N GLY A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A 452 " --> pdb=" O TRP A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 731 Processing helix chain 'B' and resid 22 through 27 removed outlier: 3.989A pdb=" N GLU B 26 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU B 27 " --> pdb=" O ASN B 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 63 removed outlier: 3.955A pdb=" N SER C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.862A pdb=" N GLN C 119 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 45 Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 removed outlier: 4.012A pdb=" N ALA D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 removed outlier: 4.002A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 129 Processing helix chain 'D' and resid 138 through 154 Processing helix chain 'D' and resid 160 through 189 Processing helix chain 'D' and resid 190 through 202 removed outlier: 3.599A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 224 removed outlier: 4.164A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.559A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 1002 through 1021 Processing helix chain 'F' and resid 1111 through 1115 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 99 removed outlier: 4.372A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 180 removed outlier: 7.688A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY A 253 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU A 247 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR A 255 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL A 245 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR A 257 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N THR A 243 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN A 259 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A 261 " --> pdb=" O ASN A 239 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN A 239 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 275 removed outlier: 6.396A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.833A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 12.679A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 338 " --> pdb=" O MET A 325 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 353 through 355 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 353 through 355 current: chain 'A' and resid 412 through 420 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 442 through 445 removed outlier: 3.724A pdb=" N GLY A 457 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 489 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A 473 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG A 488 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP A 512 " --> pdb=" O ARG A 488 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR A 531 " --> pdb=" O THR A 511 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 530 through 531 current: chain 'A' and resid 564 through 567 Processing sheet with id=AA8, first strand: chain 'A' and resid 523 through 524 removed outlier: 3.923A pdb=" N SER A 524 " --> pdb=" O THR A 577 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 580 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 618 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG A 592 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN A 594 " --> pdb=" O ASP A 614 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A 614 " --> pdb=" O ASN A 594 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 596 " --> pdb=" O THR A 612 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 628 through 629 current: chain 'A' and resid 714 through 720 removed outlier: 3.690A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY A 771 " --> pdb=" O PHE A 738 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP A 776 " --> pdb=" O LEU A 783 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 673 through 674 removed outlier: 3.777A pdb=" N CYS A 700 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.954A pdb=" N ALA B 66 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 73 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 123 through 125 removed outlier: 3.879A pdb=" N ILE B 124 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR B 132 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 131 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR B 145 " --> pdb=" O VAL B 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AB5, first strand: chain 'B' and resid 200 through 203 removed outlier: 3.673A pdb=" N VAL B 209 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 252 through 253 removed outlier: 4.294A pdb=" N LEU B 267 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B 269 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.606A pdb=" N TYR B 297 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP B 292 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 308 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 298 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET B 306 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL B 314 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 331 through 333 Processing sheet with id=AB9, first strand: chain 'B' and resid 372 through 374 removed outlier: 3.914A pdb=" N LEU B 379 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 95 through 96 removed outlier: 4.098A pdb=" N LEU C 107 " --> pdb=" O ARG C 96 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 133 through 134 removed outlier: 3.639A pdb=" N GLN C 133 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 142 " --> pdb=" O GLN C 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 145 through 148 removed outlier: 3.703A pdb=" N TYR C 157 " --> pdb=" O TRP C 148 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 182 through 183 Processing sheet with id=AC5, first strand: chain 'E' and resid 32 through 34 removed outlier: 3.587A pdb=" N ARG E 78 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN E 103 " --> pdb=" O THR E 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 1044 through 1046 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 1044 through 1046 current: chain 'F' and resid 1208 through 1213 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 1221 through 1223 current: chain 'F' and resid 1259 through 1261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 1259 through 1261 current: chain 'F' and resid 1288 through 1295 Processing sheet with id=AC7, first strand: chain 'F' and resid 1062 through 1065 removed outlier: 3.809A pdb=" N VAL F1063 " --> pdb=" O HIS F1086 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 1084 through 1087 current: chain 'F' and resid 1097 through 1105 removed outlier: 4.301A pdb=" N LYS F1101 " --> pdb=" O ASP F1129 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP F1129 " --> pdb=" O LYS F1101 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL F1103 " --> pdb=" O HIS F1127 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS F1127 " --> pdb=" O VAL F1103 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 1182 through 1185 403 hydrogen bonds defined for protein. 1080 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: 5.19 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5042 1.34 - 1.46: 3743 1.46 - 1.59: 6499 1.59 - 1.71: 0 1.71 - 1.84: 76 Bond restraints: 15360 Sorted by residual: bond pdb=" CA ILE B 380 " pdb=" CB ILE B 380 " ideal model delta sigma weight residual 1.553 1.533 0.020 7.40e-03 1.83e+04 7.19e+00 bond pdb=" CB PHE A 347 " pdb=" CG PHE A 347 " ideal model delta sigma weight residual 1.502 1.444 0.058 2.30e-02 1.89e+03 6.42e+00 bond pdb=" C PRO D 206 " pdb=" N ASP D 207 " ideal model delta sigma weight residual 1.332 1.298 0.035 1.40e-02 5.10e+03 6.18e+00 bond pdb=" CA SER C 62 " pdb=" C SER C 62 " ideal model delta sigma weight residual 1.524 1.476 0.048 2.25e-02 1.98e+03 4.49e+00 bond pdb=" CA THR A 747 " pdb=" C THR A 747 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.72e-02 3.38e+03 4.12e+00 ... (remaining 15355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 20049 2.01 - 4.01: 700 4.01 - 6.02: 96 6.02 - 8.02: 17 8.02 - 10.03: 4 Bond angle restraints: 20866 Sorted by residual: angle pdb=" C PRO A 159 " pdb=" N ARG A 160 " pdb=" CA ARG A 160 " ideal model delta sigma weight residual 121.54 129.63 -8.09 1.91e+00 2.74e-01 1.79e+01 angle pdb=" N HIS D 102 " pdb=" CA HIS D 102 " pdb=" C HIS D 102 " ideal model delta sigma weight residual 108.13 111.71 -3.58 9.00e-01 1.23e+00 1.58e+01 angle pdb=" C THR C 61 " pdb=" N SER C 62 " pdb=" CA SER C 62 " ideal model delta sigma weight residual 122.55 114.86 7.69 2.03e+00 2.43e-01 1.43e+01 angle pdb=" C TYR D 185 " pdb=" N THR D 186 " pdb=" CA THR D 186 " ideal model delta sigma weight residual 120.72 114.54 6.18 1.67e+00 3.59e-01 1.37e+01 angle pdb=" N ALA A 730 " pdb=" CA ALA A 730 " pdb=" C ALA A 730 " ideal model delta sigma weight residual 113.19 108.84 4.35 1.19e+00 7.06e-01 1.33e+01 ... (remaining 20861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 7983 17.91 - 35.83: 867 35.83 - 53.74: 131 53.74 - 71.66: 27 71.66 - 89.57: 17 Dihedral angle restraints: 9025 sinusoidal: 3491 harmonic: 5534 Sorted by residual: dihedral pdb=" CB CYS A 806 " pdb=" SG CYS A 806 " pdb=" SG CYS F1041 " pdb=" CB CYS F1041 " ideal model delta sinusoidal sigma weight residual -86.00 -154.03 68.03 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta harmonic sigma weight residual 180.00 141.65 38.35 0 5.00e+00 4.00e-02 5.88e+01 dihedral pdb=" CA THR A 434 " pdb=" C THR A 434 " pdb=" N GLU A 435 " pdb=" CA GLU A 435 " ideal model delta harmonic sigma weight residual 180.00 143.20 36.80 0 5.00e+00 4.00e-02 5.42e+01 ... (remaining 9022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1322 0.037 - 0.073: 612 0.073 - 0.110: 244 0.110 - 0.146: 68 0.146 - 0.183: 15 Chirality restraints: 2261 Sorted by residual: chirality pdb=" CA VAL A 593 " pdb=" N VAL A 593 " pdb=" C VAL A 593 " pdb=" CB VAL A 593 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CA VAL A 744 " pdb=" N VAL A 744 " pdb=" C VAL A 744 " pdb=" CB VAL A 744 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CA ILE F1045 " pdb=" N ILE F1045 " pdb=" C ILE F1045 " pdb=" CB ILE F1045 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.27e-01 ... (remaining 2258 not shown) Planarity restraints: 2753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 91 " 0.058 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO A 92 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 92 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 92 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F1168 " -0.043 5.00e-02 4.00e+02 6.58e-02 6.92e+00 pdb=" N PRO F1169 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO F1169 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO F1169 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 789 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO A 790 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 790 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 790 " 0.032 5.00e-02 4.00e+02 ... (remaining 2750 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 328 2.61 - 3.18: 14620 3.18 - 3.75: 22171 3.75 - 4.33: 30110 4.33 - 4.90: 48518 Nonbonded interactions: 115747 Sorted by model distance: nonbonded pdb=" OE2 GLU A 521 " pdb=" OH TYR E 28 " model vdw 2.032 3.040 nonbonded pdb=" O ASN E 33 " pdb=" NE2 GLN E 34 " model vdw 2.105 3.120 nonbonded pdb=" OG SER F1051 " pdb=" O ASN F1287 " model vdw 2.125 3.040 nonbonded pdb=" O VAL F1095 " pdb=" OG1 THR F1135 " model vdw 2.134 3.040 nonbonded pdb=" OH TYR A 674 " pdb=" OD2 ASP A 704 " model vdw 2.145 3.040 ... (remaining 115742 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 ========== 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=0.50 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: 1.630 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 36.690 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.007 0.062 15360 Z= 0.491 Angle : 0.875 10.030 20866 Z= 0.493 Chirality : 0.050 0.183 2261 Planarity : 0.005 0.089 2753 Dihedral : 15.123 89.569 5514 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 17.60 % Favored : 82.19 % Rotamer: Outliers : 0.32 % Allowed : 10.53 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.45 % Twisted General : 0.16 % 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: -5.91 (0.14), residues: 1923 helix: -2.12 (0.22), residues: 364 sheet: -4.02 (0.17), residues: 565 loop : -4.68 (0.13), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 449 HIS 0.007 0.001 HIS B 64 PHE 0.026 0.002 PHE B 289 TYR 0.035 0.002 TYR A 432 ARG 0.012 0.001 ARG E 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 209 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 TYR cc_start: 0.7448 (m-10) cc_final: 0.7215 (m-10) REVERT: A 545 MET cc_start: 0.8532 (mtt) cc_final: 0.8031 (mtt) REVERT: A 677 HIS cc_start: 0.6398 (t-170) cc_final: 0.5945 (t70) REVERT: A 768 MET cc_start: 0.8504 (mtm) cc_final: 0.8292 (mtp) REVERT: B 278 MET cc_start: 0.7788 (mmt) cc_final: 0.7474 (mmt) REVERT: B 306 MET cc_start: 0.8158 (ppp) cc_final: 0.7334 (ppp) REVERT: C 56 MET cc_start: 0.8076 (mpp) cc_final: 0.7627 (mpp) REVERT: C 81 ASP cc_start: 0.8571 (p0) cc_final: 0.8319 (p0) REVERT: D 205 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.8538 (m-80) REVERT: E 53 GLN cc_start: 0.8663 (tp40) cc_final: 0.8399 (tp40) REVERT: F 1124 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8715 (ttmm) REVERT: F 1127 HIS cc_start: 0.8773 (p90) cc_final: 0.8268 (p90) REVERT: F 1166 TRP cc_start: 0.8752 (m-10) cc_final: 0.8465 (m100) REVERT: F 1230 GLN cc_start: 0.8616 (tt0) cc_final: 0.8362 (tt0) REVERT: F 1256 SER cc_start: 0.7853 (p) cc_final: 0.7427 (p) outliers start: 5 outliers final: 1 residues processed: 212 average time/residue: 0.2703 time to fit residues: 84.2420 Evaluate side-chains 167 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain D residue 205 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 173 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15360 Z= 0.234 Angle : 0.718 9.610 20866 Z= 0.380 Chirality : 0.047 0.169 2261 Planarity : 0.005 0.088 2753 Dihedral : 6.325 36.304 2122 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.19 % Favored : 87.66 % Rotamer: Outliers : 1.89 % Allowed : 15.26 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.45 % Twisted General : 0.11 % 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: -4.75 (0.16), residues: 1923 helix: -0.41 (0.25), residues: 367 sheet: -3.47 (0.19), residues: 559 loop : -4.17 (0.15), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 546 HIS 0.004 0.001 HIS B 347 PHE 0.031 0.002 PHE F1082 TYR 0.037 0.002 TYR A 432 ARG 0.007 0.001 ARG F1205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 197 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 TYR cc_start: 0.7366 (m-10) cc_final: 0.7088 (m-10) REVERT: A 545 MET cc_start: 0.8311 (mtt) cc_final: 0.7831 (mtt) REVERT: A 677 HIS cc_start: 0.6702 (t-170) cc_final: 0.6262 (t70) REVERT: A 738 PHE cc_start: 0.9140 (p90) cc_final: 0.8778 (p90) REVERT: A 768 MET cc_start: 0.8413 (mtm) cc_final: 0.8193 (mtp) REVERT: B 221 MET cc_start: 0.7683 (ttm) cc_final: 0.7397 (mtp) REVERT: B 263 TYR cc_start: 0.5592 (t80) cc_final: 0.5039 (t80) REVERT: C 56 MET cc_start: 0.7915 (mpp) cc_final: 0.7490 (mpp) REVERT: C 81 ASP cc_start: 0.8540 (p0) cc_final: 0.8303 (p0) REVERT: C 83 ARG cc_start: 0.7659 (ptt-90) cc_final: 0.7136 (ttp-110) REVERT: D 56 GLU cc_start: 0.8772 (tp30) cc_final: 0.8562 (tp30) REVERT: D 205 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.8537 (m-80) REVERT: D 222 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.8729 (m-80) REVERT: E 53 GLN cc_start: 0.8599 (tp40) cc_final: 0.8293 (tp40) REVERT: F 1034 ASP cc_start: 0.7421 (t0) cc_final: 0.7137 (t0) REVERT: F 1046 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7120 (ttp) REVERT: F 1112 MET cc_start: 0.7825 (ptp) cc_final: 0.7525 (ptp) REVERT: F 1212 LYS cc_start: 0.7080 (mttm) cc_final: 0.6811 (ptmm) outliers start: 30 outliers final: 13 residues processed: 216 average time/residue: 0.2578 time to fit residues: 84.3634 Evaluate side-chains 191 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 175 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 1046 MET Chi-restraints excluded: chain F residue 1107 LEU Chi-restraints excluded: chain F residue 1268 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 7.9990 chunk 53 optimal weight: 0.0970 chunk 144 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 187 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15360 Z= 0.227 Angle : 0.675 9.266 20866 Z= 0.356 Chirality : 0.045 0.166 2261 Planarity : 0.005 0.085 2753 Dihedral : 5.975 36.499 2122 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.08 % Favored : 87.76 % Rotamer: Outliers : 3.09 % Allowed : 17.72 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.45 % Twisted General : 0.11 % 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: -4.18 (0.17), residues: 1923 helix: 0.26 (0.26), residues: 367 sheet: -3.15 (0.19), residues: 560 loop : -3.86 (0.15), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 546 HIS 0.006 0.001 HIS D 102 PHE 0.012 0.001 PHE C 99 TYR 0.037 0.002 TYR A 432 ARG 0.006 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 183 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 TYR cc_start: 0.7411 (m-10) cc_final: 0.7140 (m-10) REVERT: A 677 HIS cc_start: 0.6697 (t-170) cc_final: 0.6160 (t70) REVERT: A 768 MET cc_start: 0.8360 (mtm) cc_final: 0.8097 (mtp) REVERT: B 263 TYR cc_start: 0.5713 (t80) cc_final: 0.5241 (t80) REVERT: B 278 MET cc_start: 0.8802 (mtp) cc_final: 0.8438 (mtm) REVERT: C 56 MET cc_start: 0.8133 (mpp) cc_final: 0.7674 (mpp) REVERT: C 83 ARG cc_start: 0.7656 (ptt-90) cc_final: 0.7182 (ttp-110) REVERT: D 56 GLU cc_start: 0.8773 (tp30) cc_final: 0.8527 (tp30) REVERT: D 205 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.8536 (m-80) REVERT: E 53 GLN cc_start: 0.8651 (tp40) cc_final: 0.8378 (tp40) REVERT: F 1034 ASP cc_start: 0.7302 (t0) cc_final: 0.7013 (t0) REVERT: F 1046 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7218 (ttp) REVERT: F 1112 MET cc_start: 0.7909 (ptp) cc_final: 0.7640 (ptp) REVERT: F 1212 LYS cc_start: 0.7042 (mttm) cc_final: 0.6797 (ptmm) outliers start: 49 outliers final: 32 residues processed: 218 average time/residue: 0.2419 time to fit residues: 82.2804 Evaluate side-chains 205 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 171 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 1046 MET Chi-restraints excluded: chain F residue 1107 LEU Chi-restraints excluded: chain F residue 1174 VAL Chi-restraints excluded: chain F residue 1256 SER Chi-restraints excluded: chain F residue 1262 VAL Chi-restraints excluded: chain F residue 1268 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 5.9990 chunk 130 optimal weight: 40.0000 chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 82 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 184 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 165 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15360 Z= 0.294 Angle : 0.686 8.947 20866 Z= 0.362 Chirality : 0.046 0.221 2261 Planarity : 0.005 0.084 2753 Dihedral : 5.948 37.015 2122 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.12 % Favored : 86.72 % Rotamer: Outliers : 3.66 % Allowed : 18.28 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.45 % Twisted General : 0.11 % 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: -3.91 (0.17), residues: 1923 helix: 0.48 (0.27), residues: 367 sheet: -2.94 (0.20), residues: 557 loop : -3.71 (0.16), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 546 HIS 0.005 0.001 HIS B 64 PHE 0.015 0.002 PHE A 648 TYR 0.037 0.002 TYR A 432 ARG 0.005 0.000 ARG F1044 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 178 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 TYR cc_start: 0.7350 (m-10) cc_final: 0.7067 (m-10) REVERT: A 677 HIS cc_start: 0.6259 (t-170) cc_final: 0.5788 (t70) REVERT: A 768 MET cc_start: 0.8438 (mtm) cc_final: 0.8162 (mtp) REVERT: B 263 TYR cc_start: 0.5753 (t80) cc_final: 0.5266 (t80) REVERT: B 278 MET cc_start: 0.8833 (mtp) cc_final: 0.8519 (mtm) REVERT: C 56 MET cc_start: 0.8292 (mpp) cc_final: 0.7741 (mpp) REVERT: C 81 ASP cc_start: 0.8458 (p0) cc_final: 0.8185 (p0) REVERT: C 83 ARG cc_start: 0.7673 (ptt-90) cc_final: 0.7202 (ttp-110) REVERT: D 26 GLU cc_start: 0.7113 (tp30) cc_final: 0.6417 (tt0) REVERT: D 56 GLU cc_start: 0.8808 (tp30) cc_final: 0.8384 (tp30) REVERT: D 222 TYR cc_start: 0.9036 (OUTLIER) cc_final: 0.8794 (m-10) REVERT: E 53 GLN cc_start: 0.8718 (tp40) cc_final: 0.8451 (tp40) REVERT: F 1034 ASP cc_start: 0.7298 (t0) cc_final: 0.7017 (t0) REVERT: F 1046 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7300 (ttp) REVERT: F 1112 MET cc_start: 0.7922 (ptp) cc_final: 0.7669 (ptp) REVERT: F 1212 LYS cc_start: 0.7069 (mttm) cc_final: 0.6743 (ptmm) outliers start: 58 outliers final: 44 residues processed: 224 average time/residue: 0.2464 time to fit residues: 85.8793 Evaluate side-chains 219 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 173 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 83 HIS Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 1046 MET Chi-restraints excluded: chain F residue 1107 LEU Chi-restraints excluded: chain F residue 1146 THR Chi-restraints excluded: chain F residue 1174 VAL Chi-restraints excluded: chain F residue 1256 SER Chi-restraints excluded: chain F residue 1262 VAL Chi-restraints excluded: chain F residue 1268 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 0.1980 chunk 104 optimal weight: 0.7980 chunk 2 optimal weight: 30.0000 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 157 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 94 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15360 Z= 0.275 Angle : 0.667 9.008 20866 Z= 0.353 Chirality : 0.045 0.165 2261 Planarity : 0.005 0.082 2753 Dihedral : 5.854 37.154 2122 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.92 % Favored : 86.93 % Rotamer: Outliers : 3.97 % Allowed : 19.42 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.45 % Twisted General : 0.11 % 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: -3.69 (0.18), residues: 1923 helix: 0.63 (0.27), residues: 361 sheet: -2.78 (0.20), residues: 552 loop : -3.54 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 546 HIS 0.004 0.001 HIS B 64 PHE 0.017 0.001 PHE B 289 TYR 0.037 0.002 TYR A 432 ARG 0.006 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 173 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 TYR cc_start: 0.7266 (m-10) cc_final: 0.6955 (m-10) REVERT: A 545 MET cc_start: 0.8428 (mtm) cc_final: 0.6960 (mtm) REVERT: A 677 HIS cc_start: 0.6212 (t-170) cc_final: 0.5702 (t70) REVERT: B 221 MET cc_start: 0.8110 (mtp) cc_final: 0.7620 (mtp) REVERT: B 263 TYR cc_start: 0.5853 (t80) cc_final: 0.5278 (t80) REVERT: B 278 MET cc_start: 0.8843 (mtp) cc_final: 0.8525 (mtm) REVERT: C 39 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7915 (mm-30) REVERT: C 56 MET cc_start: 0.8295 (mpp) cc_final: 0.7724 (mpp) REVERT: C 80 LEU cc_start: 0.9126 (tp) cc_final: 0.8684 (tt) REVERT: C 83 ARG cc_start: 0.7637 (ptt-90) cc_final: 0.7224 (ttp-110) REVERT: D 56 GLU cc_start: 0.8756 (tp30) cc_final: 0.8342 (tp30) REVERT: D 222 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.8817 (m-10) REVERT: E 53 GLN cc_start: 0.8697 (tp40) cc_final: 0.8423 (tp40) REVERT: F 1034 ASP cc_start: 0.7332 (t0) cc_final: 0.7062 (t0) REVERT: F 1046 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7279 (ttp) REVERT: F 1112 MET cc_start: 0.7878 (ptp) cc_final: 0.7590 (ptp) REVERT: F 1212 LYS cc_start: 0.7093 (mttm) cc_final: 0.6763 (ptmm) outliers start: 63 outliers final: 45 residues processed: 224 average time/residue: 0.2350 time to fit residues: 82.5618 Evaluate side-chains 214 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 167 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 83 HIS Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 1046 MET Chi-restraints excluded: chain F residue 1107 LEU Chi-restraints excluded: chain F residue 1146 THR Chi-restraints excluded: chain F residue 1174 VAL Chi-restraints excluded: chain F residue 1256 SER Chi-restraints excluded: chain F residue 1262 VAL Chi-restraints excluded: chain F residue 1268 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 0.3980 chunk 166 optimal weight: 0.0070 chunk 36 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 45 optimal weight: 0.0870 chunk 184 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 15 optimal weight: 0.0060 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 overall best weight: 0.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN B 347 HIS ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN E 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 15360 Z= 0.161 Angle : 0.636 14.509 20866 Z= 0.328 Chirality : 0.044 0.179 2261 Planarity : 0.004 0.082 2753 Dihedral : 5.306 36.638 2122 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.96 % Favored : 90.99 % Rotamer: Outliers : 2.33 % Allowed : 21.82 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.45 % Twisted General : 0.11 % 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: -3.21 (0.18), residues: 1923 helix: 0.99 (0.28), residues: 360 sheet: -2.38 (0.22), residues: 511 loop : -3.28 (0.16), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 449 HIS 0.005 0.001 HIS B 347 PHE 0.019 0.001 PHE A 738 TYR 0.057 0.001 TYR A 432 ARG 0.004 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 203 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 ASN cc_start: 0.8455 (t0) cc_final: 0.8150 (t0) REVERT: A 449 TRP cc_start: 0.8670 (t60) cc_final: 0.8444 (t60) REVERT: A 465 TYR cc_start: 0.7224 (m-10) cc_final: 0.6901 (m-10) REVERT: A 539 MET cc_start: 0.7961 (ptt) cc_final: 0.6134 (ttp) REVERT: A 545 MET cc_start: 0.8310 (mtm) cc_final: 0.7234 (ptp) REVERT: A 619 VAL cc_start: 0.9347 (t) cc_final: 0.8915 (m) REVERT: A 677 HIS cc_start: 0.6229 (t-170) cc_final: 0.5824 (t70) REVERT: A 769 SER cc_start: 0.9392 (t) cc_final: 0.8899 (m) REVERT: B 80 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8056 (pt) REVERT: B 263 TYR cc_start: 0.5696 (t80) cc_final: 0.5208 (t80) REVERT: B 278 MET cc_start: 0.8836 (mtp) cc_final: 0.8419 (mtm) REVERT: B 306 MET cc_start: 0.8293 (ppp) cc_final: 0.7644 (ppp) REVERT: B 356 PHE cc_start: 0.8653 (m-10) cc_final: 0.8285 (m-10) REVERT: C 56 MET cc_start: 0.8126 (mpp) cc_final: 0.7631 (mpp) REVERT: C 81 ASP cc_start: 0.8272 (p0) cc_final: 0.8066 (p0) REVERT: C 83 ARG cc_start: 0.7483 (ptt-90) cc_final: 0.7199 (ttp-110) REVERT: D 56 GLU cc_start: 0.8691 (tp30) cc_final: 0.8418 (tp30) REVERT: E 53 GLN cc_start: 0.8565 (tp40) cc_final: 0.8320 (tp40) REVERT: E 113 ASN cc_start: 0.6957 (m-40) cc_final: 0.6451 (t0) REVERT: F 1034 ASP cc_start: 0.7278 (t0) cc_final: 0.7042 (t0) REVERT: F 1112 MET cc_start: 0.7786 (ptp) cc_final: 0.7532 (ptp) REVERT: F 1212 LYS cc_start: 0.6822 (mttm) cc_final: 0.6528 (ptmm) outliers start: 37 outliers final: 26 residues processed: 231 average time/residue: 0.2346 time to fit residues: 84.8911 Evaluate side-chains 202 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 1107 LEU Chi-restraints excluded: chain F residue 1146 THR Chi-restraints excluded: chain F residue 1174 VAL Chi-restraints excluded: chain F residue 1262 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 134 optimal weight: 0.0070 chunk 104 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 overall best weight: 2.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 15360 Z= 0.329 Angle : 0.685 11.167 20866 Z= 0.357 Chirality : 0.046 0.165 2261 Planarity : 0.005 0.082 2753 Dihedral : 5.565 36.773 2120 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.40 % Favored : 87.45 % Rotamer: Outliers : 3.09 % Allowed : 21.75 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.45 % Twisted General : 0.11 % 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: -3.24 (0.18), residues: 1923 helix: 0.88 (0.27), residues: 361 sheet: -2.50 (0.21), residues: 568 loop : -3.20 (0.17), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 546 HIS 0.005 0.001 HIS B 64 PHE 0.023 0.002 PHE F1082 TYR 0.046 0.002 TYR A 432 ARG 0.006 0.000 ARG F1044 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 170 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7963 (mmtm) REVERT: A 465 TYR cc_start: 0.7233 (m-10) cc_final: 0.6930 (m-10) REVERT: A 545 MET cc_start: 0.8465 (mtm) cc_final: 0.7378 (mtm) REVERT: A 677 HIS cc_start: 0.6248 (t-170) cc_final: 0.5904 (t70) REVERT: B 263 TYR cc_start: 0.6051 (t80) cc_final: 0.5549 (t80) REVERT: B 278 MET cc_start: 0.8851 (mtp) cc_final: 0.8532 (mtm) REVERT: C 56 MET cc_start: 0.8293 (mpp) cc_final: 0.7663 (mpp) REVERT: C 80 LEU cc_start: 0.9143 (tp) cc_final: 0.8740 (tt) REVERT: D 56 GLU cc_start: 0.8733 (tp30) cc_final: 0.8320 (tp30) REVERT: E 53 GLN cc_start: 0.8706 (tp40) cc_final: 0.8441 (tp40) REVERT: E 113 ASN cc_start: 0.7200 (m-40) cc_final: 0.6658 (t0) REVERT: F 1034 ASP cc_start: 0.7264 (t0) cc_final: 0.6989 (t0) REVERT: F 1112 MET cc_start: 0.7908 (ptp) cc_final: 0.7659 (ptp) REVERT: F 1196 ASP cc_start: 0.8159 (m-30) cc_final: 0.7738 (t0) REVERT: F 1212 LYS cc_start: 0.7049 (mttm) cc_final: 0.6684 (ptmm) outliers start: 49 outliers final: 43 residues processed: 210 average time/residue: 0.2398 time to fit residues: 79.0007 Evaluate side-chains 209 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 166 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 1107 LEU Chi-restraints excluded: chain F residue 1146 THR Chi-restraints excluded: chain F residue 1174 VAL Chi-restraints excluded: chain F residue 1262 VAL Chi-restraints excluded: chain F residue 1268 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 144 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15360 Z= 0.166 Angle : 0.633 10.980 20866 Z= 0.328 Chirality : 0.044 0.213 2261 Planarity : 0.004 0.081 2753 Dihedral : 5.320 37.022 2120 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.69 % Favored : 90.26 % Rotamer: Outliers : 2.33 % Allowed : 22.45 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.45 % Twisted General : 0.11 % 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: -2.97 (0.18), residues: 1923 helix: 1.10 (0.28), residues: 360 sheet: -2.20 (0.22), residues: 533 loop : -3.10 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 546 HIS 0.002 0.000 HIS F1086 PHE 0.017 0.001 PHE A 738 TYR 0.041 0.001 TYR A 432 ARG 0.005 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 187 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 ASN cc_start: 0.8412 (t0) cc_final: 0.8179 (t0) REVERT: A 449 TRP cc_start: 0.8670 (t60) cc_final: 0.8388 (t-100) REVERT: A 465 TYR cc_start: 0.7217 (m-10) cc_final: 0.6891 (m-10) REVERT: A 539 MET cc_start: 0.8113 (ttp) cc_final: 0.5959 (ttp) REVERT: A 677 HIS cc_start: 0.6436 (t-170) cc_final: 0.5964 (t70) REVERT: A 768 MET cc_start: 0.8174 (mpp) cc_final: 0.7970 (mpp) REVERT: B 263 TYR cc_start: 0.5869 (t80) cc_final: 0.5252 (t80) REVERT: B 278 MET cc_start: 0.8847 (mtp) cc_final: 0.8524 (mtm) REVERT: B 306 MET cc_start: 0.8388 (ppp) cc_final: 0.7792 (ppp) REVERT: B 356 PHE cc_start: 0.8635 (m-10) cc_final: 0.8333 (m-10) REVERT: C 56 MET cc_start: 0.8198 (mpp) cc_final: 0.7620 (mpp) REVERT: C 83 ARG cc_start: 0.7418 (ptp-110) cc_final: 0.7188 (mtm180) REVERT: D 56 GLU cc_start: 0.8724 (tp30) cc_final: 0.8308 (tp30) REVERT: E 53 GLN cc_start: 0.8602 (tp40) cc_final: 0.8343 (tp40) REVERT: E 113 ASN cc_start: 0.6914 (m-40) cc_final: 0.6655 (t0) REVERT: F 1034 ASP cc_start: 0.7198 (t0) cc_final: 0.6952 (t0) REVERT: F 1046 MET cc_start: 0.7605 (ttp) cc_final: 0.7033 (tmm) REVERT: F 1112 MET cc_start: 0.7847 (ptp) cc_final: 0.7591 (ptp) REVERT: F 1196 ASP cc_start: 0.8223 (m-30) cc_final: 0.7838 (t0) REVERT: F 1212 LYS cc_start: 0.6850 (mttm) cc_final: 0.6535 (ptmm) outliers start: 37 outliers final: 32 residues processed: 215 average time/residue: 0.2300 time to fit residues: 77.2984 Evaluate side-chains 212 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 1107 LEU Chi-restraints excluded: chain F residue 1146 THR Chi-restraints excluded: chain F residue 1174 VAL Chi-restraints excluded: chain F residue 1262 VAL Chi-restraints excluded: chain F residue 1268 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 134 optimal weight: 0.0050 chunk 52 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 162 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 15360 Z= 0.249 Angle : 0.665 10.256 20866 Z= 0.346 Chirality : 0.045 0.221 2261 Planarity : 0.004 0.082 2753 Dihedral : 5.408 36.293 2120 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.20 % Favored : 88.70 % Rotamer: Outliers : 2.52 % Allowed : 22.38 % Favored : 75.09 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.45 % Twisted General : 0.11 % 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: -2.96 (0.18), residues: 1923 helix: 0.97 (0.27), residues: 363 sheet: -2.22 (0.22), residues: 549 loop : -3.02 (0.17), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 546 HIS 0.003 0.001 HIS A 533 PHE 0.035 0.002 PHE F1274 TYR 0.070 0.002 TYR A 432 ARG 0.007 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 178 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TRP cc_start: 0.8715 (t60) cc_final: 0.8429 (t-100) REVERT: A 465 TYR cc_start: 0.7252 (m-10) cc_final: 0.6922 (m-10) REVERT: A 677 HIS cc_start: 0.6107 (t-170) cc_final: 0.5694 (t70) REVERT: A 768 MET cc_start: 0.8258 (mpp) cc_final: 0.8055 (mpp) REVERT: B 263 TYR cc_start: 0.5911 (t80) cc_final: 0.5511 (t80) REVERT: B 278 MET cc_start: 0.8847 (mtp) cc_final: 0.8529 (mtm) REVERT: B 306 MET cc_start: 0.8357 (ppp) cc_final: 0.7710 (ppp) REVERT: B 356 PHE cc_start: 0.8658 (m-10) cc_final: 0.8372 (m-10) REVERT: C 56 MET cc_start: 0.8247 (mpp) cc_final: 0.7652 (mpp) REVERT: C 83 ARG cc_start: 0.7502 (ptp-170) cc_final: 0.7180 (mtm180) REVERT: D 109 MET cc_start: 0.8433 (mtp) cc_final: 0.8170 (mtp) REVERT: E 53 GLN cc_start: 0.8689 (tp40) cc_final: 0.8423 (tp40) REVERT: E 113 ASN cc_start: 0.6883 (m-40) cc_final: 0.6624 (t0) REVERT: F 1034 ASP cc_start: 0.7206 (t0) cc_final: 0.6959 (t0) REVERT: F 1046 MET cc_start: 0.7701 (ttp) cc_final: 0.7003 (tmm) REVERT: F 1112 MET cc_start: 0.7785 (ptp) cc_final: 0.7540 (ptp) REVERT: F 1196 ASP cc_start: 0.8226 (m-30) cc_final: 0.7822 (t0) REVERT: F 1212 LYS cc_start: 0.6938 (mttm) cc_final: 0.6591 (ptmm) outliers start: 40 outliers final: 39 residues processed: 210 average time/residue: 0.2431 time to fit residues: 79.3649 Evaluate side-chains 214 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 175 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 1107 LEU Chi-restraints excluded: chain F residue 1146 THR Chi-restraints excluded: chain F residue 1174 VAL Chi-restraints excluded: chain F residue 1262 VAL Chi-restraints excluded: chain F residue 1268 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.2980 chunk 181 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 126 optimal weight: 40.0000 chunk 190 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 151 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 15360 Z= 0.246 Angle : 0.668 10.448 20866 Z= 0.347 Chirality : 0.045 0.199 2261 Planarity : 0.004 0.080 2753 Dihedral : 5.431 37.687 2120 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.56 % Favored : 88.33 % Rotamer: Outliers : 2.84 % Allowed : 22.57 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.45 % Twisted General : 0.11 % 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: -2.94 (0.18), residues: 1923 helix: 0.95 (0.27), residues: 363 sheet: -2.22 (0.21), residues: 563 loop : -2.99 (0.17), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 546 HIS 0.003 0.001 HIS A 533 PHE 0.035 0.002 PHE F1274 TYR 0.060 0.002 TYR A 432 ARG 0.003 0.000 ARG F1044 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 173 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TRP cc_start: 0.8699 (t60) cc_final: 0.8448 (t-100) REVERT: A 465 TYR cc_start: 0.7207 (m-10) cc_final: 0.6890 (m-10) REVERT: A 677 HIS cc_start: 0.6142 (t-170) cc_final: 0.5773 (t70) REVERT: B 263 TYR cc_start: 0.5975 (t80) cc_final: 0.5561 (t80) REVERT: B 278 MET cc_start: 0.8849 (mtp) cc_final: 0.8529 (mtm) REVERT: B 306 MET cc_start: 0.8315 (ppp) cc_final: 0.7677 (ppp) REVERT: B 356 PHE cc_start: 0.8672 (m-10) cc_final: 0.8374 (m-10) REVERT: C 56 MET cc_start: 0.8252 (mpp) cc_final: 0.7653 (mpp) REVERT: C 83 ARG cc_start: 0.7551 (ptp-170) cc_final: 0.7303 (mtm180) REVERT: D 109 MET cc_start: 0.8435 (mtp) cc_final: 0.8141 (mtp) REVERT: E 53 GLN cc_start: 0.8682 (tp40) cc_final: 0.8391 (tp40) REVERT: E 113 ASN cc_start: 0.7031 (m-40) cc_final: 0.6815 (t0) REVERT: F 1034 ASP cc_start: 0.7200 (t0) cc_final: 0.6950 (t0) REVERT: F 1112 MET cc_start: 0.7792 (ptp) cc_final: 0.7544 (ptp) REVERT: F 1196 ASP cc_start: 0.8266 (m-30) cc_final: 0.7936 (t0) REVERT: F 1212 LYS cc_start: 0.7002 (mttm) cc_final: 0.6663 (ptmm) outliers start: 45 outliers final: 39 residues processed: 209 average time/residue: 0.2442 time to fit residues: 79.9711 Evaluate side-chains 212 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 173 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 1107 LEU Chi-restraints excluded: chain F residue 1146 THR Chi-restraints excluded: chain F residue 1174 VAL Chi-restraints excluded: chain F residue 1262 VAL Chi-restraints excluded: chain F residue 1268 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 0.9990 chunk 161 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 22 optimal weight: 0.0970 chunk 42 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 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 = 0.4205 r_free = 0.4205 target = 0.159724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.119496 restraints weight = 29943.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.118217 restraints weight = 17791.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.119158 restraints weight = 16323.118| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15360 Z= 0.166 Angle : 0.641 10.225 20866 Z= 0.329 Chirality : 0.044 0.205 2261 Planarity : 0.004 0.080 2753 Dihedral : 5.188 39.222 2120 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.90 % Favored : 90.05 % Rotamer: Outliers : 2.33 % Allowed : 23.20 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.45 % Twisted General : 0.11 % 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: -2.73 (0.19), residues: 1923 helix: 1.04 (0.28), residues: 363 sheet: -2.02 (0.22), residues: 542 loop : -2.87 (0.17), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 449 HIS 0.002 0.000 HIS A 533 PHE 0.034 0.001 PHE F1274 TYR 0.059 0.001 TYR A 432 ARG 0.004 0.000 ARG D 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2993.38 seconds wall clock time: 54 minutes 14.40 seconds (3254.40 seconds total)