Starting phenix.real_space_refine on Sat Aug 3 22:20:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y92_39067/08_2024/8y92_39067.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y92_39067/08_2024/8y92_39067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y92_39067/08_2024/8y92_39067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y92_39067/08_2024/8y92_39067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y92_39067/08_2024/8y92_39067.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y92_39067/08_2024/8y92_39067.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.046 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 S 40 5.16 5 Cl 2 4.86 5 Na 1 4.78 5 C 6086 2.51 5 N 1414 2.21 5 O 1535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 75": "OD1" <-> "OD2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9078 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "B" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' CL': 1, 'A1LX4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' CL': 1, ' NA': 1, 'A1LX4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.54, per 1000 atoms: 0.61 Number of scatterers: 9078 At special positions: 0 Unit cell: (80.3, 116.8, 89.06, 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) Cl 2 17.00 S 40 16.00 Na 1 11.00 O 1535 8.00 N 1414 7.00 C 6086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 1.6 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 80.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.683A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 90 through 93 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 134 removed outlier: 3.707A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 135 through 166 removed outlier: 3.766A pdb=" N TYR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.835A pdb=" N ASP A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.642A pdb=" N TYR A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.627A pdb=" N GLU A 223 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 220 through 224' Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 255 through 283 removed outlier: 3.575A pdb=" N SER A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TRP A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 4.074A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.911A pdb=" N ARG A 301 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 303 " --> pdb=" O TYR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 320 removed outlier: 3.863A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 331 removed outlier: 4.233A pdb=" N ILE A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 372 Processing helix chain 'A' and resid 375 through 380 removed outlier: 3.652A pdb=" N VAL A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 Processing helix chain 'A' and resid 389 through 398 Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.672A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 removed outlier: 3.705A pdb=" N LYS A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 458 Processing helix chain 'A' and resid 464 through 494 removed outlier: 4.527A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 removed outlier: 3.544A pdb=" N PHE A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 580 removed outlier: 4.166A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Proline residue: A 570 - end of helix removed outlier: 3.625A pdb=" N THR A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 598 through 602 removed outlier: 3.898A pdb=" N ALA A 602 " --> pdb=" O HIS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.960A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 74 removed outlier: 3.674A pdb=" N PHE B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 81 removed outlier: 3.696A pdb=" N VAL B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 90 through 93 Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.667A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 120 removed outlier: 3.613A pdb=" N MET B 112 " --> pdb=" O PRO B 108 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 removed outlier: 3.529A pdb=" N TRP B 128 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 129 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE B 130 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Proline residue: B 132 - end of helix Processing helix chain 'B' and resid 134 through 166 removed outlier: 3.924A pdb=" N ILE B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR B 151 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL B 154 " --> pdb=" O PHE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.788A pdb=" N TYR B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.543A pdb=" N SER B 224 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 253 Processing helix chain 'B' and resid 255 through 283 removed outlier: 3.645A pdb=" N SER B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Proline residue: B 270 - end of helix removed outlier: 4.049A pdb=" N THR B 283 " --> pdb=" O VAL B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.578A pdb=" N ARG B 301 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 303 " --> pdb=" O TYR B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 320 removed outlier: 4.152A pdb=" N TRP B 308 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA B 312 " --> pdb=" O TRP B 308 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 332 removed outlier: 4.284A pdb=" N ILE B 327 " --> pdb=" O PHE B 323 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 372 removed outlier: 3.508A pdb=" N ASP B 342 " --> pdb=" O ASN B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 380 removed outlier: 3.687A pdb=" N VAL B 379 " --> pdb=" O ASN B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 Processing helix chain 'B' and resid 389 through 398 Processing helix chain 'B' and resid 400 through 435 removed outlier: 3.606A pdb=" N TRP B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 441 removed outlier: 3.794A pdb=" N LYS B 439 " --> pdb=" O PHE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 458 Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 465 through 496 Processing helix chain 'B' and resid 497 through 509 Processing helix chain 'B' and resid 514 through 523 Processing helix chain 'B' and resid 523 through 539 Processing helix chain 'B' and resid 553 through 580 Proline residue: B 570 - end of helix removed outlier: 3.506A pdb=" N THR B 580 " --> pdb=" O LYS B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 593 removed outlier: 3.729A pdb=" N TYR B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 602 removed outlier: 3.524A pdb=" N VAL B 601 " --> pdb=" O HIS B 598 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 602 " --> pdb=" O HIS B 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 598 through 602' Processing helix chain 'B' and resid 610 through 616 removed outlier: 4.170A pdb=" N TRP B 614 " --> pdb=" O GLN B 610 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1342 1.32 - 1.44: 2934 1.44 - 1.56: 5028 1.56 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 9366 Sorted by residual: bond pdb=" CA VAL A 74 " pdb=" C VAL A 74 " ideal model delta sigma weight residual 1.523 1.416 0.107 1.27e-02 6.20e+03 7.13e+01 bond pdb=" CA ASP A 75 " pdb=" C ASP A 75 " ideal model delta sigma weight residual 1.524 1.433 0.091 1.35e-02 5.49e+03 4.57e+01 bond pdb=" N ASP A 75 " pdb=" CA ASP A 75 " ideal model delta sigma weight residual 1.456 1.371 0.084 1.44e-02 4.82e+03 3.44e+01 bond pdb=" CA ALA A 77 " pdb=" C ALA A 77 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.40e-02 5.10e+03 1.62e+01 bond pdb=" N ALA A 73 " pdb=" CA ALA A 73 " ideal model delta sigma weight residual 1.459 1.420 0.039 1.17e-02 7.31e+03 1.12e+01 ... (remaining 9361 not shown) Histogram of bond angle deviations from ideal: 85.18 - 94.95: 1 94.95 - 104.71: 123 104.71 - 114.48: 5510 114.48 - 124.24: 6899 124.24 - 134.01: 243 Bond angle restraints: 12776 Sorted by residual: angle pdb=" N ASP A 75 " pdb=" CA ASP A 75 " pdb=" C ASP A 75 " ideal model delta sigma weight residual 109.18 85.18 24.00 1.42e+00 4.96e-01 2.86e+02 angle pdb=" CA ALA A 73 " pdb=" C ALA A 73 " pdb=" N VAL A 74 " ideal model delta sigma weight residual 116.92 121.89 -4.97 1.16e+00 7.43e-01 1.83e+01 angle pdb=" N ASP A 75 " pdb=" CA ASP A 75 " pdb=" CB ASP A 75 " ideal model delta sigma weight residual 111.22 105.08 6.14 1.58e+00 4.01e-01 1.51e+01 angle pdb=" CA ALA A 73 " pdb=" C ALA A 73 " pdb=" O ALA A 73 " ideal model delta sigma weight residual 121.00 117.29 3.71 1.05e+00 9.07e-01 1.25e+01 angle pdb=" C ASN B 198 " pdb=" N HIS B 199 " pdb=" CA HIS B 199 " ideal model delta sigma weight residual 120.79 125.70 -4.91 1.39e+00 5.18e-01 1.25e+01 ... (remaining 12771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.60: 5111 28.60 - 57.19: 117 57.19 - 85.79: 9 85.79 - 114.38: 0 114.38 - 142.98: 1 Dihedral angle restraints: 5238 sinusoidal: 1974 harmonic: 3264 Sorted by residual: dihedral pdb=" N ASP A 75 " pdb=" C ASP A 75 " pdb=" CA ASP A 75 " pdb=" CB ASP A 75 " ideal model delta harmonic sigma weight residual 122.80 104.46 18.34 0 2.50e+00 1.60e-01 5.38e+01 dihedral pdb=" C10 A1LX4 B 701 " pdb=" C11 A1LX4 B 701 " pdb=" N12 A1LX4 B 701 " pdb=" C13 A1LX4 B 701 " ideal model delta sinusoidal sigma weight residual -79.57 63.41 -142.98 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C VAL A 74 " pdb=" N VAL A 74 " pdb=" CA VAL A 74 " pdb=" CB VAL A 74 " ideal model delta harmonic sigma weight residual -122.00 -130.95 8.95 0 2.50e+00 1.60e-01 1.28e+01 ... (remaining 5235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1342 0.070 - 0.139: 75 0.139 - 0.208: 1 0.208 - 0.278: 1 0.278 - 0.347: 1 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA VAL A 74 " pdb=" N VAL A 74 " pdb=" C VAL A 74 " pdb=" CB VAL A 74 " both_signs ideal model delta sigma weight residual False 2.44 2.09 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA LEU A 76 " pdb=" N LEU A 76 " pdb=" C LEU A 76 " pdb=" CB LEU A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ALA A 77 " pdb=" N ALA A 77 " pdb=" C ALA A 77 " pdb=" CB ALA A 77 " both_signs ideal model delta sigma weight residual False 2.48 2.32 0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 1417 not shown) Planarity restraints: 1556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 71 " 0.015 2.00e-02 2.50e+03 2.89e-02 8.35e+00 pdb=" C GLY A 71 " -0.050 2.00e-02 2.50e+03 pdb=" O GLY A 71 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE A 72 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 107 " -0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO A 108 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 569 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO B 570 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 570 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 570 " 0.021 5.00e-02 4.00e+02 ... (remaining 1553 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 65 2.54 - 3.13: 7267 3.13 - 3.72: 15084 3.72 - 4.31: 20518 4.31 - 4.90: 34248 Nonbonded interactions: 77182 Sorted by model distance: nonbonded pdb=" N ASP A 75 " pdb=" O ASP A 75 " model vdw 1.954 2.496 nonbonded pdb=" OG SER B 318 " pdb="CL CL B 703 " model vdw 2.152 3.190 nonbonded pdb=" OG SER A 583 " pdb=" OE1 GLU A 586 " model vdw 2.190 3.040 nonbonded pdb=" OG SER A 318 " pdb="CL CL A 702 " model vdw 2.215 3.190 nonbonded pdb=" O LEU A 163 " pdb=" OG SER A 166 " model vdw 2.236 3.040 ... (remaining 77177 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 53 through 617 or resid 701)) selection = (chain 'B' and (resid 53 through 617 or resid 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.590 Find NCS groups from input model: 0.370 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 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 : 0.003 0.107 9366 Z= 0.212 Angle : 0.636 24.001 12776 Z= 0.389 Chirality : 0.037 0.347 1420 Planarity : 0.004 0.042 1556 Dihedral : 11.667 142.975 3162 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.73 % Allowed : 7.77 % Favored : 87.50 % Cbeta Deviations : 0.10 % 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: -1.19 (0.23), residues: 1126 helix: -0.36 (0.17), residues: 766 sheet: None (None), residues: 0 loop : -1.50 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 308 HIS 0.001 0.000 HIS B 199 PHE 0.012 0.001 PHE B 362 TYR 0.006 0.001 TYR B 572 ARG 0.002 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 268 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 126 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7614 (p) REVERT: A 306 THR cc_start: 0.7747 (p) cc_final: 0.7434 (t) REVERT: A 455 LEU cc_start: 0.7424 (mt) cc_final: 0.7219 (mt) REVERT: B 507 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: B 586 GLU cc_start: 0.7668 (mp0) cc_final: 0.7034 (mp0) outliers start: 45 outliers final: 9 residues processed: 298 average time/residue: 0.1816 time to fit residues: 77.5906 Evaluate side-chains 179 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 168 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 531 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9366 Z= 0.200 Angle : 0.565 7.555 12776 Z= 0.288 Chirality : 0.039 0.135 1420 Planarity : 0.004 0.040 1556 Dihedral : 7.388 107.710 1265 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.89 % Allowed : 14.71 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1126 helix: 0.83 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -0.94 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 128 HIS 0.005 0.001 HIS B 280 PHE 0.016 0.001 PHE B 316 TYR 0.013 0.001 TYR A 111 ARG 0.005 0.001 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 175 time to evaluate : 0.971 Fit side-chains REVERT: A 126 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7742 (p) REVERT: A 365 LEU cc_start: 0.7643 (mt) cc_final: 0.7273 (mt) REVERT: A 425 GLU cc_start: 0.6816 (tt0) cc_final: 0.6442 (tt0) REVERT: B 153 ASN cc_start: 0.8819 (m110) cc_final: 0.8618 (m110) REVERT: B 202 TYR cc_start: 0.4780 (OUTLIER) cc_final: 0.3122 (t80) REVERT: B 364 ILE cc_start: 0.8468 (mp) cc_final: 0.8236 (mp) REVERT: B 365 LEU cc_start: 0.7743 (mt) cc_final: 0.7384 (mt) REVERT: B 507 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7630 (tm-30) REVERT: B 601 VAL cc_start: 0.8496 (t) cc_final: 0.8203 (m) outliers start: 37 outliers final: 22 residues processed: 200 average time/residue: 0.1720 time to fit residues: 53.3308 Evaluate side-chains 167 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 531 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 90 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9366 Z= 0.186 Angle : 0.540 7.555 12776 Z= 0.276 Chirality : 0.039 0.140 1420 Planarity : 0.004 0.038 1556 Dihedral : 6.279 78.624 1255 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.83 % Allowed : 15.02 % Favored : 80.15 % 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: 1126 helix: 1.11 (0.18), residues: 794 sheet: None (None), residues: 0 loop : -0.74 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 128 HIS 0.011 0.001 HIS A 199 PHE 0.022 0.002 PHE B 275 TYR 0.018 0.001 TYR A 111 ARG 0.004 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 158 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 566 MET cc_start: 0.5214 (mtt) cc_final: 0.4927 (mtt) REVERT: B 122 GLU cc_start: 0.7967 (mp0) cc_final: 0.7506 (mp0) REVERT: B 153 ASN cc_start: 0.8809 (m110) cc_final: 0.8601 (m110) REVERT: B 202 TYR cc_start: 0.4754 (OUTLIER) cc_final: 0.3044 (t80) REVERT: B 365 LEU cc_start: 0.7758 (mt) cc_final: 0.7424 (mt) REVERT: B 425 GLU cc_start: 0.6974 (tt0) cc_final: 0.6635 (tt0) REVERT: B 486 LEU cc_start: 0.7108 (tp) cc_final: 0.6824 (tp) REVERT: B 507 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: B 566 MET cc_start: 0.4993 (mtt) cc_final: 0.4768 (mtt) REVERT: B 601 VAL cc_start: 0.8490 (t) cc_final: 0.8205 (m) outliers start: 46 outliers final: 33 residues processed: 190 average time/residue: 0.1568 time to fit residues: 45.2409 Evaluate side-chains 179 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 144 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 531 PHE Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9366 Z= 0.229 Angle : 0.563 7.846 12776 Z= 0.292 Chirality : 0.040 0.134 1420 Planarity : 0.004 0.036 1556 Dihedral : 6.200 79.634 1254 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.67 % Allowed : 15.23 % Favored : 79.10 % 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: 0.90 (0.26), residues: 1126 helix: 1.15 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -0.59 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 128 HIS 0.003 0.001 HIS A 370 PHE 0.019 0.002 PHE A 409 TYR 0.019 0.002 TYR A 111 ARG 0.005 0.001 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 148 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8293 (m-80) REVERT: A 473 ASP cc_start: 0.6531 (OUTLIER) cc_final: 0.6197 (t0) REVERT: A 481 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7842 (tp) REVERT: A 566 MET cc_start: 0.5806 (mtt) cc_final: 0.5522 (mtt) REVERT: A 588 LEU cc_start: 0.7973 (mt) cc_final: 0.7726 (mt) REVERT: B 122 GLU cc_start: 0.8211 (mp0) cc_final: 0.7732 (mp0) REVERT: B 133 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7869 (m-80) REVERT: B 202 TYR cc_start: 0.4757 (OUTLIER) cc_final: 0.3126 (t80) REVERT: B 473 ASP cc_start: 0.6553 (OUTLIER) cc_final: 0.6194 (t0) REVERT: B 481 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7930 (tp) REVERT: B 507 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7579 (tm-30) outliers start: 54 outliers final: 35 residues processed: 186 average time/residue: 0.1464 time to fit residues: 42.3098 Evaluate side-chains 180 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 137 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 531 PHE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9366 Z= 0.236 Angle : 0.583 8.427 12776 Z= 0.297 Chirality : 0.040 0.145 1420 Planarity : 0.004 0.034 1556 Dihedral : 6.264 82.704 1254 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.25 % Allowed : 17.33 % Favored : 77.42 % 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: 1.00 (0.26), residues: 1126 helix: 1.18 (0.19), residues: 794 sheet: None (None), residues: 0 loop : -0.47 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 128 HIS 0.003 0.001 HIS A 220 PHE 0.021 0.002 PHE B 275 TYR 0.019 0.001 TYR A 111 ARG 0.004 0.001 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 147 time to evaluate : 0.937 Fit side-chains REVERT: A 133 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8401 (m-80) REVERT: A 473 ASP cc_start: 0.6664 (OUTLIER) cc_final: 0.6342 (t0) REVERT: A 481 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7898 (tp) REVERT: A 588 LEU cc_start: 0.7933 (mt) cc_final: 0.7721 (mt) REVERT: B 122 GLU cc_start: 0.8266 (mp0) cc_final: 0.7582 (mp0) REVERT: B 133 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: B 202 TYR cc_start: 0.4751 (OUTLIER) cc_final: 0.3173 (t80) REVERT: B 481 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7946 (tp) REVERT: B 507 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7479 (tm-30) outliers start: 50 outliers final: 33 residues processed: 186 average time/residue: 0.1548 time to fit residues: 45.0200 Evaluate side-chains 180 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 140 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 531 PHE Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 104 optimal weight: 0.0370 overall best weight: 0.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9366 Z= 0.186 Angle : 0.547 7.186 12776 Z= 0.278 Chirality : 0.039 0.152 1420 Planarity : 0.004 0.033 1556 Dihedral : 6.093 77.948 1254 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.62 % Allowed : 19.43 % Favored : 75.95 % 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: 1.18 (0.26), residues: 1126 helix: 1.33 (0.19), residues: 794 sheet: None (None), residues: 0 loop : -0.43 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 180 HIS 0.003 0.001 HIS A 222 PHE 0.030 0.002 PHE B 408 TYR 0.021 0.001 TYR B 496 ARG 0.003 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 151 time to evaluate : 0.991 Fit side-chains REVERT: A 133 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8301 (m-80) REVERT: A 225 SER cc_start: 0.8466 (m) cc_final: 0.7783 (t) REVERT: A 292 ASN cc_start: 0.7833 (m-40) cc_final: 0.7343 (m-40) REVERT: A 473 ASP cc_start: 0.6336 (OUTLIER) cc_final: 0.5712 (t0) REVERT: A 481 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7848 (tp) REVERT: A 566 MET cc_start: 0.5955 (mtm) cc_final: 0.5736 (mtt) REVERT: A 588 LEU cc_start: 0.8024 (mt) cc_final: 0.7792 (mt) REVERT: B 122 GLU cc_start: 0.8203 (mp0) cc_final: 0.7680 (mp0) REVERT: B 133 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: B 202 TYR cc_start: 0.4718 (OUTLIER) cc_final: 0.3141 (t80) REVERT: B 418 ASP cc_start: 0.7816 (m-30) cc_final: 0.7526 (m-30) REVERT: B 481 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7901 (tp) REVERT: B 507 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: B 515 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7811 (tt) REVERT: B 566 MET cc_start: 0.6065 (mtt) cc_final: 0.5856 (mtt) REVERT: B 584 LEU cc_start: 0.7288 (mm) cc_final: 0.6677 (pt) outliers start: 44 outliers final: 34 residues processed: 184 average time/residue: 0.1519 time to fit residues: 42.7180 Evaluate side-chains 180 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 138 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9366 Z= 0.206 Angle : 0.560 7.660 12776 Z= 0.286 Chirality : 0.040 0.137 1420 Planarity : 0.004 0.037 1556 Dihedral : 5.909 71.855 1252 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.73 % Allowed : 19.64 % Favored : 75.63 % 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: 1.18 (0.26), residues: 1126 helix: 1.35 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.46 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 128 HIS 0.013 0.001 HIS B 222 PHE 0.022 0.001 PHE B 408 TYR 0.013 0.001 TYR B 391 ARG 0.003 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 139 time to evaluate : 0.933 Fit side-chains REVERT: A 133 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8318 (m-80) REVERT: A 225 SER cc_start: 0.8479 (m) cc_final: 0.7793 (t) REVERT: A 292 ASN cc_start: 0.7782 (m-40) cc_final: 0.7312 (m-40) REVERT: A 473 ASP cc_start: 0.6494 (OUTLIER) cc_final: 0.6166 (t0) REVERT: A 481 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7874 (tp) REVERT: A 588 LEU cc_start: 0.8004 (mt) cc_final: 0.7774 (mt) REVERT: B 112 MET cc_start: 0.7356 (ttp) cc_final: 0.7047 (ttt) REVERT: B 122 GLU cc_start: 0.8267 (mp0) cc_final: 0.7632 (mp0) REVERT: B 133 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: B 202 TYR cc_start: 0.4804 (OUTLIER) cc_final: 0.3185 (t80) REVERT: B 280 HIS cc_start: 0.5729 (t70) cc_final: 0.5359 (m-70) REVERT: B 297 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7819 (mt) REVERT: B 481 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7983 (tp) REVERT: B 507 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: B 515 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7851 (tt) REVERT: B 584 LEU cc_start: 0.7302 (mm) cc_final: 0.6773 (pt) outliers start: 45 outliers final: 34 residues processed: 173 average time/residue: 0.1555 time to fit residues: 41.7654 Evaluate side-chains 180 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 137 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9366 Z= 0.215 Angle : 0.567 7.811 12776 Z= 0.289 Chirality : 0.040 0.142 1420 Planarity : 0.004 0.040 1556 Dihedral : 5.951 72.123 1252 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.94 % Allowed : 19.85 % Favored : 75.21 % 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: 1.20 (0.26), residues: 1126 helix: 1.34 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -0.40 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 128 HIS 0.013 0.001 HIS B 222 PHE 0.024 0.002 PHE A 275 TYR 0.017 0.001 TYR A 111 ARG 0.003 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 142 time to evaluate : 0.966 Fit side-chains REVERT: A 133 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8378 (m-80) REVERT: A 225 SER cc_start: 0.8478 (m) cc_final: 0.7792 (t) REVERT: A 292 ASN cc_start: 0.7855 (m-40) cc_final: 0.7391 (m-40) REVERT: A 473 ASP cc_start: 0.6586 (OUTLIER) cc_final: 0.6255 (t0) REVERT: A 481 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7906 (tp) REVERT: A 588 LEU cc_start: 0.7991 (mt) cc_final: 0.7763 (mt) REVERT: B 122 GLU cc_start: 0.8358 (mp0) cc_final: 0.7746 (mp0) REVERT: B 133 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.7869 (m-80) REVERT: B 202 TYR cc_start: 0.4796 (OUTLIER) cc_final: 0.3113 (t80) REVERT: B 280 HIS cc_start: 0.5728 (t70) cc_final: 0.5367 (m-70) REVERT: B 481 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7989 (tp) REVERT: B 507 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7405 (tm-30) REVERT: B 515 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7873 (tt) REVERT: B 566 MET cc_start: 0.6069 (mtt) cc_final: 0.5606 (mtp) REVERT: B 584 LEU cc_start: 0.7301 (mm) cc_final: 0.6796 (pt) outliers start: 47 outliers final: 33 residues processed: 175 average time/residue: 0.1526 time to fit residues: 41.3743 Evaluate side-chains 182 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 141 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9366 Z= 0.208 Angle : 0.564 8.306 12776 Z= 0.288 Chirality : 0.040 0.140 1420 Planarity : 0.004 0.042 1556 Dihedral : 5.884 73.926 1250 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.52 % Allowed : 20.27 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1126 helix: 1.34 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -0.38 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 128 HIS 0.013 0.001 HIS B 222 PHE 0.017 0.001 PHE B 408 TYR 0.013 0.001 TYR A 590 ARG 0.002 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 144 time to evaluate : 0.910 Fit side-chains REVERT: A 133 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8375 (m-80) REVERT: A 225 SER cc_start: 0.8484 (m) cc_final: 0.7804 (t) REVERT: A 292 ASN cc_start: 0.7857 (m-40) cc_final: 0.7395 (m-40) REVERT: A 473 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.6228 (t0) REVERT: A 481 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7898 (tp) REVERT: A 566 MET cc_start: 0.5978 (mtm) cc_final: 0.5707 (mtt) REVERT: A 588 LEU cc_start: 0.7984 (mt) cc_final: 0.7737 (mt) REVERT: B 122 GLU cc_start: 0.8358 (mp0) cc_final: 0.7707 (mp0) REVERT: B 133 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.7848 (m-80) REVERT: B 202 TYR cc_start: 0.4710 (OUTLIER) cc_final: 0.3089 (t80) REVERT: B 280 HIS cc_start: 0.5648 (t70) cc_final: 0.5288 (m-70) REVERT: B 481 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7978 (tp) REVERT: B 507 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: B 515 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7867 (tt) REVERT: B 566 MET cc_start: 0.6089 (mtt) cc_final: 0.5666 (mtp) REVERT: B 584 LEU cc_start: 0.7307 (mm) cc_final: 0.6795 (pt) outliers start: 43 outliers final: 35 residues processed: 175 average time/residue: 0.1524 time to fit residues: 41.0119 Evaluate side-chains 181 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 138 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9366 Z= 0.306 Angle : 0.624 7.700 12776 Z= 0.323 Chirality : 0.042 0.149 1420 Planarity : 0.005 0.100 1556 Dihedral : 6.116 75.627 1250 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.73 % Allowed : 20.06 % Favored : 75.21 % 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: 0.98 (0.26), residues: 1126 helix: 1.14 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -0.40 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 128 HIS 0.014 0.001 HIS B 222 PHE 0.046 0.002 PHE B 408 TYR 0.032 0.002 TYR B 391 ARG 0.003 0.001 ARG B 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 139 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8522 (m-80) REVERT: A 225 SER cc_start: 0.8476 (m) cc_final: 0.7770 (t) REVERT: A 292 ASN cc_start: 0.7864 (m-40) cc_final: 0.7377 (m-40) REVERT: A 473 ASP cc_start: 0.6938 (OUTLIER) cc_final: 0.6685 (t0) REVERT: A 481 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7984 (tp) REVERT: B 112 MET cc_start: 0.7398 (ttp) cc_final: 0.7189 (ttm) REVERT: B 133 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: B 202 TYR cc_start: 0.4673 (OUTLIER) cc_final: 0.3035 (t80) REVERT: B 280 HIS cc_start: 0.5749 (t70) cc_final: 0.5385 (m-70) REVERT: B 418 ASP cc_start: 0.7552 (m-30) cc_final: 0.7267 (m-30) REVERT: B 481 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.8053 (tp) REVERT: B 507 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: B 566 MET cc_start: 0.6357 (mtt) cc_final: 0.5961 (mtp) REVERT: B 584 LEU cc_start: 0.7372 (mm) cc_final: 0.6794 (pt) outliers start: 45 outliers final: 34 residues processed: 172 average time/residue: 0.1536 time to fit residues: 40.6735 Evaluate side-chains 174 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 133 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 0.0050 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.4216 r_free = 0.4216 target = 0.181434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.156217 restraints weight = 12837.470| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.27 r_work: 0.3791 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9366 Z= 0.187 Angle : 0.582 10.680 12776 Z= 0.292 Chirality : 0.039 0.144 1420 Planarity : 0.005 0.071 1556 Dihedral : 5.979 77.690 1250 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.99 % Allowed : 20.69 % Favored : 75.32 % 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: 1.16 (0.26), residues: 1126 helix: 1.31 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -0.41 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.010 0.001 HIS B 222 PHE 0.042 0.001 PHE B 408 TYR 0.028 0.001 TYR B 391 ARG 0.002 0.000 ARG A 216 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 1913.41 seconds wall clock time: 34 minutes 47.35 seconds (2087.35 seconds total)