Starting phenix.real_space_refine on Mon Jul 28 14:32:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pm9_13525/07_2025/7pm9_13525.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pm9_13525/07_2025/7pm9_13525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pm9_13525/07_2025/7pm9_13525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pm9_13525/07_2025/7pm9_13525.map" model { file = "/net/cci-nas-00/data/ceres_data/7pm9_13525/07_2025/7pm9_13525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pm9_13525/07_2025/7pm9_13525.cif" } resolution = 3.7 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= 0.001 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 4 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 6422 2.51 5 N 1713 2.21 5 O 1883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10086 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 6007 Classifications: {'peptide': 735} Link IDs: {'PTRANS': 27, 'TRANS': 707} Chain breaks: 6 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.92, per 1000 atoms: 0.69 Number of scatterers: 10086 At special positions: 0 Unit cell: (109.18, 137.8, 149.46, 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 62 16.00 P 4 15.00 Mg 2 11.99 O 1883 8.00 N 1713 7.00 C 6422 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 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.3 seconds 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2358 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 14 sheets defined 55.5% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.174A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.742A pdb=" N GLY A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 153 removed outlier: 4.139A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 185 removed outlier: 3.621A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.571A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 249 removed outlier: 3.684A pdb=" N ARG A 248 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.386A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 4.166A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.679A pdb=" N GLU A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 336 removed outlier: 3.530A pdb=" N GLY A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 removed outlier: 3.527A pdb=" N THR A 358 " --> pdb=" O HIS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 removed outlier: 3.526A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 removed outlier: 3.769A pdb=" N ASP A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 480 removed outlier: 3.968A pdb=" N GLN A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 480 " --> pdb=" O GLU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 504 through 515 Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.938A pdb=" N LYS A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.587A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.350A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 653 Processing helix chain 'A' and resid 674 through 684 removed outlier: 3.521A pdb=" N ALA A 678 " --> pdb=" O ASP A 674 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 removed outlier: 3.976A pdb=" N GLY A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 723 through 736 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 removed outlier: 3.793A pdb=" N ARG A 784 " --> pdb=" O GLY A 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 93 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.856A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.568A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 196 removed outlier: 3.926A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.859A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.770A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix removed outlier: 4.196A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.658A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 removed outlier: 3.773A pdb=" N ARG C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.828A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.755A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.671A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 13 through 16 removed outlier: 3.580A pdb=" N LEU A 40 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 103 removed outlier: 7.783A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 344 removed outlier: 3.603A pdb=" N ARG A 343 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 378 through 382 Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.637A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.852A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.526A pdb=" N VAL C 152 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241 514 hydrogen bonds defined for protein. 1443 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: 3.32 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1676 1.32 - 1.44: 2734 1.44 - 1.56: 5784 1.56 - 1.69: 6 1.69 - 1.81: 100 Bond restraints: 10300 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.450 0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.201 0.062 2.00e-02 2.50e+03 9.49e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.463 0.062 2.10e-02 2.27e+03 8.71e+00 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.370 -0.041 1.40e-02 5.10e+03 8.43e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.75e+00 ... (remaining 10295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 13503 2.38 - 4.75: 349 4.75 - 7.13: 50 7.13 - 9.51: 8 9.51 - 11.88: 4 Bond angle restraints: 13914 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 109.82 11.88 1.80e+00 3.09e-01 4.36e+01 angle pdb=" N LEU A 782 " pdb=" CA LEU A 782 " pdb=" C LEU A 782 " ideal model delta sigma weight residual 111.14 117.11 -5.97 1.08e+00 8.57e-01 3.05e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.77 -4.77 1.10e+00 8.26e-01 1.88e+01 angle pdb=" CA TYR A 787 " pdb=" CB TYR A 787 " pdb=" CG TYR A 787 " ideal model delta sigma weight residual 113.90 121.55 -7.65 1.80e+00 3.09e-01 1.81e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 102.08 8.02 1.90e+00 2.77e-01 1.78e+01 ... (remaining 13909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 6066 34.88 - 69.76: 108 69.76 - 104.64: 31 104.64 - 139.53: 4 139.53 - 174.41: 1 Dihedral angle restraints: 6210 sinusoidal: 2553 harmonic: 3657 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 114.40 -174.41 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 72.24 -132.24 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 172.66 127.34 1 2.00e+01 2.50e-03 3.86e+01 ... (remaining 6207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1102 0.050 - 0.101: 312 0.101 - 0.151: 92 0.151 - 0.202: 9 0.202 - 0.252: 5 Chirality restraints: 1520 Sorted by residual: chirality pdb=" CA MET A 648 " pdb=" N MET A 648 " pdb=" C MET A 648 " pdb=" CB MET A 648 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA TYR A 787 " pdb=" N TYR A 787 " pdb=" C TYR A 787 " pdb=" CB TYR A 787 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA HIS A 418 " pdb=" N HIS A 418 " pdb=" C HIS A 418 " pdb=" CB HIS A 418 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1517 not shown) Planarity restraints: 1776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 116 " 0.138 9.50e-02 1.11e+02 7.90e-02 3.26e+01 pdb=" NE ARG C 116 " -0.040 2.00e-02 2.50e+03 pdb=" CZ ARG C 116 " 0.094 2.00e-02 2.50e+03 pdb=" NH1 ARG C 116 " -0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG C 116 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 306 " -0.003 2.00e-02 2.50e+03 3.90e-02 3.04e+01 pdb=" CG TYR C 306 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR C 306 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR C 306 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 306 " 0.053 2.00e-02 2.50e+03 pdb=" CE2 TYR C 306 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 306 " 0.058 2.00e-02 2.50e+03 pdb=" OH TYR C 306 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 231 " 0.121 9.50e-02 1.11e+02 7.00e-02 2.64e+01 pdb=" NE ARG A 231 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 231 " 0.085 2.00e-02 2.50e+03 pdb=" NH1 ARG A 231 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG A 231 " -0.024 2.00e-02 2.50e+03 ... (remaining 1773 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 26 2.37 - 3.00: 5491 3.00 - 3.63: 15183 3.63 - 4.27: 22416 4.27 - 4.90: 37848 Nonbonded interactions: 80964 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.731 3.620 nonbonded pdb=" OG1 THR A 170 " pdb="MG MG A1901 " model vdw 2.157 2.170 nonbonded pdb=" OH TYR A 100 " pdb=" OH TYR A 119 " model vdw 2.170 3.040 nonbonded pdb=" OG SER A 165 " pdb=" O ASN A 216 " model vdw 2.175 3.040 nonbonded pdb=" NZ LYS A 633 " pdb=" O GLY C 23 " model vdw 2.182 3.120 ... (remaining 80959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.240 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 10302 Z= 0.225 Angle : 0.931 11.883 13920 Z= 0.543 Chirality : 0.052 0.252 1520 Planarity : 0.008 0.085 1774 Dihedral : 16.175 174.408 3846 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.81 % Cbeta Deviations : 0.08 % 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: -1.87 (0.20), residues: 1221 helix: -1.55 (0.16), residues: 614 sheet: 0.01 (0.41), residues: 141 loop : -0.92 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 356 HIS 0.007 0.001 HIS A 418 PHE 0.028 0.003 PHE C 266 TYR 0.059 0.007 TYR C 306 ARG 0.095 0.012 ARG C 116 Details of bonding type rmsd link_TRANS : bond 0.00930 ( 2) link_TRANS : angle 4.22393 ( 6) hydrogen bonds : bond 0.15774 ( 512) hydrogen bonds : angle 6.99107 ( 1443) covalent geometry : bond 0.00459 (10300) covalent geometry : angle 0.92723 (13914) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.8173 (p0) cc_final: 0.7937 (t70) REVERT: A 759 LEU cc_start: 0.9142 (mt) cc_final: 0.8774 (tt) REVERT: C 80 ASP cc_start: 0.7890 (p0) cc_final: 0.7686 (p0) outliers start: 1 outliers final: 1 residues processed: 178 average time/residue: 0.2525 time to fit residues: 61.6022 Evaluate side-chains 101 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 75 GLN A 72 ASN A 156 ASN A 252 GLN A 264 GLN A 395 HIS A 525 GLN C 41 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 280 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.066503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048499 restraints weight = 48369.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.050258 restraints weight = 24197.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.051428 restraints weight = 15127.055| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10302 Z= 0.151 Angle : 0.689 10.158 13920 Z= 0.359 Chirality : 0.045 0.273 1520 Planarity : 0.004 0.044 1774 Dihedral : 10.546 167.646 1395 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.58 % Allowed : 6.15 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.31 (0.23), residues: 1221 helix: 0.47 (0.20), residues: 619 sheet: 0.52 (0.38), residues: 168 loop : -0.09 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 484 HIS 0.005 0.001 HIS A 354 PHE 0.016 0.002 PHE A 564 TYR 0.031 0.002 TYR A 787 ARG 0.009 0.001 ARG A 155 Details of bonding type rmsd link_TRANS : bond 0.00206 ( 2) link_TRANS : angle 1.54600 ( 6) hydrogen bonds : bond 0.04221 ( 512) hydrogen bonds : angle 5.15619 ( 1443) covalent geometry : bond 0.00334 (10300) covalent geometry : angle 0.68809 (13914) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.8075 (p0) cc_final: 0.7872 (t70) REVERT: A 305 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8827 (tmm) REVERT: A 363 LEU cc_start: 0.9331 (mt) cc_final: 0.9113 (tp) REVERT: A 507 ASP cc_start: 0.8242 (t0) cc_final: 0.7985 (t0) REVERT: A 744 PHE cc_start: 0.8639 (m-80) cc_final: 0.8016 (m-80) REVERT: A 759 LEU cc_start: 0.9191 (mt) cc_final: 0.8892 (pp) REVERT: C 57 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8831 (tp30) REVERT: C 355 MET cc_start: 0.8932 (mmm) cc_final: 0.8616 (mmm) outliers start: 17 outliers final: 7 residues processed: 126 average time/residue: 0.2052 time to fit residues: 38.5809 Evaluate side-chains 103 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 679 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 12 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 HIS A 418 HIS ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.063720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.046103 restraints weight = 49085.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.047705 restraints weight = 25075.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.048763 restraints weight = 15870.904| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10302 Z= 0.207 Angle : 0.664 12.633 13920 Z= 0.341 Chirality : 0.044 0.180 1520 Planarity : 0.004 0.043 1774 Dihedral : 9.214 129.579 1394 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.58 % Allowed : 8.38 % Favored : 90.04 % 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: 0.68 (0.23), residues: 1221 helix: 0.96 (0.21), residues: 618 sheet: 0.44 (0.38), residues: 166 loop : -0.12 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 484 HIS 0.006 0.001 HIS A 354 PHE 0.015 0.002 PHE C 255 TYR 0.027 0.002 TYR A 787 ARG 0.004 0.000 ARG A 155 Details of bonding type rmsd link_TRANS : bond 0.00267 ( 2) link_TRANS : angle 0.97041 ( 6) hydrogen bonds : bond 0.04108 ( 512) hydrogen bonds : angle 4.95351 ( 1443) covalent geometry : bond 0.00455 (10300) covalent geometry : angle 0.66399 (13914) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.8054 (p0) cc_final: 0.7847 (t70) REVERT: A 305 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8804 (tmm) REVERT: A 478 MET cc_start: 0.8619 (mmm) cc_final: 0.8367 (mmm) REVERT: A 744 PHE cc_start: 0.8481 (m-80) cc_final: 0.7991 (m-80) REVERT: A 759 LEU cc_start: 0.9190 (mt) cc_final: 0.8913 (pp) REVERT: A 767 LEU cc_start: 0.8710 (pp) cc_final: 0.8362 (tt) REVERT: C 47 MET cc_start: 0.8083 (ppp) cc_final: 0.7834 (ppp) outliers start: 17 outliers final: 11 residues processed: 108 average time/residue: 0.1941 time to fit residues: 32.0383 Evaluate side-chains 99 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 737 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 66 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 HIS ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN A 430 HIS A 463 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.064527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.046930 restraints weight = 48751.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.048560 restraints weight = 24927.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.049640 restraints weight = 15815.603| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10302 Z= 0.138 Angle : 0.610 12.239 13920 Z= 0.308 Chirality : 0.042 0.173 1520 Planarity : 0.004 0.043 1774 Dihedral : 8.039 108.116 1394 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.77 % Allowed : 9.78 % Favored : 88.45 % 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: 0.93 (0.24), residues: 1221 helix: 1.25 (0.21), residues: 618 sheet: 0.42 (0.38), residues: 167 loop : -0.08 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.008 0.001 HIS B 111 PHE 0.013 0.001 PHE B 93 TYR 0.023 0.001 TYR A 787 ARG 0.004 0.000 ARG A 327 Details of bonding type rmsd link_TRANS : bond 0.00211 ( 2) link_TRANS : angle 0.89987 ( 6) hydrogen bonds : bond 0.03619 ( 512) hydrogen bonds : angle 4.74696 ( 1443) covalent geometry : bond 0.00313 (10300) covalent geometry : angle 0.61005 (13914) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8771 (tmm) REVERT: A 671 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7620 (t80) REVERT: A 744 PHE cc_start: 0.8469 (m-80) cc_final: 0.7997 (m-80) REVERT: A 759 LEU cc_start: 0.9183 (mt) cc_final: 0.8909 (pp) REVERT: C 47 MET cc_start: 0.8137 (ppp) cc_final: 0.7923 (ppp) outliers start: 19 outliers final: 9 residues processed: 111 average time/residue: 0.1785 time to fit residues: 30.3516 Evaluate side-chains 91 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 679 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 91 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 111 HIS ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.064595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.046996 restraints weight = 48319.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.048652 restraints weight = 24789.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.049732 restraints weight = 15671.212| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10302 Z= 0.131 Angle : 0.606 11.439 13920 Z= 0.302 Chirality : 0.041 0.188 1520 Planarity : 0.004 0.041 1774 Dihedral : 7.344 93.656 1394 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.49 % Allowed : 12.29 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.24), residues: 1221 helix: 1.30 (0.21), residues: 618 sheet: 0.37 (0.38), residues: 162 loop : -0.03 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 484 HIS 0.005 0.001 HIS B 111 PHE 0.012 0.001 PHE C 255 TYR 0.022 0.001 TYR A 787 ARG 0.003 0.000 ARG B 64 Details of bonding type rmsd link_TRANS : bond 0.00210 ( 2) link_TRANS : angle 0.87566 ( 6) hydrogen bonds : bond 0.03454 ( 512) hydrogen bonds : angle 4.70688 ( 1443) covalent geometry : bond 0.00300 (10300) covalent geometry : angle 0.60542 (13914) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.7336 (tpt) cc_final: 0.6939 (tpt) REVERT: A 150 MET cc_start: 0.8637 (ttp) cc_final: 0.8388 (ttp) REVERT: A 305 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8756 (tmm) REVERT: A 478 MET cc_start: 0.8932 (mmm) cc_final: 0.8675 (tpt) REVERT: A 671 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7472 (t80) REVERT: A 744 PHE cc_start: 0.8449 (m-80) cc_final: 0.7986 (m-80) REVERT: A 759 LEU cc_start: 0.9177 (mt) cc_final: 0.8907 (pp) REVERT: C 47 MET cc_start: 0.8149 (ppp) cc_final: 0.7910 (ppp) REVERT: C 117 GLU cc_start: 0.8430 (mp0) cc_final: 0.8160 (mm-30) outliers start: 16 outliers final: 10 residues processed: 102 average time/residue: 0.1825 time to fit residues: 28.6686 Evaluate side-chains 96 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 19 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 46 optimal weight: 0.0770 chunk 81 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 HIS ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.064118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.046710 restraints weight = 48795.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.048318 restraints weight = 24983.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.049405 restraints weight = 15775.051| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10302 Z= 0.141 Angle : 0.599 9.274 13920 Z= 0.299 Chirality : 0.041 0.169 1520 Planarity : 0.004 0.039 1774 Dihedral : 7.168 88.463 1394 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.68 % Allowed : 11.55 % Favored : 86.78 % 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: 1.05 (0.24), residues: 1221 helix: 1.34 (0.21), residues: 618 sheet: 0.40 (0.39), residues: 159 loop : 0.05 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 374 HIS 0.011 0.001 HIS B 111 PHE 0.012 0.001 PHE C 255 TYR 0.021 0.001 TYR A 787 ARG 0.003 0.000 ARG B 64 Details of bonding type rmsd link_TRANS : bond 0.00225 ( 2) link_TRANS : angle 0.87008 ( 6) hydrogen bonds : bond 0.03403 ( 512) hydrogen bonds : angle 4.69886 ( 1443) covalent geometry : bond 0.00318 (10300) covalent geometry : angle 0.59850 (13914) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.7427 (tpt) cc_final: 0.6996 (tpt) REVERT: A 305 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8750 (tmm) REVERT: A 478 MET cc_start: 0.8908 (mmm) cc_final: 0.8656 (tpt) REVERT: A 671 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7431 (t80) REVERT: A 744 PHE cc_start: 0.8416 (m-80) cc_final: 0.8027 (m-80) REVERT: A 759 LEU cc_start: 0.9173 (mt) cc_final: 0.8905 (pp) REVERT: C 117 GLU cc_start: 0.8448 (mp0) cc_final: 0.8166 (mm-30) outliers start: 18 outliers final: 11 residues processed: 99 average time/residue: 0.2040 time to fit residues: 30.4333 Evaluate side-chains 95 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 43 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 6 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 92 optimal weight: 0.0770 chunk 83 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 111 HIS ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.064795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.047197 restraints weight = 49253.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.048843 restraints weight = 25199.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.049940 restraints weight = 15851.590| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10302 Z= 0.117 Angle : 0.609 12.192 13920 Z= 0.299 Chirality : 0.041 0.184 1520 Planarity : 0.004 0.042 1774 Dihedral : 6.956 84.065 1394 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.30 % Allowed : 12.76 % Favored : 85.94 % 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: 1.08 (0.24), residues: 1221 helix: 1.36 (0.21), residues: 618 sheet: 0.39 (0.39), residues: 159 loop : 0.06 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.004 0.001 HIS C 161 PHE 0.011 0.001 PHE C 255 TYR 0.020 0.001 TYR A 787 ARG 0.003 0.000 ARG C 206 Details of bonding type rmsd link_TRANS : bond 0.00212 ( 2) link_TRANS : angle 0.85583 ( 6) hydrogen bonds : bond 0.03258 ( 512) hydrogen bonds : angle 4.62903 ( 1443) covalent geometry : bond 0.00272 (10300) covalent geometry : angle 0.60887 (13914) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.7036 (tpt) cc_final: 0.6616 (tpt) REVERT: A 305 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8755 (tmm) REVERT: A 478 MET cc_start: 0.8884 (mmm) cc_final: 0.8620 (tpt) REVERT: A 744 PHE cc_start: 0.8397 (m-80) cc_final: 0.8013 (m-80) REVERT: A 759 LEU cc_start: 0.9188 (mt) cc_final: 0.8935 (pp) REVERT: C 117 GLU cc_start: 0.8503 (mp0) cc_final: 0.8079 (mm-30) outliers start: 14 outliers final: 9 residues processed: 99 average time/residue: 0.1881 time to fit residues: 28.5563 Evaluate side-chains 93 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 HIS ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.064032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.046479 restraints weight = 49200.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.048108 restraints weight = 25257.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.049173 restraints weight = 15977.538| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10302 Z= 0.156 Angle : 0.619 11.339 13920 Z= 0.306 Chirality : 0.041 0.188 1520 Planarity : 0.004 0.042 1774 Dihedral : 6.950 82.672 1394 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.49 % Allowed : 12.38 % Favored : 86.13 % 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: 1.04 (0.24), residues: 1221 helix: 1.34 (0.21), residues: 620 sheet: 0.32 (0.39), residues: 159 loop : 0.04 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 374 HIS 0.005 0.001 HIS A 354 PHE 0.013 0.001 PHE A 671 TYR 0.020 0.001 TYR A 787 ARG 0.003 0.000 ARG B 110 Details of bonding type rmsd link_TRANS : bond 0.00241 ( 2) link_TRANS : angle 0.86619 ( 6) hydrogen bonds : bond 0.03388 ( 512) hydrogen bonds : angle 4.65606 ( 1443) covalent geometry : bond 0.00358 (10300) covalent geometry : angle 0.61880 (13914) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.6726 (tpt) cc_final: 0.6287 (tpp) REVERT: A 305 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8763 (tmm) REVERT: A 478 MET cc_start: 0.8897 (mmm) cc_final: 0.8634 (tpt) REVERT: A 671 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7560 (t80) REVERT: A 744 PHE cc_start: 0.8429 (m-80) cc_final: 0.8031 (m-80) REVERT: A 759 LEU cc_start: 0.9206 (mt) cc_final: 0.8920 (pp) REVERT: C 117 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8180 (mm-30) outliers start: 16 outliers final: 11 residues processed: 95 average time/residue: 0.2208 time to fit residues: 32.6444 Evaluate side-chains 96 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 81 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 HIS ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.063706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.045979 restraints weight = 49506.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.047589 restraints weight = 25582.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.048635 restraints weight = 16288.677| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10302 Z= 0.166 Angle : 0.640 11.763 13920 Z= 0.314 Chirality : 0.042 0.189 1520 Planarity : 0.004 0.042 1774 Dihedral : 6.960 81.962 1394 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.49 % Allowed : 12.94 % Favored : 85.57 % 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: 0.97 (0.24), residues: 1221 helix: 1.30 (0.21), residues: 621 sheet: 0.21 (0.40), residues: 162 loop : 0.02 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.005 0.001 HIS B 111 PHE 0.027 0.001 PHE B 12 TYR 0.019 0.001 TYR A 787 ARG 0.003 0.000 ARG C 177 Details of bonding type rmsd link_TRANS : bond 0.00251 ( 2) link_TRANS : angle 0.86891 ( 6) hydrogen bonds : bond 0.03403 ( 512) hydrogen bonds : angle 4.70316 ( 1443) covalent geometry : bond 0.00379 (10300) covalent geometry : angle 0.64009 (13914) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.6807 (tpt) cc_final: 0.6095 (tpt) REVERT: A 305 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8750 (tmm) REVERT: A 478 MET cc_start: 0.8894 (mmm) cc_final: 0.8633 (tpt) REVERT: A 671 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7632 (t80) REVERT: A 744 PHE cc_start: 0.8441 (m-80) cc_final: 0.8037 (m-80) REVERT: A 759 LEU cc_start: 0.9197 (mt) cc_final: 0.8899 (pp) outliers start: 16 outliers final: 12 residues processed: 97 average time/residue: 0.1917 time to fit residues: 28.5311 Evaluate side-chains 97 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 98 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 HIS ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.063923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.046576 restraints weight = 48879.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.048158 restraints weight = 25190.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.049208 restraints weight = 16019.076| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10302 Z= 0.138 Angle : 0.636 12.072 13920 Z= 0.312 Chirality : 0.042 0.217 1520 Planarity : 0.004 0.041 1774 Dihedral : 6.874 78.947 1394 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.40 % Allowed : 13.31 % Favored : 85.29 % 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 (0.24), residues: 1221 helix: 1.32 (0.21), residues: 619 sheet: 0.29 (0.40), residues: 161 loop : 0.01 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.004 0.001 HIS A 354 PHE 0.025 0.001 PHE B 12 TYR 0.015 0.001 TYR A 408 ARG 0.003 0.000 ARG C 147 Details of bonding type rmsd link_TRANS : bond 0.00231 ( 2) link_TRANS : angle 0.85474 ( 6) hydrogen bonds : bond 0.03413 ( 512) hydrogen bonds : angle 4.70838 ( 1443) covalent geometry : bond 0.00322 (10300) covalent geometry : angle 0.63564 (13914) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8742 (tmm) REVERT: A 478 MET cc_start: 0.8871 (mmm) cc_final: 0.8613 (tpt) REVERT: A 648 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8537 (mmm) REVERT: A 671 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7571 (t80) REVERT: A 744 PHE cc_start: 0.8423 (m-80) cc_final: 0.8025 (m-80) REVERT: A 759 LEU cc_start: 0.9202 (mt) cc_final: 0.8910 (pp) REVERT: C 176 MET cc_start: 0.8166 (ppp) cc_final: 0.7841 (ppp) outliers start: 15 outliers final: 11 residues processed: 95 average time/residue: 0.1857 time to fit residues: 27.1766 Evaluate side-chains 95 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 107 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 60 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 HIS ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.064320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.046947 restraints weight = 48638.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.048542 restraints weight = 25076.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.049581 restraints weight = 15949.794| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10302 Z= 0.124 Angle : 0.634 12.069 13920 Z= 0.311 Chirality : 0.042 0.225 1520 Planarity : 0.004 0.041 1774 Dihedral : 6.741 78.048 1394 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.40 % Allowed : 13.50 % Favored : 85.10 % 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: 1.08 (0.24), residues: 1221 helix: 1.37 (0.21), residues: 618 sheet: 0.31 (0.40), residues: 161 loop : 0.09 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 79 HIS 0.004 0.001 HIS A 354 PHE 0.023 0.001 PHE B 12 TYR 0.014 0.001 TYR A 787 ARG 0.003 0.000 ARG B 64 Details of bonding type rmsd link_TRANS : bond 0.00225 ( 2) link_TRANS : angle 0.84979 ( 6) hydrogen bonds : bond 0.03319 ( 512) hydrogen bonds : angle 4.69851 ( 1443) covalent geometry : bond 0.00291 (10300) covalent geometry : angle 0.63421 (13914) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3523.30 seconds wall clock time: 62 minutes 1.52 seconds (3721.52 seconds total)