Starting phenix.real_space_refine on Thu Jul 2 15:21:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yvu_34138/07_2026/7yvu_34138.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvu_34138/07_2026/7yvu_34138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7yvu_34138/07_2026/7yvu_34138.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yvu_34138/07_2026/7yvu_34138.cif" model { file = "/net/cci-nas-00/data/ceres_data/7yvu_34138/07_2026/7yvu_34138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvu_34138/07_2026/7yvu_34138.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yvu_34138/07_2026/7yvu_34138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvu_34138/07_2026/7yvu_34138.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3164 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4124 2.51 5 N 1081 2.21 5 O 1213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6456 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4856 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.00, per 1000 atoms: 0.15 Number of scatterers: 6456 At special positions: 0 Unit cell: (81.07, 90.45, 114.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1213 8.00 N 1081 7.00 C 4124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 546 " " NAG B 601 " - " ASN B 343 " Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 261.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 378 " 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 57.3% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 4.352A pdb=" N ASN A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.571A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.597A pdb=" N SER A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.842A pdb=" N ALA A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.741A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 221 through 232 removed outlier: 3.713A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.656A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 removed outlier: 4.397A pdb=" N ILE A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 283 Proline residue: A 280 - end of helix removed outlier: 4.109A pdb=" N VAL A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.580A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.591A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 411 removed outlier: 3.521A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.839A pdb=" N ILE A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.549A pdb=" N ALA A 501 " --> pdb=" O CYS A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.571A pdb=" N ASN A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.594A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.078A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 552 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.810A pdb=" N ALA A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 570 " --> pdb=" O TRP A 566 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.608A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.629A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.711A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.041A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.681A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.277A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.059A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.774A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 284 hydrogen bonds defined for protein. 792 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: 0.61 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2080 1.35 - 1.48: 1820 1.48 - 1.61: 2680 1.61 - 1.73: 0 1.73 - 1.86: 58 Bond restraints: 6638 Sorted by residual: bond pdb=" CA ASN A 49 " pdb=" C ASN A 49 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.35e-02 5.49e+03 8.43e+00 bond pdb=" N GLU A 402 " pdb=" CA GLU A 402 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.96e+00 bond pdb=" CB PRO B 521 " pdb=" CG PRO B 521 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.41e+00 bond pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 1.808 1.859 -0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 ... (remaining 6633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 8831 1.97 - 3.94: 158 3.94 - 5.91: 23 5.91 - 7.88: 5 7.88 - 9.84: 1 Bond angle restraints: 9018 Sorted by residual: angle pdb=" N ILE B 468 " pdb=" CA ILE B 468 " pdb=" C ILE B 468 " ideal model delta sigma weight residual 113.20 108.38 4.82 9.60e-01 1.09e+00 2.52e+01 angle pdb=" C ASP A 509 " pdb=" CA ASP A 509 " pdb=" CB ASP A 509 " ideal model delta sigma weight residual 116.34 110.19 6.15 1.40e+00 5.10e-01 1.93e+01 angle pdb=" C LEU A 144 " pdb=" N GLU A 145 " pdb=" CA GLU A 145 " ideal model delta sigma weight residual 121.80 131.64 -9.84 2.44e+00 1.68e-01 1.63e+01 angle pdb=" N CYS B 432 " pdb=" CA CYS B 432 " pdb=" C CYS B 432 " ideal model delta sigma weight residual 108.14 114.18 -6.04 1.52e+00 4.33e-01 1.58e+01 angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 121.85 -7.45 2.30e+00 1.89e-01 1.05e+01 ... (remaining 9013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 3465 17.49 - 34.98: 351 34.98 - 52.46: 64 52.46 - 69.95: 12 69.95 - 87.44: 10 Dihedral angle restraints: 3902 sinusoidal: 1577 harmonic: 2325 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 152.96 -59.96 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 42.17 50.83 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 129.29 -36.29 1 1.00e+01 1.00e-02 1.86e+01 ... (remaining 3899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 609 0.037 - 0.073: 235 0.073 - 0.110: 73 0.110 - 0.147: 23 0.147 - 0.183: 3 Chirality restraints: 943 Sorted by residual: chirality pdb=" CA PRO B 521 " pdb=" N PRO B 521 " pdb=" C PRO B 521 " pdb=" CB PRO B 521 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" C2 NAG A 701 " pdb=" C1 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" N2 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA CYS B 432 " pdb=" N CYS B 432 " pdb=" C CYS B 432 " pdb=" CB CYS B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 940 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " 0.078 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO B 521 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " 0.070 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO A 146 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 252 " 0.038 5.00e-02 4.00e+02 5.86e-02 5.50e+00 pdb=" N PRO A 253 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " 0.032 5.00e-02 4.00e+02 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 77 2.66 - 3.22: 6007 3.22 - 3.78: 9260 3.78 - 4.34: 12549 4.34 - 4.90: 21450 Nonbonded interactions: 49343 Sorted by model distance: nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 703 " model vdw 2.103 2.230 nonbonded pdb=" O PHE A 327 " pdb=" OG SER A 331 " model vdw 2.153 3.040 nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.215 3.120 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.253 3.120 nonbonded pdb=" O PRO B 384 " pdb=" OG1 THR B 385 " model vdw 2.292 3.040 ... (remaining 49338 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: 11.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.570 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 0.167 6650 Z= 0.209 Angle : 0.641 9.844 9041 Z= 0.343 Chirality : 0.045 0.183 943 Planarity : 0.007 0.117 1169 Dihedral : 14.727 87.438 2389 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.46 % Favored : 94.03 % Rotamer: Outliers : 0.29 % Allowed : 0.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.30), residues: 787 helix: 0.61 (0.28), residues: 388 sheet: 0.04 (0.71), residues: 50 loop : -1.64 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 246 TYR 0.017 0.001 TYR A 381 PHE 0.023 0.001 PHE A 308 TRP 0.028 0.002 TRP A 594 HIS 0.006 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 ( 6638) covalent geometry : angle 0.63556 / 0.34 ( 9018) SS BOND : bond 0.00558 / 0.41 ( 7) SS BOND : angle 1.58627 / 0.91 ( 14) hydrogen bonds : bond 0.17931 / 11.63 ( 284) hydrogen bonds : angle 6.07070 / 4.25 ( 792) metal coordination : bond 0.16530 / 8.31 ( 2) link_NAG-ASN : bond 0.00293 / 0.14 ( 3) link_NAG-ASN : angle 1.96507 / 1.04 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 0.174 Fit side-chains REVERT: A 78 LYS cc_start: 0.8354 (tptm) cc_final: 0.8014 (tptm) REVERT: A 216 ASN cc_start: 0.7667 (m-40) cc_final: 0.7430 (m-40) REVERT: A 402 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6351 (mm-30) REVERT: A 421 ILE cc_start: 0.8013 (tp) cc_final: 0.7812 (tp) REVERT: A 455 MET cc_start: 0.7398 (tmm) cc_final: 0.6951 (tmm) REVERT: A 479 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7153 (tm-30) REVERT: A 508 ASN cc_start: 0.7589 (m-40) cc_final: 0.7296 (t0) REVERT: B 357 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7901 (ttp80) REVERT: B 438 SER cc_start: 0.7762 (t) cc_final: 0.7441 (t) REVERT: B 443 SER cc_start: 0.8240 (m) cc_final: 0.7986 (m) outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 0.0620 time to fit residues: 17.2150 Evaluate side-chains 191 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.0270 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 HIS A 374 HIS A 601 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.104612 restraints weight = 9803.426| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.18 r_work: 0.3198 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 6650 Z= 0.180 Angle : 0.617 10.225 9041 Z= 0.311 Chirality : 0.045 0.286 943 Planarity : 0.007 0.117 1169 Dihedral : 4.365 49.086 869 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.59 % Favored : 93.90 % Rotamer: Outliers : 1.60 % Allowed : 11.21 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.30), residues: 787 helix: 0.91 (0.27), residues: 391 sheet: 0.06 (0.69), residues: 50 loop : -1.53 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 465 TYR 0.019 0.001 TYR A 385 PHE 0.012 0.001 PHE A 308 TRP 0.015 0.001 TRP A 594 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 ( 6638) covalent geometry : angle 0.61276 / 0.31 ( 9018) SS BOND : bond 0.00519 / 0.39 ( 7) SS BOND : angle 1.37328 / 0.78 ( 14) hydrogen bonds : bond 0.05411 / 3.45 ( 284) hydrogen bonds : angle 4.34870 / 3.06 ( 792) metal coordination : bond 0.12770 / 6.72 ( 2) link_NAG-ASN : bond 0.00297 / 0.14 ( 3) link_NAG-ASN : angle 1.84105 / 1.01 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 54 ILE cc_start: 0.7915 (mt) cc_final: 0.7681 (tt) REVERT: A 75 GLU cc_start: 0.8439 (tp30) cc_final: 0.8165 (tp30) REVERT: A 78 LYS cc_start: 0.8617 (tptm) cc_final: 0.8283 (tptm) REVERT: A 87 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7107 (tm-30) REVERT: A 111 ASP cc_start: 0.8289 (m-30) cc_final: 0.8014 (t70) REVERT: A 149 ASP cc_start: 0.8044 (t70) cc_final: 0.7840 (t70) REVERT: A 421 ILE cc_start: 0.8726 (tp) cc_final: 0.8495 (tp) REVERT: A 455 MET cc_start: 0.8455 (tmm) cc_final: 0.8084 (tmm) REVERT: A 470 LYS cc_start: 0.8808 (tttm) cc_final: 0.8512 (tttp) REVERT: A 479 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7958 (tm-30) REVERT: A 508 ASN cc_start: 0.8111 (m-40) cc_final: 0.7676 (t0) REVERT: A 556 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8246 (mtpp) REVERT: B 347 PHE cc_start: 0.8439 (m-10) cc_final: 0.8142 (m-10) REVERT: B 438 SER cc_start: 0.8084 (t) cc_final: 0.7840 (t) REVERT: B 443 SER cc_start: 0.8479 (m) cc_final: 0.8211 (m) outliers start: 11 outliers final: 7 residues processed: 194 average time/residue: 0.0681 time to fit residues: 17.5872 Evaluate side-chains 192 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 185 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 0.0470 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 HIS A 601 ASN ** B 422 ASN ** 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 = 0.3489 r_free = 0.3489 target = 0.116077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.103991 restraints weight = 9726.967| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.16 r_work: 0.3192 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 6650 Z= 0.184 Angle : 0.613 10.296 9041 Z= 0.308 Chirality : 0.045 0.271 943 Planarity : 0.006 0.118 1169 Dihedral : 4.008 19.903 866 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.59 % Favored : 93.90 % Rotamer: Outliers : 2.18 % Allowed : 12.95 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.30), residues: 787 helix: 0.86 (0.27), residues: 392 sheet: -0.16 (0.65), residues: 53 loop : -1.50 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 465 TYR 0.019 0.001 TYR A 385 PHE 0.012 0.001 PHE A 308 TRP 0.015 0.001 TRP A 477 HIS 0.006 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 ( 6638) covalent geometry : angle 0.60780 / 0.31 ( 9018) SS BOND : bond 0.00458 / 0.33 ( 7) SS BOND : angle 1.40965 / 0.79 ( 14) hydrogen bonds : bond 0.05554 / 3.54 ( 284) hydrogen bonds : angle 4.29912 / 3.04 ( 792) metal coordination : bond 0.00161 / 0.08 ( 2) link_NAG-ASN : bond 0.00292 / 0.14 ( 3) link_NAG-ASN : angle 1.94840 / 1.04 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8418 (tp30) cc_final: 0.8132 (tp30) REVERT: A 78 LYS cc_start: 0.8617 (tptm) cc_final: 0.8280 (tptm) REVERT: A 87 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7035 (tm-30) REVERT: A 111 ASP cc_start: 0.8332 (m-30) cc_final: 0.8073 (t70) REVERT: A 149 ASP cc_start: 0.8100 (t70) cc_final: 0.7878 (t70) REVERT: A 287 GLN cc_start: 0.8303 (mm-40) cc_final: 0.8036 (mm-40) REVERT: A 455 MET cc_start: 0.8474 (tmm) cc_final: 0.8110 (tmm) REVERT: A 470 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8442 (tttp) REVERT: A 479 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7961 (tm-30) REVERT: A 508 ASN cc_start: 0.8059 (m-40) cc_final: 0.7645 (t0) REVERT: A 556 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8258 (mtpp) REVERT: B 347 PHE cc_start: 0.8445 (m-10) cc_final: 0.8112 (m-10) REVERT: B 438 SER cc_start: 0.8125 (t) cc_final: 0.7872 (t) REVERT: B 443 SER cc_start: 0.8510 (m) cc_final: 0.8271 (m) outliers start: 15 outliers final: 10 residues processed: 186 average time/residue: 0.0574 time to fit residues: 14.4575 Evaluate side-chains 187 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 0.1980 chunk 24 optimal weight: 0.0470 chunk 43 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 28 optimal weight: 0.4980 chunk 60 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 17 optimal weight: 0.1980 overall best weight: 0.2056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 HIS A 601 ASN B 394 ASN B 422 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.118973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106554 restraints weight = 9897.410| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.23 r_work: 0.3229 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6650 Z= 0.116 Angle : 0.579 10.397 9041 Z= 0.289 Chirality : 0.042 0.284 943 Planarity : 0.006 0.117 1169 Dihedral : 3.749 18.669 866 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.32 % Favored : 95.17 % Rotamer: Outliers : 2.18 % Allowed : 15.43 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.30), residues: 787 helix: 1.09 (0.27), residues: 384 sheet: 0.71 (0.68), residues: 45 loop : -1.56 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 246 TYR 0.018 0.001 TYR A 535 PHE 0.008 0.001 PHE A 308 TRP 0.010 0.001 TRP A 594 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 6638) covalent geometry : angle 0.57497 / 0.29 ( 9018) SS BOND : bond 0.00524 / 0.40 ( 7) SS BOND : angle 1.24448 / 0.71 ( 14) hydrogen bonds : bond 0.04153 / 2.65 ( 284) hydrogen bonds : angle 4.11209 / 2.89 ( 792) metal coordination : bond 0.00052 / 0.03 ( 2) link_NAG-ASN : bond 0.00284 / 0.14 ( 3) link_NAG-ASN : angle 1.78693 / 0.97 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8449 (tp30) cc_final: 0.8175 (tp30) REVERT: A 78 LYS cc_start: 0.8564 (tptm) cc_final: 0.8221 (tptm) REVERT: A 287 GLN cc_start: 0.8275 (mm-40) cc_final: 0.8047 (mm-40) REVERT: A 455 MET cc_start: 0.8480 (tmm) cc_final: 0.8136 (tmm) REVERT: A 470 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8433 (tttp) REVERT: A 479 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7873 (tm-30) REVERT: A 508 ASN cc_start: 0.8005 (m-40) cc_final: 0.7682 (t0) REVERT: A 556 LYS cc_start: 0.8569 (ttmm) cc_final: 0.8231 (mtpp) REVERT: B 438 SER cc_start: 0.8147 (t) cc_final: 0.7855 (t) REVERT: B 443 SER cc_start: 0.8443 (m) cc_final: 0.8181 (m) outliers start: 15 outliers final: 9 residues processed: 188 average time/residue: 0.0581 time to fit residues: 15.1110 Evaluate side-chains 190 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 0.0270 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 59 optimal weight: 0.0980 chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 11 optimal weight: 5.9990 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 HIS A 601 ASN B 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.105438 restraints weight = 9973.596| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.24 r_work: 0.3218 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 6650 Z= 0.131 Angle : 0.598 10.334 9041 Z= 0.297 Chirality : 0.043 0.263 943 Planarity : 0.006 0.117 1169 Dihedral : 3.742 18.982 866 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.45 % Favored : 95.04 % Rotamer: Outliers : 2.62 % Allowed : 16.16 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.30), residues: 787 helix: 1.05 (0.27), residues: 391 sheet: 0.25 (0.66), residues: 52 loop : -1.41 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 246 TYR 0.018 0.001 TYR A 385 PHE 0.010 0.001 PHE A 308 TRP 0.011 0.001 TRP A 477 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 6638) covalent geometry : angle 0.59420 / 0.30 ( 9018) SS BOND : bond 0.00417 / 0.31 ( 7) SS BOND : angle 1.17482 / 0.66 ( 14) hydrogen bonds : bond 0.04423 / 2.82 ( 284) hydrogen bonds : angle 4.08398 / 2.87 ( 792) metal coordination : bond 0.00057 / 0.03 ( 2) link_NAG-ASN : bond 0.00281 / 0.13 ( 3) link_NAG-ASN : angle 1.75428 / 0.94 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8428 (tp30) cc_final: 0.8151 (tp30) REVERT: A 78 LYS cc_start: 0.8551 (tptm) cc_final: 0.8220 (tptm) REVERT: A 111 ASP cc_start: 0.8296 (m-30) cc_final: 0.8030 (t70) REVERT: A 287 GLN cc_start: 0.8253 (mm-40) cc_final: 0.8045 (mm-40) REVERT: A 455 MET cc_start: 0.8456 (tmm) cc_final: 0.8106 (tmm) REVERT: A 470 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8412 (tttp) REVERT: A 479 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7869 (tm-30) REVERT: A 508 ASN cc_start: 0.7961 (m-40) cc_final: 0.7707 (t0) REVERT: A 556 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8238 (mtpp) REVERT: B 438 SER cc_start: 0.8109 (t) cc_final: 0.7870 (t) REVERT: B 443 SER cc_start: 0.8427 (m) cc_final: 0.8170 (m) outliers start: 18 outliers final: 10 residues processed: 185 average time/residue: 0.0611 time to fit residues: 15.3178 Evaluate side-chains 187 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 0.1980 chunk 38 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 chunk 58 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 75 optimal weight: 0.0870 chunk 10 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 HIS A 601 ASN B 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.105298 restraints weight = 10013.622| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.24 r_work: 0.3212 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 6650 Z= 0.135 Angle : 0.589 10.308 9041 Z= 0.292 Chirality : 0.044 0.270 943 Planarity : 0.006 0.117 1169 Dihedral : 3.757 19.624 866 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.57 % Favored : 94.92 % Rotamer: Outliers : 2.33 % Allowed : 17.47 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.30), residues: 787 helix: 1.05 (0.27), residues: 391 sheet: 0.87 (0.68), residues: 45 loop : -1.45 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.017 0.001 TYR A 385 PHE 0.010 0.001 PHE A 308 TRP 0.011 0.001 TRP A 477 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.13 ( 6638) covalent geometry : angle 0.58425 / 0.29 ( 9018) SS BOND : bond 0.00481 / 0.36 ( 7) SS BOND : angle 1.35070 / 0.77 ( 14) hydrogen bonds : bond 0.04474 / 2.86 ( 284) hydrogen bonds : angle 4.07313 / 2.87 ( 792) metal coordination : bond 0.00083 / 0.04 ( 2) link_NAG-ASN : bond 0.00270 / 0.13 ( 3) link_NAG-ASN : angle 1.78219 / 0.97 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8447 (tp30) cc_final: 0.8167 (tp30) REVERT: A 78 LYS cc_start: 0.8586 (tptm) cc_final: 0.8259 (tptm) REVERT: A 111 ASP cc_start: 0.8342 (m-30) cc_final: 0.8072 (t70) REVERT: A 287 GLN cc_start: 0.8251 (mm-40) cc_final: 0.8045 (mm-40) REVERT: A 455 MET cc_start: 0.8480 (tmm) cc_final: 0.8142 (tmm) REVERT: A 470 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8454 (tttp) REVERT: A 479 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7863 (tm-30) REVERT: A 508 ASN cc_start: 0.7954 (m-40) cc_final: 0.7727 (t0) REVERT: A 556 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8245 (mtpp) REVERT: B 438 SER cc_start: 0.8124 (t) cc_final: 0.7877 (t) REVERT: B 443 SER cc_start: 0.8420 (m) cc_final: 0.8162 (m) outliers start: 16 outliers final: 14 residues processed: 181 average time/residue: 0.0559 time to fit residues: 13.8693 Evaluate side-chains 189 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.3980 chunk 65 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 HIS A 601 ASN B 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104589 restraints weight = 9871.133| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.21 r_work: 0.3199 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6650 Z= 0.154 Angle : 0.608 10.224 9041 Z= 0.302 Chirality : 0.045 0.264 943 Planarity : 0.006 0.117 1169 Dihedral : 3.825 19.693 866 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.72 % Favored : 93.77 % Rotamer: Outliers : 2.62 % Allowed : 17.32 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.30), residues: 787 helix: 1.03 (0.27), residues: 392 sheet: 0.19 (0.64), residues: 52 loop : -1.34 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.019 0.001 TYR A 385 PHE 0.012 0.001 PHE A 308 TRP 0.013 0.001 TRP A 477 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 ( 6638) covalent geometry : angle 0.60409 / 0.30 ( 9018) SS BOND : bond 0.00535 / 0.40 ( 7) SS BOND : angle 1.43652 / 0.82 ( 14) hydrogen bonds : bond 0.04843 / 3.09 ( 284) hydrogen bonds : angle 4.10058 / 2.89 ( 792) metal coordination : bond 0.00070 / 0.03 ( 2) link_NAG-ASN : bond 0.00271 / 0.13 ( 3) link_NAG-ASN : angle 1.73970 / 0.94 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8428 (tp30) cc_final: 0.8146 (tp30) REVERT: A 78 LYS cc_start: 0.8597 (tptm) cc_final: 0.8257 (tptm) REVERT: A 111 ASP cc_start: 0.8306 (m-30) cc_final: 0.8043 (t70) REVERT: A 287 GLN cc_start: 0.8258 (mm-40) cc_final: 0.8032 (mm-40) REVERT: A 402 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7228 (mm-30) REVERT: A 421 ILE cc_start: 0.8602 (tp) cc_final: 0.8281 (tp) REVERT: A 455 MET cc_start: 0.8494 (tmm) cc_final: 0.8150 (tmm) REVERT: A 470 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8465 (tttp) REVERT: A 479 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7860 (tm-30) REVERT: A 508 ASN cc_start: 0.7958 (m-40) cc_final: 0.7717 (t0) REVERT: A 556 LYS cc_start: 0.8586 (ttmm) cc_final: 0.8245 (mtpp) REVERT: B 438 SER cc_start: 0.8151 (t) cc_final: 0.7866 (t) REVERT: B 443 SER cc_start: 0.8471 (m) cc_final: 0.8215 (m) outliers start: 18 outliers final: 15 residues processed: 193 average time/residue: 0.0556 time to fit residues: 14.6485 Evaluate side-chains 198 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN A 345 HIS A 601 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.115091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.103051 restraints weight = 9909.633| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.18 r_work: 0.3177 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 6650 Z= 0.201 Angle : 0.656 10.109 9041 Z= 0.328 Chirality : 0.046 0.269 943 Planarity : 0.006 0.119 1169 Dihedral : 3.979 20.119 866 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.72 % Favored : 93.77 % Rotamer: Outliers : 2.62 % Allowed : 18.05 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.30), residues: 787 helix: 0.98 (0.27), residues: 392 sheet: 0.26 (0.64), residues: 52 loop : -1.42 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.019 0.001 TYR A 385 PHE 0.014 0.002 PHE A 308 TRP 0.015 0.001 TRP A 477 HIS 0.006 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 ( 6638) covalent geometry : angle 0.65048 / 0.33 ( 9018) SS BOND : bond 0.00450 / 0.32 ( 7) SS BOND : angle 1.68575 / 0.96 ( 14) hydrogen bonds : bond 0.05512 / 3.50 ( 284) hydrogen bonds : angle 4.21231 / 2.98 ( 792) metal coordination : bond 0.00089 / 0.04 ( 2) link_NAG-ASN : bond 0.00284 / 0.14 ( 3) link_NAG-ASN : angle 1.88845 / 1.00 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8434 (tp30) cc_final: 0.8136 (tp30) REVERT: A 78 LYS cc_start: 0.8622 (tptm) cc_final: 0.8256 (tptm) REVERT: A 87 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7030 (tm-30) REVERT: A 111 ASP cc_start: 0.8268 (m-30) cc_final: 0.8068 (t70) REVERT: A 219 ARG cc_start: 0.8587 (ptt180) cc_final: 0.7988 (ptt180) REVERT: A 402 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7400 (mm-30) REVERT: A 455 MET cc_start: 0.8502 (tmm) cc_final: 0.8153 (tmm) REVERT: A 470 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8478 (tttp) REVERT: A 479 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7894 (tm-30) REVERT: A 508 ASN cc_start: 0.7974 (m-40) cc_final: 0.7735 (t0) REVERT: A 556 LYS cc_start: 0.8611 (ttmm) cc_final: 0.8273 (mtpp) REVERT: B 347 PHE cc_start: 0.8478 (m-10) cc_final: 0.8086 (m-80) REVERT: B 438 SER cc_start: 0.8145 (t) cc_final: 0.7904 (t) REVERT: B 443 SER cc_start: 0.8487 (m) cc_final: 0.8239 (m) outliers start: 18 outliers final: 15 residues processed: 188 average time/residue: 0.0809 time to fit residues: 20.4490 Evaluate side-chains 195 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 35 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 70 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 HIS A 601 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.104056 restraints weight = 10068.615| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.23 r_work: 0.3194 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6650 Z= 0.162 Angle : 0.632 10.109 9041 Z= 0.316 Chirality : 0.045 0.264 943 Planarity : 0.006 0.119 1169 Dihedral : 3.915 19.978 866 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.34 % Favored : 94.16 % Rotamer: Outliers : 2.91 % Allowed : 17.76 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.30), residues: 787 helix: 0.98 (0.27), residues: 392 sheet: 0.31 (0.66), residues: 52 loop : -1.41 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 577 TYR 0.018 0.001 TYR A 385 PHE 0.012 0.001 PHE A 308 TRP 0.012 0.001 TRP A 477 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 6638) covalent geometry : angle 0.62713 / 0.31 ( 9018) SS BOND : bond 0.00478 / 0.35 ( 7) SS BOND : angle 1.60401 / 0.92 ( 14) hydrogen bonds : bond 0.05008 / 3.18 ( 284) hydrogen bonds : angle 4.18149 / 2.95 ( 792) metal coordination : bond 0.00068 / 0.03 ( 2) link_NAG-ASN : bond 0.00291 / 0.14 ( 3) link_NAG-ASN : angle 1.77920 / 0.96 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8432 (tp30) cc_final: 0.8135 (tp30) REVERT: A 78 LYS cc_start: 0.8612 (tptm) cc_final: 0.8246 (tptm) REVERT: A 87 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7068 (tm-30) REVERT: A 111 ASP cc_start: 0.8254 (m-30) cc_final: 0.8053 (t70) REVERT: A 287 GLN cc_start: 0.8291 (mm-40) cc_final: 0.7890 (mm-40) REVERT: A 421 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8414 (tp) REVERT: A 455 MET cc_start: 0.8496 (tmm) cc_final: 0.8157 (tmm) REVERT: A 479 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7864 (tm-30) REVERT: A 508 ASN cc_start: 0.7967 (m-40) cc_final: 0.7738 (t0) REVERT: A 556 LYS cc_start: 0.8623 (ttmm) cc_final: 0.8284 (mtpp) REVERT: B 368 LEU cc_start: 0.7523 (tp) cc_final: 0.7265 (tt) REVERT: B 443 SER cc_start: 0.8466 (m) cc_final: 0.8219 (m) outliers start: 20 outliers final: 16 residues processed: 188 average time/residue: 0.0771 time to fit residues: 19.5915 Evaluate side-chains 196 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 0.2980 chunk 56 optimal weight: 0.4980 chunk 49 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 chunk 30 optimal weight: 0.0870 chunk 66 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 HIS B 422 ASN B 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.117457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.105280 restraints weight = 9885.713| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.21 r_work: 0.3219 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6650 Z= 0.130 Angle : 0.611 10.109 9041 Z= 0.303 Chirality : 0.044 0.267 943 Planarity : 0.006 0.118 1169 Dihedral : 3.767 19.810 866 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.83 % Favored : 94.66 % Rotamer: Outliers : 2.04 % Allowed : 18.78 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.30), residues: 787 helix: 1.14 (0.27), residues: 385 sheet: 0.33 (0.66), residues: 52 loop : -1.40 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 577 TYR 0.016 0.001 TYR A 385 PHE 0.014 0.001 PHE B 486 TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 6638) covalent geometry : angle 0.60688 / 0.30 ( 9018) SS BOND : bond 0.00404 / 0.30 ( 7) SS BOND : angle 1.38123 / 0.79 ( 14) hydrogen bonds : bond 0.04378 / 2.79 ( 284) hydrogen bonds : angle 4.08824 / 2.88 ( 792) metal coordination : bond 0.00049 / 0.02 ( 2) link_NAG-ASN : bond 0.00306 / 0.15 ( 3) link_NAG-ASN : angle 1.57562 / 0.87 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8445 (tp30) cc_final: 0.8142 (tp30) REVERT: A 78 LYS cc_start: 0.8565 (tptm) cc_final: 0.8224 (tptm) REVERT: A 87 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7101 (tm-30) REVERT: A 219 ARG cc_start: 0.8472 (ptt180) cc_final: 0.7917 (ptt180) REVERT: A 287 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7889 (mm-40) REVERT: A 455 MET cc_start: 0.8471 (tmm) cc_final: 0.8126 (tmm) REVERT: A 479 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7820 (tm-30) REVERT: A 508 ASN cc_start: 0.7949 (m-40) cc_final: 0.7526 (t0) REVERT: A 510 TYR cc_start: 0.8664 (m-80) cc_final: 0.8281 (m-80) REVERT: A 556 LYS cc_start: 0.8607 (ttmm) cc_final: 0.8269 (mtpp) REVERT: B 443 SER cc_start: 0.8460 (m) cc_final: 0.8209 (m) outliers start: 14 outliers final: 12 residues processed: 178 average time/residue: 0.0769 time to fit residues: 18.6026 Evaluate side-chains 184 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 0.0270 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 HIS B 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.117846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105718 restraints weight = 9798.086| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.20 r_work: 0.3219 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.204 6650 Z= 0.212 Angle : 1.086 59.197 9041 Z= 0.615 Chirality : 0.049 0.556 943 Planarity : 0.006 0.117 1169 Dihedral : 3.849 19.756 866 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.96 % Favored : 94.54 % Rotamer: Outliers : 1.89 % Allowed : 18.78 % Favored : 79.33 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.30), residues: 787 helix: 1.15 (0.27), residues: 385 sheet: 0.39 (0.67), residues: 52 loop : -1.41 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 219 TYR 0.019 0.001 TYR B 421 PHE 0.011 0.001 PHE A 308 TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 ( 6638) covalent geometry : angle 1.05651 / 0.60 ( 9018) SS BOND : bond 0.01323 / 1.02 ( 7) SS BOND : angle 6.41072 / 3.83 ( 14) hydrogen bonds : bond 0.04683 / 3.04 ( 284) hydrogen bonds : angle 4.18268 / 2.93 ( 792) metal coordination : bond 0.00061 / 0.03 ( 2) link_NAG-ASN : bond 0.00294 / 0.14 ( 3) link_NAG-ASN : angle 1.58806 / 0.87 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1742.27 seconds wall clock time: 30 minutes 30.20 seconds (1830.20 seconds total)