Starting phenix.real_space_refine on Mon May 12 20:49:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nsc_12564/05_2025/7nsc_12564.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nsc_12564/05_2025/7nsc_12564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nsc_12564/05_2025/7nsc_12564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nsc_12564/05_2025/7nsc_12564.map" model { file = "/net/cci-nas-00/data/ceres_data/7nsc_12564/05_2025/7nsc_12564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nsc_12564/05_2025/7nsc_12564.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 62 5.16 5 C 5955 2.51 5 N 1607 2.21 5 O 1703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9327 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2065 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 17, 'TRANS': 258} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "E" Number of atoms: 4631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4631 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 18, 'TRANS': 596} Chain breaks: 2 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 20, 'ASN:plan1': 5, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 127 Chain: "H" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1178 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "D" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1453 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain breaks: 3 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 5.90, per 1000 atoms: 0.63 Number of scatterers: 9327 At special positions: 0 Unit cell: (83.3, 136.85, 118.15, 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 62 16.00 O 1703 8.00 N 1607 7.00 C 5955 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.1 seconds 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2324 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 3 sheets defined 55.0% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 143 through 154 Processing helix chain 'A' and resid 338 through 356 removed outlier: 3.903A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 696 through 713 removed outlier: 3.668A pdb=" N ALA A 700 " --> pdb=" O PRO A 696 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 721 No H-bonds generated for 'chain 'A' and resid 718 through 721' Processing helix chain 'A' and resid 724 through 727 No H-bonds generated for 'chain 'A' and resid 724 through 727' Processing helix chain 'E' and resid 21 through 33 Processing helix chain 'E' and resid 37 through 43 Processing helix chain 'E' and resid 63 through 78 Processing helix chain 'E' and resid 81 through 90 removed outlier: 3.648A pdb=" N CYS E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 100 Processing helix chain 'E' and resid 105 through 120 Processing helix chain 'E' and resid 127 through 131 removed outlier: 4.272A pdb=" N THR E 131 " --> pdb=" O GLU E 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 127 through 131' Processing helix chain 'E' and resid 134 through 143 Processing helix chain 'E' and resid 147 through 161 Processing helix chain 'E' and resid 164 through 173 removed outlier: 3.556A pdb=" N HIS E 173 " --> pdb=" O ILE E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 removed outlier: 4.669A pdb=" N HIS E 181 " --> pdb=" O GLN E 177 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU E 182 " --> pdb=" O ASN E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 202 Processing helix chain 'E' and resid 206 through 214 removed outlier: 3.817A pdb=" N THR E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ASN E 214 " --> pdb=" O MET E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 230 removed outlier: 3.815A pdb=" N VAL E 227 " --> pdb=" O PRO E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 252 Processing helix chain 'E' and resid 262 through 274 removed outlier: 3.911A pdb=" N THR E 266 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU E 267 " --> pdb=" O VAL E 263 " (cutoff:3.500A) Proline residue: E 268 - end of helix removed outlier: 3.965A pdb=" N CYS E 274 " --> pdb=" O LEU E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 293 removed outlier: 3.825A pdb=" N GLU E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 287 " --> pdb=" O ARG E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 306 removed outlier: 3.766A pdb=" N ILE E 306 " --> pdb=" O ARG E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 317 Processing helix chain 'E' and resid 334 through 338 Processing helix chain 'E' and resid 340 through 355 removed outlier: 4.102A pdb=" N ARG E 344 " --> pdb=" O ALA E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 367 Processing helix chain 'E' and resid 371 through 379 Processing helix chain 'E' and resid 384 through 398 removed outlier: 4.347A pdb=" N ALA E 389 " --> pdb=" O LYS E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 411 removed outlier: 4.608A pdb=" N PHE E 408 " --> pdb=" O LEU E 404 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN E 409 " --> pdb=" O ARG E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.794A pdb=" N MET E 418 " --> pdb=" O TRP E 414 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS E 419 " --> pdb=" O LYS E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 439 removed outlier: 4.066A pdb=" N VAL E 431 " --> pdb=" O GLU E 427 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET E 435 " --> pdb=" O VAL E 431 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU E 436 " --> pdb=" O ALA E 432 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS E 437 " --> pdb=" O SER E 433 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ASN E 438 " --> pdb=" O SER E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 452 removed outlier: 4.512A pdb=" N ILE E 450 " --> pdb=" O SER E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 464 removed outlier: 3.679A pdb=" N THR E 463 " --> pdb=" O LEU E 459 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLN E 464 " --> pdb=" O CYS E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 482 removed outlier: 4.774A pdb=" N ASN E 473 " --> pdb=" O ALA E 469 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU E 478 " --> pdb=" O GLY E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 496 removed outlier: 4.847A pdb=" N ASP E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 506 Processing helix chain 'E' and resid 511 through 525 removed outlier: 3.804A pdb=" N LEU E 525 " --> pdb=" O LEU E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 538 removed outlier: 3.604A pdb=" N ASP E 532 " --> pdb=" O ARG E 528 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR E 537 " --> pdb=" O LYS E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 551 removed outlier: 3.816A pdb=" N GLN E 544 " --> pdb=" O LYS E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 571 Processing helix chain 'E' and resid 575 through 581 removed outlier: 3.767A pdb=" N ILE E 579 " --> pdb=" O ALA E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 592 Processing helix chain 'E' and resid 598 through 611 removed outlier: 3.763A pdb=" N CYS E 607 " --> pdb=" O ALA E 603 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE E 608 " --> pdb=" O ALA E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 629 removed outlier: 3.967A pdb=" N MET E 629 " --> pdb=" O LYS E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 639 Processing helix chain 'E' and resid 645 through 656 Processing helix chain 'H' and resid 27 through 38 Processing helix chain 'H' and resid 44 through 52 removed outlier: 3.871A pdb=" N LYS H 48 " --> pdb=" O GLU H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 63 No H-bonds generated for 'chain 'H' and resid 60 through 63' Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 79 through 87 Processing helix chain 'H' and resid 92 through 96 removed outlier: 5.089A pdb=" N THR H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 92 through 96' Processing helix chain 'H' and resid 98 through 114 Processing helix chain 'H' and resid 166 through 183 Processing helix chain 'H' and resid 191 through 209 removed outlier: 4.164A pdb=" N LYS H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 219 No H-bonds generated for 'chain 'H' and resid 216 through 219' Processing helix chain 'D' and resid 195 through 204 removed outlier: 3.888A pdb=" N LYS D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 214 Processing helix chain 'D' and resid 222 through 227 removed outlier: 3.935A pdb=" N ASN D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 175 removed outlier: 5.760A pdb=" N ASP A 173 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER A 201 " --> pdb=" O PHE A 175 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 200 through 203 current: chain 'A' and resid 314 through 319 removed outlier: 6.714A pdb=" N TYR A 229 " --> pdb=" O GLN A 319 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N HIS A 250 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER A 251 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 181 removed outlier: 4.696A pdb=" N ARG A 186 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLU A 323 " --> pdb=" O TYR A 189 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP A 279 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL A 280 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ASN A 290 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 126 through 133 removed outlier: 3.801A pdb=" N SER D 126 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS D 156 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N THR D 172 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU D 240 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE D 174 " --> pdb=" O GLN D 238 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG D 234 " --> pdb=" O GLU D 178 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASP D 229 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU D 237 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY D 256 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 268 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA D 267 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN D 282 " --> pdb=" O TYR D 273 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1383 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: 2.43 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1519 1.30 - 1.43: 2422 1.43 - 1.56: 5480 1.56 - 1.68: 0 1.68 - 1.81: 97 Bond restraints: 9518 Sorted by residual: bond pdb=" C TYR A 254 " pdb=" O TYR A 254 " ideal model delta sigma weight residual 1.236 1.175 0.061 1.14e-02 7.69e+03 2.82e+01 bond pdb=" N TYR A 727 " pdb=" CA TYR A 727 " ideal model delta sigma weight residual 1.457 1.389 0.068 1.29e-02 6.01e+03 2.81e+01 bond pdb=" CA TYR A 727 " pdb=" C TYR A 727 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.34e-02 5.57e+03 9.28e+00 bond pdb=" CG TYR A 254 " pdb=" CD1 TYR A 254 " ideal model delta sigma weight residual 1.389 1.338 0.051 2.10e-02 2.27e+03 5.96e+00 bond pdb=" CE2 TYR A 254 " pdb=" CZ TYR A 254 " ideal model delta sigma weight residual 1.378 1.321 0.057 2.40e-02 1.74e+03 5.72e+00 ... (remaining 9513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 12545 1.76 - 3.51: 317 3.51 - 5.27: 52 5.27 - 7.03: 15 7.03 - 8.79: 4 Bond angle restraints: 12933 Sorted by residual: angle pdb=" N HIS E 181 " pdb=" CA HIS E 181 " pdb=" C HIS E 181 " ideal model delta sigma weight residual 114.56 106.20 8.36 1.27e+00 6.20e-01 4.33e+01 angle pdb=" CA ASP A 726 " pdb=" C ASP A 726 " pdb=" N TYR A 727 " ideal model delta sigma weight residual 118.08 112.46 5.62 1.30e+00 5.92e-01 1.87e+01 angle pdb=" O GLY A 253 " pdb=" C GLY A 253 " pdb=" N TYR A 254 " ideal model delta sigma weight residual 123.54 126.90 -3.36 9.20e-01 1.18e+00 1.33e+01 angle pdb=" CA HIS E 181 " pdb=" C HIS E 181 " pdb=" N LEU E 182 " ideal model delta sigma weight residual 119.26 115.12 4.14 1.14e+00 7.69e-01 1.32e+01 angle pdb=" O ASP A 726 " pdb=" C ASP A 726 " pdb=" N TYR A 727 " ideal model delta sigma weight residual 122.39 127.03 -4.64 1.30e+00 5.92e-01 1.27e+01 ... (remaining 12928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 5079 17.59 - 35.17: 495 35.17 - 52.76: 102 52.76 - 70.34: 15 70.34 - 87.93: 4 Dihedral angle restraints: 5695 sinusoidal: 2107 harmonic: 3588 Sorted by residual: dihedral pdb=" CA ASP E 316 " pdb=" C ASP E 316 " pdb=" N TYR E 317 " pdb=" CA TYR E 317 " ideal model delta harmonic sigma weight residual 180.00 154.11 25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA MET H 73 " pdb=" C MET H 73 " pdb=" N ILE H 74 " pdb=" CA ILE H 74 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA LEU H 89 " pdb=" C LEU H 89 " pdb=" N HIS H 90 " pdb=" CA HIS H 90 " ideal model delta harmonic sigma weight residual 180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 5692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 984 0.038 - 0.076: 411 0.076 - 0.113: 91 0.113 - 0.151: 19 0.151 - 0.189: 1 Chirality restraints: 1506 Sorted by residual: chirality pdb=" CG LEU H 164 " pdb=" CB LEU H 164 " pdb=" CD1 LEU H 164 " pdb=" CD2 LEU H 164 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CG LEU A 318 " pdb=" CB LEU A 318 " pdb=" CD1 LEU A 318 " pdb=" CD2 LEU A 318 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CB ILE A 232 " pdb=" CA ILE A 232 " pdb=" CG1 ILE A 232 " pdb=" CG2 ILE A 232 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 1503 not shown) Planarity restraints: 1648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 317 " 0.023 2.00e-02 2.50e+03 1.71e-02 5.82e+00 pdb=" CG TYR E 317 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR E 317 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR E 317 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 317 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 317 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 317 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR E 317 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 695 " 0.037 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO A 696 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 696 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 696 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 726 " -0.010 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C ASP A 726 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP A 726 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR A 727 " -0.013 2.00e-02 2.50e+03 ... (remaining 1645 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 22 2.37 - 3.00: 5071 3.00 - 3.63: 13713 3.63 - 4.27: 20345 4.27 - 4.90: 34848 Nonbonded interactions: 73999 Sorted by model distance: nonbonded pdb=" NE2 GLN A 350 " pdb=" OH TYR A 727 " model vdw 1.732 3.120 nonbonded pdb=" OE1 GLU A 344 " pdb=" NH1 ARG E 232 " model vdw 2.212 3.120 nonbonded pdb=" O SER E 526 " pdb=" OG1 THR E 527 " model vdw 2.228 3.040 nonbonded pdb=" O ALA E 352 " pdb=" OG SER E 396 " model vdw 2.231 3.040 nonbonded pdb=" O HIS E 595 " pdb=" NE2 GLN E 601 " model vdw 2.231 3.120 ... (remaining 73994 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.400 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.005 0.068 9518 Z= 0.217 Angle : 0.705 8.786 12933 Z= 0.383 Chirality : 0.042 0.189 1506 Planarity : 0.004 0.057 1648 Dihedral : 14.497 87.927 3371 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.10 % Allowed : 0.62 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.24), residues: 1206 helix: 0.05 (0.20), residues: 677 sheet: -0.78 (0.46), residues: 140 loop : -2.83 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 345 HIS 0.012 0.001 HIS A 188 PHE 0.017 0.002 PHE D 186 TYR 0.041 0.002 TYR E 317 ARG 0.004 0.000 ARG E 399 Details of bonding type rmsd hydrogen bonds : bond 0.05032 ( 464) hydrogen bonds : angle 4.87291 ( 1383) covalent geometry : bond 0.00476 ( 9518) covalent geometry : angle 0.70547 (12933) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 1.068 Fit side-chains REVERT: A 727 TYR cc_start: 0.5753 (OUTLIER) cc_final: 0.5149 (m-10) REVERT: D 149 ASP cc_start: 0.6918 (p0) cc_final: 0.6208 (p0) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.1817 time to fit residues: 38.0483 Evaluate side-chains 122 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 727 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.0370 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 0.0170 chunk 57 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 380 HIS E 181 HIS ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.136328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.118557 restraints weight = 14082.175| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.82 r_work: 0.3361 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9518 Z= 0.118 Angle : 0.576 7.433 12933 Z= 0.297 Chirality : 0.039 0.139 1506 Planarity : 0.004 0.053 1648 Dihedral : 4.744 30.628 1311 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.14 % Allowed : 8.32 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.25), residues: 1206 helix: 0.44 (0.21), residues: 678 sheet: -0.58 (0.46), residues: 140 loop : -2.73 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 345 HIS 0.004 0.001 HIS A 188 PHE 0.023 0.001 PHE H 42 TYR 0.021 0.001 TYR E 317 ARG 0.005 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 464) hydrogen bonds : angle 4.57279 ( 1383) covalent geometry : bond 0.00264 ( 9518) covalent geometry : angle 0.57590 (12933) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.989 Fit side-chains REVERT: A 376 TYR cc_start: 0.8106 (t80) cc_final: 0.7620 (t80) REVERT: E 89 ASP cc_start: 0.8597 (m-30) cc_final: 0.8309 (m-30) REVERT: H 92 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8088 (tm-30) REVERT: H 111 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6999 (mm-30) REVERT: D 149 ASP cc_start: 0.7289 (p0) cc_final: 0.6925 (p0) outliers start: 11 outliers final: 7 residues processed: 139 average time/residue: 0.1854 time to fit residues: 37.8360 Evaluate side-chains 132 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain D residue 146 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 109 optimal weight: 0.0270 chunk 7 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 181 HIS ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.117214 restraints weight = 14198.221| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.82 r_work: 0.3339 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9518 Z= 0.140 Angle : 0.565 6.178 12933 Z= 0.291 Chirality : 0.039 0.165 1506 Planarity : 0.004 0.050 1648 Dihedral : 4.516 20.452 1309 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.56 % Allowed : 11.85 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.25), residues: 1206 helix: 0.56 (0.21), residues: 682 sheet: -0.50 (0.46), residues: 140 loop : -2.67 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 345 HIS 0.011 0.001 HIS A 188 PHE 0.014 0.001 PHE E 318 TYR 0.015 0.001 TYR E 317 ARG 0.004 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 464) hydrogen bonds : angle 4.47265 ( 1383) covalent geometry : bond 0.00333 ( 9518) covalent geometry : angle 0.56537 (12933) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.089 Fit side-chains REVERT: E 89 ASP cc_start: 0.8582 (m-30) cc_final: 0.8277 (m-30) REVERT: E 372 MET cc_start: 0.8291 (mmm) cc_final: 0.7953 (mmm) REVERT: E 548 LEU cc_start: 0.7943 (mt) cc_final: 0.7523 (mp) REVERT: H 73 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8000 (ttp) REVERT: H 111 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6996 (mm-30) REVERT: D 149 ASP cc_start: 0.7370 (p0) cc_final: 0.6943 (p0) outliers start: 15 outliers final: 11 residues processed: 136 average time/residue: 0.1821 time to fit residues: 36.4317 Evaluate side-chains 131 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 181 HIS Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 47 optimal weight: 0.0970 chunk 69 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS E 181 HIS ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.135501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.117789 restraints weight = 14054.664| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.74 r_work: 0.3359 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9518 Z= 0.151 Angle : 0.579 12.250 12933 Z= 0.295 Chirality : 0.040 0.135 1506 Planarity : 0.004 0.049 1648 Dihedral : 4.508 21.005 1309 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.70 % Allowed : 13.83 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.25), residues: 1206 helix: 0.62 (0.21), residues: 681 sheet: -0.51 (0.46), residues: 140 loop : -2.67 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 345 HIS 0.004 0.001 HIS A 188 PHE 0.015 0.001 PHE E 318 TYR 0.017 0.001 TYR A 376 ARG 0.004 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 464) hydrogen bonds : angle 4.46180 ( 1383) covalent geometry : bond 0.00362 ( 9518) covalent geometry : angle 0.57866 (12933) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 1.013 Fit side-chains REVERT: E 89 ASP cc_start: 0.8547 (m-30) cc_final: 0.8291 (m-30) REVERT: E 548 LEU cc_start: 0.8013 (mt) cc_final: 0.7610 (mp) REVERT: H 73 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8054 (ptp) REVERT: H 111 GLU cc_start: 0.7311 (mm-30) cc_final: 0.7079 (mm-30) REVERT: D 149 ASP cc_start: 0.7349 (p0) cc_final: 0.6971 (p0) outliers start: 26 outliers final: 14 residues processed: 142 average time/residue: 0.1746 time to fit residues: 36.9837 Evaluate side-chains 136 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 233 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 83 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS E 181 HIS ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.135401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.117769 restraints weight = 14073.176| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.74 r_work: 0.3360 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9518 Z= 0.144 Angle : 0.570 9.160 12933 Z= 0.290 Chirality : 0.040 0.167 1506 Planarity : 0.004 0.048 1648 Dihedral : 4.505 28.678 1309 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.60 % Allowed : 15.59 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.25), residues: 1206 helix: 0.67 (0.21), residues: 683 sheet: -0.50 (0.46), residues: 140 loop : -2.64 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 345 HIS 0.004 0.001 HIS A 188 PHE 0.014 0.001 PHE E 318 TYR 0.016 0.001 TYR A 376 ARG 0.004 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 464) hydrogen bonds : angle 4.43807 ( 1383) covalent geometry : bond 0.00344 ( 9518) covalent geometry : angle 0.57028 (12933) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.078 Fit side-chains REVERT: E 89 ASP cc_start: 0.8596 (m-30) cc_final: 0.8315 (m-30) REVERT: E 548 LEU cc_start: 0.8023 (mt) cc_final: 0.7617 (mp) REVERT: H 73 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8212 (ttp) REVERT: H 111 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7096 (mm-30) REVERT: D 149 ASP cc_start: 0.7374 (p0) cc_final: 0.6996 (p0) REVERT: D 152 ASN cc_start: 0.8184 (m110) cc_final: 0.7868 (m110) outliers start: 25 outliers final: 17 residues processed: 145 average time/residue: 0.1755 time to fit residues: 37.9323 Evaluate side-chains 142 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.5612 > 50: distance: 44 - 63: 31.198 distance: 49 - 71: 31.027 distance: 52 - 55: 20.253 distance: 53 - 79: 30.633 distance: 55 - 56: 17.411 distance: 56 - 57: 11.006 distance: 56 - 59: 23.400 distance: 57 - 58: 16.800 distance: 57 - 63: 10.054 distance: 58 - 90: 33.630 distance: 59 - 60: 33.448 distance: 60 - 61: 14.074 distance: 60 - 62: 23.693 distance: 63 - 64: 29.218 distance: 64 - 65: 23.381 distance: 64 - 67: 24.250 distance: 65 - 66: 11.045 distance: 65 - 71: 39.707 distance: 67 - 68: 22.366 distance: 67 - 69: 17.823 distance: 68 - 70: 34.209 distance: 71 - 72: 3.294 distance: 72 - 73: 52.992 distance: 72 - 75: 54.967 distance: 73 - 79: 27.753 distance: 75 - 76: 19.363 distance: 76 - 77: 21.089 distance: 76 - 78: 18.866 distance: 79 - 80: 6.262 distance: 80 - 83: 20.469 distance: 81 - 82: 5.929 distance: 81 - 90: 33.927 distance: 83 - 84: 35.342 distance: 84 - 85: 14.082 distance: 86 - 87: 40.332 distance: 87 - 88: 24.033 distance: 87 - 89: 5.565 distance: 90 - 91: 30.570 distance: 91 - 92: 35.322 distance: 91 - 94: 37.711 distance: 92 - 93: 36.074 distance: 92 - 96: 12.239 distance: 94 - 95: 6.290 distance: 96 - 97: 17.348 distance: 97 - 98: 22.899 distance: 97 - 100: 41.614 distance: 98 - 99: 8.623 distance: 98 - 104: 27.275 distance: 100 - 101: 34.262 distance: 101 - 102: 50.487 distance: 101 - 103: 59.040 distance: 104 - 105: 4.344 distance: 105 - 106: 60.990 distance: 105 - 108: 17.119 distance: 106 - 109: 56.956 distance: 110 - 111: 21.343 distance: 111 - 112: 4.917 distance: 111 - 114: 39.977 distance: 112 - 135: 31.106 distance: 115 - 116: 41.550 distance: 115 - 118: 7.789 distance: 116 - 117: 20.944 distance: 116 - 119: 17.501 distance: 117 - 143: 30.120 distance: 119 - 120: 10.075 distance: 120 - 123: 18.479 distance: 121 - 122: 18.490 distance: 121 - 128: 28.610 distance: 122 - 154: 15.940 distance: 123 - 124: 26.625 distance: 124 - 125: 6.698 distance: 125 - 126: 19.861 distance: 125 - 127: 10.619