Starting phenix.real_space_refine on Sat Jun 7 14:33:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wam_37397/06_2025/8wam_37397.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wam_37397/06_2025/8wam_37397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wam_37397/06_2025/8wam_37397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wam_37397/06_2025/8wam_37397.map" model { file = "/net/cci-nas-00/data/ceres_data/8wam_37397/06_2025/8wam_37397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wam_37397/06_2025/8wam_37397.cif" } resolution = 3.23 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= -0.002 sd= 0.071 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 5612 2.51 5 N 1448 2.21 5 O 1528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8650 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4293 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain breaks: 4 Chain: "B" Number of atoms: 4293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4293 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain breaks: 4 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.18, per 1000 atoms: 0.71 Number of scatterers: 8650 At special positions: 0 Unit cell: (97.455, 77.745, 124.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 6 15.00 Mg 2 11.99 O 1528 8.00 N 1448 7.00 C 5612 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: 2.55 Conformation dependent library (CDL) restraints added in 1.1 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 65.1% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 174 through 189 removed outlier: 3.511A pdb=" N LYS A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.671A pdb=" N LYS A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 255 Processing helix chain 'A' and resid 268 through 274 removed outlier: 3.810A pdb=" N MET A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 4.474A pdb=" N ALA A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 338 through 357 removed outlier: 4.228A pdb=" N ALA A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Proline residue: A 351 - end of helix Processing helix chain 'A' and resid 379 through 402 removed outlier: 3.577A pdb=" N ILE A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 4.106A pdb=" N ILE A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 456 removed outlier: 3.790A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.671A pdb=" N VAL A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 473 removed outlier: 3.551A pdb=" N GLU A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILE A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 493 removed outlier: 3.665A pdb=" N TYR A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N MET A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 removed outlier: 3.844A pdb=" N ALA A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 541 removed outlier: 3.593A pdb=" N ILE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 562 removed outlier: 3.945A pdb=" N THR A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 579 removed outlier: 3.973A pdb=" N VAL A 574 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N TRP A 575 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N MET A 576 " --> pdb=" O MET A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 595 removed outlier: 4.223A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 removed outlier: 4.004A pdb=" N MET A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 634 through 660 removed outlier: 3.590A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 174 through 189 Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.724A pdb=" N LYS B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 255 Processing helix chain 'B' and resid 268 through 274 removed outlier: 3.854A pdb=" N MET B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.619A pdb=" N PHE B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.525A pdb=" N PHE B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 358 removed outlier: 4.391A pdb=" N ALA B 350 " --> pdb=" O ASP B 346 " (cutoff:3.500A) Proline residue: B 351 - end of helix removed outlier: 3.942A pdb=" N GLU B 358 " --> pdb=" O LYS B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 402 removed outlier: 3.656A pdb=" N ILE B 383 " --> pdb=" O ILE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 removed outlier: 4.468A pdb=" N ILE B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 455 removed outlier: 3.754A pdb=" N GLY B 438 " --> pdb=" O HIS B 434 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU B 439 " --> pdb=" O ASP B 435 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 440 " --> pdb=" O ARG B 436 " (cutoff:3.500A) Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 457 through 473 removed outlier: 3.854A pdb=" N GLU B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA B 464 " --> pdb=" O PRO B 460 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE B 465 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 467 " --> pdb=" O ARG B 463 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 493 removed outlier: 3.719A pdb=" N TYR B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 489 " --> pdb=" O VAL B 485 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 493 " --> pdb=" O LEU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 507 removed outlier: 3.838A pdb=" N ALA B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TRP B 505 " --> pdb=" O THR B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 541 removed outlier: 3.513A pdb=" N ILE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 561 removed outlier: 3.717A pdb=" N THR B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 579 Processing helix chain 'B' and resid 580 through 595 removed outlier: 4.015A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 621 through 630 Processing helix chain 'B' and resid 634 through 660 removed outlier: 3.614A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 91 removed outlier: 3.599A pdb=" N LEU A 84 " --> pdb=" O TYR A 47 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL A 45 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR A 88 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 43 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET A 90 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS A 41 " --> pdb=" O MET A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.124A pdb=" N MET A 97 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 280 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 91 removed outlier: 3.567A pdb=" N LEU B 84 " --> pdb=" O TYR B 47 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 86 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL B 45 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR B 88 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 43 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET B 90 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS B 41 " --> pdb=" O MET B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.271A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N MET B 97 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 278 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL B 289 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 280 " --> pdb=" O LEU B 287 " (cutoff:3.500A) 481 hydrogen bonds defined for protein. 1410 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: 2.50 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2689 1.34 - 1.46: 1657 1.46 - 1.58: 4386 1.58 - 1.69: 10 1.69 - 1.81: 88 Bond restraints: 8830 Sorted by residual: bond pdb=" CA PHE A 646 " pdb=" C PHE A 646 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.30e-02 5.92e+03 1.13e+00 bond pdb=" CA PHE A 647 " pdb=" C PHE A 647 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.27e-02 6.20e+03 8.79e-01 bond pdb=" C GLU B 599 " pdb=" O GLU B 599 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.26e-02 6.30e+03 7.70e-01 bond pdb=" C ILE B 383 " pdb=" O ILE B 383 " ideal model delta sigma weight residual 1.237 1.246 -0.009 1.13e-02 7.83e+03 6.73e-01 bond pdb=" CE1 PHE A 646 " pdb=" CZ PHE A 646 " ideal model delta sigma weight residual 1.382 1.404 -0.022 3.00e-02 1.11e+03 5.17e-01 ... (remaining 8825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 11759 1.28 - 2.55: 155 2.55 - 3.83: 43 3.83 - 5.10: 19 5.10 - 6.38: 4 Bond angle restraints: 11980 Sorted by residual: angle pdb=" CA GLU B 492 " pdb=" CB GLU B 492 " pdb=" CG GLU B 492 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" C VAL B 43 " pdb=" N ASP B 44 " pdb=" CA ASP B 44 " ideal model delta sigma weight residual 122.46 125.78 -3.32 1.41e+00 5.03e-01 5.56e+00 angle pdb=" C VAL A 43 " pdb=" N ASP A 44 " pdb=" CA ASP A 44 " ideal model delta sigma weight residual 122.46 125.72 -3.26 1.41e+00 5.03e-01 5.35e+00 angle pdb=" N PHE A 647 " pdb=" CA PHE A 647 " pdb=" C PHE A 647 " ideal model delta sigma weight residual 111.07 112.96 -1.89 1.07e+00 8.73e-01 3.12e+00 angle pdb=" C PHE A 646 " pdb=" CA PHE A 646 " pdb=" CB PHE A 646 " ideal model delta sigma weight residual 110.79 113.68 -2.89 1.66e+00 3.63e-01 3.04e+00 ... (remaining 11975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4369 17.92 - 35.84: 637 35.84 - 53.77: 186 53.77 - 71.69: 25 71.69 - 89.61: 7 Dihedral angle restraints: 5224 sinusoidal: 2072 harmonic: 3152 Sorted by residual: dihedral pdb=" CA TRP B 447 " pdb=" C TRP B 447 " pdb=" N GLY B 448 " pdb=" CA GLY B 448 " ideal model delta harmonic sigma weight residual 180.00 163.29 16.71 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CG ARG A 171 " pdb=" CD ARG A 171 " pdb=" NE ARG A 171 " pdb=" CZ ARG A 171 " ideal model delta sinusoidal sigma weight residual 180.00 135.33 44.67 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA ASP A 44 " pdb=" CB ASP A 44 " pdb=" CG ASP A 44 " pdb=" OD1 ASP A 44 " ideal model delta sinusoidal sigma weight residual -30.00 -85.64 55.64 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 5221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 898 0.026 - 0.052: 303 0.052 - 0.078: 145 0.078 - 0.104: 56 0.104 - 0.130: 18 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA ILE B 129 " pdb=" N ILE B 129 " pdb=" C ILE B 129 " pdb=" CB ILE B 129 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE A 129 " pdb=" N ILE A 129 " pdb=" C ILE A 129 " pdb=" CB ILE A 129 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA VAL A 261 " pdb=" N VAL A 261 " pdb=" C VAL A 261 " pdb=" CB VAL A 261 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1417 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 646 " 0.014 2.00e-02 2.50e+03 1.53e-02 4.08e+00 pdb=" CG PHE A 646 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE A 646 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 646 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 646 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 646 " -0.021 2.00e-02 2.50e+03 pdb=" CZ PHE A 646 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 492 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.60e+00 pdb=" C GLU B 492 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU B 492 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU B 493 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 305 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO A 306 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 306 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 306 " -0.026 5.00e-02 4.00e+02 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 899 2.75 - 3.29: 8168 3.29 - 3.82: 14286 3.82 - 4.36: 15239 4.36 - 4.90: 27932 Nonbonded interactions: 66524 Sorted by model distance: nonbonded pdb=" OG SER A 108 " pdb=" OD2 ASP A 231 " model vdw 2.211 3.040 nonbonded pdb=" O GLU B 599 " pdb=" NE ARG B 602 " model vdw 2.232 3.120 nonbonded pdb=" O SER B 596 " pdb=" OG SER B 596 " model vdw 2.395 3.040 nonbonded pdb=" OG1 THR A 240 " pdb=" OD1 ASN B 321 " model vdw 2.400 3.040 nonbonded pdb=" O SER B 548 " pdb=" OG1 THR B 552 " model vdw 2.405 3.040 ... (remaining 66519 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.870 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8830 Z= 0.095 Angle : 0.450 6.377 11980 Z= 0.230 Chirality : 0.036 0.130 1420 Planarity : 0.003 0.047 1460 Dihedral : 17.901 89.612 3200 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.11 % Allowed : 27.09 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.26), residues: 1082 helix: 2.22 (0.21), residues: 638 sheet: 1.47 (0.62), residues: 80 loop : -1.00 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 505 HIS 0.002 0.000 HIS B 219 PHE 0.021 0.001 PHE A 647 TYR 0.004 0.001 TYR A 430 ARG 0.006 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.12619 ( 481) hydrogen bonds : angle 4.72009 ( 1410) covalent geometry : bond 0.00176 ( 8830) covalent geometry : angle 0.45025 (11980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.899 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.2444 time to fit residues: 36.9776 Evaluate side-chains 110 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 0.0980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN B 147 GLN B 484 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.187499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.149806 restraints weight = 10668.532| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.41 r_work: 0.3622 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8830 Z= 0.177 Angle : 0.544 6.277 11980 Z= 0.275 Chirality : 0.041 0.143 1420 Planarity : 0.004 0.042 1460 Dihedral : 9.927 88.229 1265 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.36 % Allowed : 25.59 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.37 (0.26), residues: 1082 helix: 1.81 (0.20), residues: 662 sheet: 1.17 (0.59), residues: 80 loop : -0.97 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 447 HIS 0.004 0.001 HIS B 154 PHE 0.019 0.001 PHE A 499 TYR 0.013 0.002 TYR B 594 ARG 0.007 0.001 ARG B 602 Details of bonding type rmsd hydrogen bonds : bond 0.05071 ( 481) hydrogen bonds : angle 3.83918 ( 1410) covalent geometry : bond 0.00423 ( 8830) covalent geometry : angle 0.54439 (11980) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.925 Fit side-chains REVERT: A 170 PRO cc_start: 0.6860 (Cg_exo) cc_final: 0.6651 (Cg_endo) REVERT: A 573 MET cc_start: 0.7516 (mmt) cc_final: 0.7114 (mmt) REVERT: B 265 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.6576 (t-170) outliers start: 22 outliers final: 13 residues processed: 125 average time/residue: 0.2362 time to fit residues: 39.9271 Evaluate side-chains 119 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 0.0370 chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN A 265 HIS A 454 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.190303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.152334 restraints weight = 10999.011| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.44 r_work: 0.3647 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8830 Z= 0.107 Angle : 0.463 5.537 11980 Z= 0.234 Chirality : 0.038 0.127 1420 Planarity : 0.003 0.038 1460 Dihedral : 9.322 89.875 1262 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.03 % Allowed : 25.16 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.26), residues: 1082 helix: 1.97 (0.21), residues: 660 sheet: 1.13 (0.57), residues: 80 loop : -0.99 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 505 HIS 0.003 0.001 HIS B 265 PHE 0.011 0.001 PHE A 499 TYR 0.008 0.001 TYR B 594 ARG 0.006 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 481) hydrogen bonds : angle 3.60105 ( 1410) covalent geometry : bond 0.00238 ( 8830) covalent geometry : angle 0.46271 (11980) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.989 Fit side-chains REVERT: A 310 MET cc_start: 0.4627 (ppp) cc_final: 0.3695 (ppp) REVERT: A 573 MET cc_start: 0.7736 (mmt) cc_final: 0.7211 (mmt) REVERT: A 603 MET cc_start: 0.5227 (mpp) cc_final: 0.4090 (mtt) REVERT: B 265 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.6602 (t-170) outliers start: 19 outliers final: 13 residues processed: 129 average time/residue: 0.2548 time to fit residues: 43.6318 Evaluate side-chains 118 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN A 484 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.188265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.150165 restraints weight = 10963.627| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.45 r_work: 0.3606 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8830 Z= 0.150 Angle : 0.506 5.881 11980 Z= 0.255 Chirality : 0.039 0.132 1420 Planarity : 0.003 0.037 1460 Dihedral : 9.169 89.937 1262 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.57 % Allowed : 24.73 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.26), residues: 1082 helix: 1.82 (0.20), residues: 662 sheet: 0.95 (0.57), residues: 80 loop : -0.98 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 505 HIS 0.007 0.001 HIS A 265 PHE 0.016 0.001 PHE A 499 TYR 0.015 0.001 TYR B 594 ARG 0.006 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 481) hydrogen bonds : angle 3.58784 ( 1410) covalent geometry : bond 0.00359 ( 8830) covalent geometry : angle 0.50565 (11980) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 1.003 Fit side-chains REVERT: A 97 MET cc_start: 0.7531 (tpt) cc_final: 0.7095 (tpt) REVERT: A 310 MET cc_start: 0.4675 (ppp) cc_final: 0.3676 (ppp) REVERT: A 573 MET cc_start: 0.7632 (mmt) cc_final: 0.7135 (mmt) REVERT: A 603 MET cc_start: 0.5302 (mpp) cc_final: 0.4139 (mtt) REVERT: B 265 HIS cc_start: 0.7735 (OUTLIER) cc_final: 0.6653 (t-170) REVERT: B 310 MET cc_start: 0.3955 (ppp) cc_final: 0.3226 (ppp) REVERT: B 528 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7931 (mp) outliers start: 24 outliers final: 17 residues processed: 123 average time/residue: 0.2540 time to fit residues: 41.5585 Evaluate side-chains 121 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.190151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.152217 restraints weight = 10908.046| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.45 r_work: 0.3637 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8830 Z= 0.104 Angle : 0.459 5.764 11980 Z= 0.232 Chirality : 0.037 0.129 1420 Planarity : 0.003 0.038 1460 Dihedral : 8.815 86.040 1262 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.68 % Allowed : 24.52 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.26), residues: 1082 helix: 1.97 (0.21), residues: 660 sheet: 0.83 (0.56), residues: 78 loop : -0.97 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 505 HIS 0.002 0.001 HIS B 265 PHE 0.012 0.001 PHE A 481 TYR 0.012 0.001 TYR B 594 ARG 0.006 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 481) hydrogen bonds : angle 3.44757 ( 1410) covalent geometry : bond 0.00235 ( 8830) covalent geometry : angle 0.45902 (11980) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.901 Fit side-chains REVERT: A 97 MET cc_start: 0.7580 (tpt) cc_final: 0.7171 (tpt) REVERT: A 310 MET cc_start: 0.4582 (ppp) cc_final: 0.3594 (ppp) REVERT: A 573 MET cc_start: 0.7589 (mmt) cc_final: 0.7059 (mmt) REVERT: A 603 MET cc_start: 0.5257 (mpp) cc_final: 0.4191 (mtt) REVERT: A 623 ARG cc_start: 0.5613 (OUTLIER) cc_final: 0.5334 (ptm160) REVERT: B 196 ASN cc_start: 0.8253 (t0) cc_final: 0.7916 (t0) REVERT: B 265 HIS cc_start: 0.7584 (OUTLIER) cc_final: 0.6641 (t-170) REVERT: B 310 MET cc_start: 0.4305 (ppp) cc_final: 0.3594 (ppp) REVERT: B 394 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8136 (mm) outliers start: 25 outliers final: 15 residues processed: 134 average time/residue: 0.2517 time to fit residues: 44.4244 Evaluate side-chains 126 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 0.0870 chunk 13 optimal weight: 4.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.185567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.147153 restraints weight = 10953.189| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.46 r_work: 0.3582 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8830 Z= 0.183 Angle : 0.546 6.649 11980 Z= 0.276 Chirality : 0.040 0.141 1420 Planarity : 0.004 0.045 1460 Dihedral : 8.974 86.745 1262 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.21 % Allowed : 23.77 % Favored : 73.02 % 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: 1.17 (0.26), residues: 1082 helix: 1.67 (0.20), residues: 662 sheet: 0.63 (0.57), residues: 82 loop : -0.98 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 447 HIS 0.006 0.001 HIS A 484 PHE 0.019 0.002 PHE A 499 TYR 0.019 0.002 TYR B 594 ARG 0.006 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.04583 ( 481) hydrogen bonds : angle 3.57286 ( 1410) covalent geometry : bond 0.00452 ( 8830) covalent geometry : angle 0.54570 (11980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.984 Fit side-chains REVERT: A 97 MET cc_start: 0.7671 (tpt) cc_final: 0.7187 (ttm) REVERT: A 196 ASN cc_start: 0.8251 (t0) cc_final: 0.7970 (t0) REVERT: A 265 HIS cc_start: 0.7516 (OUTLIER) cc_final: 0.6862 (t-170) REVERT: A 310 MET cc_start: 0.4645 (ppp) cc_final: 0.3665 (ppp) REVERT: A 603 MET cc_start: 0.5305 (mpp) cc_final: 0.4220 (mtt) REVERT: A 623 ARG cc_start: 0.5667 (OUTLIER) cc_final: 0.5367 (ptp-170) REVERT: B 196 ASN cc_start: 0.8259 (t0) cc_final: 0.7949 (t0) REVERT: B 265 HIS cc_start: 0.7853 (OUTLIER) cc_final: 0.6773 (t-170) REVERT: B 310 MET cc_start: 0.4381 (ppp) cc_final: 0.3619 (ppp) REVERT: B 528 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7866 (mp) outliers start: 30 outliers final: 21 residues processed: 136 average time/residue: 0.2711 time to fit residues: 48.1950 Evaluate side-chains 131 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.183325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.144418 restraints weight = 11008.589| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.48 r_work: 0.3544 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8830 Z= 0.215 Angle : 0.594 6.475 11980 Z= 0.300 Chirality : 0.042 0.157 1420 Planarity : 0.004 0.046 1460 Dihedral : 9.130 86.894 1262 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.75 % Allowed : 23.55 % Favored : 72.70 % 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: 0.85 (0.25), residues: 1082 helix: 1.40 (0.20), residues: 662 sheet: 0.52 (0.57), residues: 82 loop : -1.07 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 447 HIS 0.004 0.001 HIS B 427 PHE 0.020 0.002 PHE A 499 TYR 0.022 0.002 TYR B 594 ARG 0.010 0.001 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.05097 ( 481) hydrogen bonds : angle 3.72396 ( 1410) covalent geometry : bond 0.00532 ( 8830) covalent geometry : angle 0.59375 (11980) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 1.254 Fit side-chains REVERT: A 97 MET cc_start: 0.7673 (tpt) cc_final: 0.7342 (ttm) REVERT: A 196 ASN cc_start: 0.8216 (t0) cc_final: 0.7961 (t0) REVERT: A 265 HIS cc_start: 0.7574 (OUTLIER) cc_final: 0.6809 (t-170) REVERT: A 310 MET cc_start: 0.4703 (ppp) cc_final: 0.3727 (ppp) REVERT: A 492 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6721 (tp30) REVERT: A 603 MET cc_start: 0.5555 (mpp) cc_final: 0.4921 (tmm) REVERT: A 623 ARG cc_start: 0.5773 (OUTLIER) cc_final: 0.5456 (ptp-170) REVERT: B 196 ASN cc_start: 0.8223 (t0) cc_final: 0.7895 (t0) REVERT: B 224 ASN cc_start: 0.7737 (m-40) cc_final: 0.7275 (p0) REVERT: B 265 HIS cc_start: 0.7926 (OUTLIER) cc_final: 0.6762 (t-170) REVERT: B 310 MET cc_start: 0.4471 (ppp) cc_final: 0.3691 (ppp) REVERT: B 462 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: B 528 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7797 (mp) outliers start: 35 outliers final: 25 residues processed: 144 average time/residue: 0.2580 time to fit residues: 49.0451 Evaluate side-chains 141 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.183031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.144160 restraints weight = 11083.096| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.49 r_work: 0.3544 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8830 Z= 0.199 Angle : 0.579 6.744 11980 Z= 0.292 Chirality : 0.042 0.143 1420 Planarity : 0.004 0.045 1460 Dihedral : 9.128 86.532 1262 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.64 % Allowed : 23.77 % Favored : 72.59 % 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: 0.81 (0.25), residues: 1082 helix: 1.39 (0.20), residues: 660 sheet: 0.39 (0.56), residues: 82 loop : -1.10 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 505 HIS 0.004 0.001 HIS A 427 PHE 0.019 0.002 PHE B 499 TYR 0.020 0.002 TYR B 594 ARG 0.008 0.001 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.04900 ( 481) hydrogen bonds : angle 3.69755 ( 1410) covalent geometry : bond 0.00491 ( 8830) covalent geometry : angle 0.57923 (11980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 1.035 Fit side-chains REVERT: A 97 MET cc_start: 0.7557 (tpt) cc_final: 0.7264 (ttm) REVERT: A 196 ASN cc_start: 0.8183 (t0) cc_final: 0.7759 (t0) REVERT: A 265 HIS cc_start: 0.7563 (OUTLIER) cc_final: 0.6819 (t-170) REVERT: A 310 MET cc_start: 0.4856 (ppp) cc_final: 0.3905 (ppp) REVERT: A 397 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7113 (mp) REVERT: A 492 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6674 (tp30) REVERT: A 568 LYS cc_start: 0.8365 (tptp) cc_final: 0.7415 (tmtt) REVERT: A 573 MET cc_start: 0.7610 (mmt) cc_final: 0.7166 (mmt) REVERT: A 603 MET cc_start: 0.5804 (mpp) cc_final: 0.5139 (tmm) REVERT: A 623 ARG cc_start: 0.5904 (OUTLIER) cc_final: 0.5537 (ptp-170) REVERT: B 196 ASN cc_start: 0.8249 (t0) cc_final: 0.7923 (t0) REVERT: B 224 ASN cc_start: 0.7763 (m-40) cc_final: 0.7215 (p0) REVERT: B 265 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.6747 (t-170) REVERT: B 310 MET cc_start: 0.4619 (ppp) cc_final: 0.3842 (ppp) REVERT: B 462 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.6781 (mp0) REVERT: B 528 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7811 (mp) outliers start: 34 outliers final: 24 residues processed: 144 average time/residue: 0.2567 time to fit residues: 48.6144 Evaluate side-chains 141 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.185683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.147222 restraints weight = 10947.232| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.50 r_work: 0.3584 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8830 Z= 0.137 Angle : 0.518 6.922 11980 Z= 0.262 Chirality : 0.039 0.136 1420 Planarity : 0.004 0.046 1460 Dihedral : 8.984 85.819 1262 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.57 % Allowed : 25.27 % Favored : 72.16 % 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: 0.99 (0.26), residues: 1082 helix: 1.59 (0.20), residues: 662 sheet: 0.38 (0.56), residues: 82 loop : -1.13 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 505 HIS 0.003 0.001 HIS B 427 PHE 0.013 0.001 PHE B 275 TYR 0.014 0.001 TYR B 594 ARG 0.007 0.000 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 481) hydrogen bonds : angle 3.57582 ( 1410) covalent geometry : bond 0.00326 ( 8830) covalent geometry : angle 0.51840 (11980) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.082 Fit side-chains REVERT: A 97 MET cc_start: 0.7550 (tpt) cc_final: 0.7255 (ttm) REVERT: A 196 ASN cc_start: 0.8134 (t0) cc_final: 0.7827 (t0) REVERT: A 265 HIS cc_start: 0.7433 (OUTLIER) cc_final: 0.6870 (t-170) REVERT: A 310 MET cc_start: 0.4858 (ppp) cc_final: 0.3911 (ppp) REVERT: A 492 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6680 (tp30) REVERT: A 573 MET cc_start: 0.7546 (mmt) cc_final: 0.7022 (mmt) REVERT: A 603 MET cc_start: 0.5908 (mpp) cc_final: 0.5233 (tmm) REVERT: B 196 ASN cc_start: 0.8259 (t0) cc_final: 0.7947 (t0) REVERT: B 224 ASN cc_start: 0.7515 (m-40) cc_final: 0.7216 (p0) REVERT: B 265 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.6736 (t-170) REVERT: B 310 MET cc_start: 0.4624 (ppp) cc_final: 0.3822 (ppp) REVERT: B 462 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: B 528 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7696 (mp) outliers start: 24 outliers final: 18 residues processed: 135 average time/residue: 0.3124 time to fit residues: 56.3531 Evaluate side-chains 132 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 0.9980 chunk 41 optimal weight: 0.0270 chunk 4 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.186348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.147907 restraints weight = 10984.176| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.50 r_work: 0.3584 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8830 Z= 0.128 Angle : 0.509 6.816 11980 Z= 0.257 Chirality : 0.039 0.131 1420 Planarity : 0.004 0.045 1460 Dihedral : 8.864 85.292 1262 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.57 % Allowed : 25.16 % Favored : 72.27 % 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: 1.12 (0.26), residues: 1082 helix: 1.69 (0.20), residues: 662 sheet: 0.44 (0.56), residues: 82 loop : -1.09 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 505 HIS 0.003 0.001 HIS B 427 PHE 0.014 0.001 PHE B 275 TYR 0.012 0.001 TYR B 594 ARG 0.007 0.000 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 481) hydrogen bonds : angle 3.52284 ( 1410) covalent geometry : bond 0.00303 ( 8830) covalent geometry : angle 0.50886 (11980) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.000 Fit side-chains REVERT: A 97 MET cc_start: 0.7775 (tpt) cc_final: 0.7479 (ttm) REVERT: A 196 ASN cc_start: 0.8168 (t0) cc_final: 0.7791 (t0) REVERT: A 265 HIS cc_start: 0.7414 (OUTLIER) cc_final: 0.6861 (t-170) REVERT: A 310 MET cc_start: 0.4851 (ppp) cc_final: 0.3908 (ppp) REVERT: A 397 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7091 (tp) REVERT: A 492 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6670 (tp30) REVERT: A 573 MET cc_start: 0.7540 (mmt) cc_final: 0.6982 (mmt) REVERT: A 603 MET cc_start: 0.5915 (mpp) cc_final: 0.5238 (tmm) REVERT: B 196 ASN cc_start: 0.8265 (t0) cc_final: 0.7967 (t0) REVERT: B 265 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.6708 (t-170) REVERT: B 310 MET cc_start: 0.4637 (ppp) cc_final: 0.3825 (ppp) REVERT: B 462 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: B 528 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7713 (mp) outliers start: 24 outliers final: 18 residues processed: 136 average time/residue: 0.2420 time to fit residues: 43.9278 Evaluate side-chains 136 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 36 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.186520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.148798 restraints weight = 10793.846| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.44 r_work: 0.3600 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8830 Z= 0.114 Angle : 0.492 6.842 11980 Z= 0.248 Chirality : 0.038 0.128 1420 Planarity : 0.003 0.046 1460 Dihedral : 8.769 85.176 1262 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.46 % Allowed : 25.70 % Favored : 71.84 % 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: 1.23 (0.26), residues: 1082 helix: 1.82 (0.21), residues: 660 sheet: 0.45 (0.55), residues: 82 loop : -1.11 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 505 HIS 0.002 0.001 HIS B 265 PHE 0.012 0.001 PHE B 275 TYR 0.010 0.001 TYR B 594 ARG 0.008 0.000 ARG B 270 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 481) hydrogen bonds : angle 3.45163 ( 1410) covalent geometry : bond 0.00264 ( 8830) covalent geometry : angle 0.49210 (11980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4128.54 seconds wall clock time: 72 minutes 28.74 seconds (4348.74 seconds total)