Starting phenix.real_space_refine on Wed Jul 30 18:35:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k52_36893/07_2025/8k52_36893.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k52_36893/07_2025/8k52_36893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k52_36893/07_2025/8k52_36893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k52_36893/07_2025/8k52_36893.map" model { file = "/net/cci-nas-00/data/ceres_data/8k52_36893/07_2025/8k52_36893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k52_36893/07_2025/8k52_36893.cif" } resolution = 2.94 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= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 Mn 2 7.51 5 P 4 5.49 5 S 70 5.16 5 C 8108 2.51 5 N 2090 2.21 5 O 2232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12506 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 6239 Classifications: {'peptide': 775} Link IDs: {'PTRANS': 27, 'TRANS': 747} Chain breaks: 4 Chain: "B" Number of atoms: 6215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6215 Classifications: {'peptide': 773} Link IDs: {'PTRANS': 26, 'TRANS': 746} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.14, per 1000 atoms: 0.65 Number of scatterers: 12506 At special positions: 0 Unit cell: (119.6, 109.2, 122.72, 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) Mn 2 24.99 S 70 16.00 P 4 15.00 O 2232 8.00 N 2090 7.00 C 8108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.7 seconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2906 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 4 sheets defined 68.1% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 23 through 37 Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 93 through 110 Processing helix chain 'A' and resid 112 through 134 removed outlier: 3.612A pdb=" N GLU A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 163 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 242 through 262 removed outlier: 3.708A pdb=" N LEU A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 357 through 374 Processing helix chain 'A' and resid 390 through 403 Processing helix chain 'A' and resid 423 through 447 removed outlier: 3.576A pdb=" N PHE A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 479 removed outlier: 4.826A pdb=" N THR A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU A 477 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.781A pdb=" N LEU A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 493 Processing helix chain 'A' and resid 495 through 505 Processing helix chain 'A' and resid 528 through 554 removed outlier: 3.788A pdb=" N ASN A 541 " --> pdb=" O LYS A 537 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 560 removed outlier: 4.367A pdb=" N TYR A 558 " --> pdb=" O TRP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 587 removed outlier: 3.522A pdb=" N PHE A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 606 Processing helix chain 'A' and resid 619 through 646 removed outlier: 4.293A pdb=" N ASP A 623 " --> pdb=" O GLN A 619 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 681 Processing helix chain 'A' and resid 684 through 696 Processing helix chain 'A' and resid 696 through 706 Processing helix chain 'A' and resid 708 through 735 removed outlier: 5.595A pdb=" N THR A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N HIS A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) Proline residue: A 723 - end of helix Processing helix chain 'A' and resid 764 through 819 Processing helix chain 'A' and resid 820 through 853 Proline residue: A 826 - end of helix Processing helix chain 'B' and resid 24 through 37 Processing helix chain 'B' and resid 78 through 85 Processing helix chain 'B' and resid 93 through 110 Processing helix chain 'B' and resid 112 through 134 removed outlier: 3.971A pdb=" N LEU B 117 " --> pdb=" O TYR B 113 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LYS B 118 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 163 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 242 through 262 removed outlier: 3.770A pdb=" N LEU B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 311 through 319 Processing helix chain 'B' and resid 357 through 374 Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 423 through 447 removed outlier: 3.574A pdb=" N PHE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 479 removed outlier: 4.927A pdb=" N THR B 476 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU B 477 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 485 removed outlier: 3.864A pdb=" N LEU B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 493 Processing helix chain 'B' and resid 495 through 505 Processing helix chain 'B' and resid 528 through 553 removed outlier: 3.827A pdb=" N ASN B 541 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE B 545 " --> pdb=" O ASN B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 560 removed outlier: 4.337A pdb=" N TYR B 558 " --> pdb=" O TRP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 587 Processing helix chain 'B' and resid 587 through 606 Processing helix chain 'B' and resid 620 through 646 removed outlier: 3.954A pdb=" N VAL B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 680 Processing helix chain 'B' and resid 684 through 696 Processing helix chain 'B' and resid 696 through 706 Processing helix chain 'B' and resid 708 through 720 removed outlier: 5.479A pdb=" N THR B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N HIS B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 735 removed outlier: 3.713A pdb=" N THR B 730 " --> pdb=" O VAL B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 819 Processing helix chain 'B' and resid 820 through 853 Proline residue: B 826 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 180 removed outlier: 7.032A pdb=" N VAL A 284 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL A 348 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 286 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ALA A 350 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 288 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LYS A 352 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA A 290 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 232 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N CYS A 287 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 234 " --> pdb=" O CYS A 287 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL A 289 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE A 236 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N MET A 233 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N MET A 381 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N CYS A 235 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG A 461 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY A 406 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N HIS A 514 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA A 408 " --> pdb=" O HIS A 514 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL A 516 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLY A 410 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ASP A 518 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N LEU A 412 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N VAL A 520 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N VAL A 414 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG A 522 " --> pdb=" O VAL A 414 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA3, first strand: chain 'B' and resid 177 through 180 removed outlier: 8.387A pdb=" N ARG B 200 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR B 332 " --> pdb=" O ARG B 200 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 347 " --> pdb=" O HIS B 331 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN B 346 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 232 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N CYS B 287 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE B 234 " --> pdb=" O CYS B 287 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL B 289 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE B 236 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET B 233 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N MET B 381 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N CYS B 235 " --> pdb=" O MET B 381 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 461 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY B 406 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N HIS B 514 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA B 408 " --> pdb=" O HIS B 514 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL B 516 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLY B 410 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ASP B 518 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N LEU B 412 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N VAL B 520 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N VAL B 414 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG B 522 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 336 through 337 830 hydrogen bonds defined for protein. 2445 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: 3.95 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2734 1.33 - 1.45: 3100 1.45 - 1.57: 6879 1.57 - 1.69: 8 1.69 - 1.82: 110 Bond restraints: 12831 Sorted by residual: bond pdb=" O1B UDP B1001 " pdb=" PB UDP B1001 " ideal model delta sigma weight residual 1.530 1.658 -0.128 1.00e-02 1.00e+04 1.65e+02 bond pdb=" O1B UDP A1001 " pdb=" PB UDP A1001 " ideal model delta sigma weight residual 1.530 1.657 -0.127 1.00e-02 1.00e+04 1.62e+02 bond pdb=" O3A UDP B1001 " pdb=" PB UDP B1001 " ideal model delta sigma weight residual 1.584 1.638 -0.054 1.00e-02 1.00e+04 2.89e+01 bond pdb=" O3A UDP A1001 " pdb=" PB UDP A1001 " ideal model delta sigma weight residual 1.584 1.636 -0.052 1.00e-02 1.00e+04 2.70e+01 bond pdb=" O5' UDP B1001 " pdb=" PA UDP B1001 " ideal model delta sigma weight residual 1.581 1.645 -0.064 1.50e-02 4.44e+03 1.81e+01 ... (remaining 12826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 17098 2.37 - 4.75: 237 4.75 - 7.12: 47 7.12 - 9.49: 23 9.49 - 11.87: 5 Bond angle restraints: 17410 Sorted by residual: angle pdb=" O5' UDP A1001 " pdb=" PA UDP A1001 " pdb=" O3A UDP A1001 " ideal model delta sigma weight residual 104.35 92.94 11.41 1.00e+00 1.00e+00 1.30e+02 angle pdb=" O5' UDP B1001 " pdb=" PA UDP B1001 " pdb=" O3A UDP B1001 " ideal model delta sigma weight residual 104.35 93.01 11.34 1.00e+00 1.00e+00 1.29e+02 angle pdb=" O1B UDP A1001 " pdb=" PB UDP A1001 " pdb=" O3A UDP A1001 " ideal model delta sigma weight residual 102.95 92.91 10.04 1.00e+00 1.00e+00 1.01e+02 angle pdb=" O1B UDP B1001 " pdb=" PB UDP B1001 " pdb=" O3A UDP B1001 " ideal model delta sigma weight residual 102.95 93.00 9.95 1.00e+00 1.00e+00 9.90e+01 angle pdb=" O2B UDP B1001 " pdb=" PB UDP B1001 " pdb=" O3A UDP B1001 " ideal model delta sigma weight residual 102.95 110.54 -7.59 1.00e+00 1.00e+00 5.76e+01 ... (remaining 17405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 6516 17.59 - 35.17: 741 35.17 - 52.76: 221 52.76 - 70.34: 20 70.34 - 87.93: 10 Dihedral angle restraints: 7508 sinusoidal: 2988 harmonic: 4520 Sorted by residual: dihedral pdb=" CA GLU B 353 " pdb=" C GLU B 353 " pdb=" N ASN B 354 " pdb=" CA ASN B 354 " ideal model delta harmonic sigma weight residual 180.00 -162.20 -17.80 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA GLN B 602 " pdb=" C GLN B 602 " pdb=" N GLY B 603 " pdb=" CA GLY B 603 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA GLN A 602 " pdb=" C GLN A 602 " pdb=" N GLY A 603 " pdb=" CA GLY A 603 " ideal model delta harmonic sigma weight residual 180.00 163.61 16.39 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 7505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1597 0.057 - 0.115: 283 0.115 - 0.172: 21 0.172 - 0.229: 6 0.229 - 0.286: 1 Chirality restraints: 1908 Sorted by residual: chirality pdb=" CG LEU B 665 " pdb=" CB LEU B 665 " pdb=" CD1 LEU B 665 " pdb=" CD2 LEU B 665 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA ALA A 543 " pdb=" N ALA A 543 " pdb=" C ALA A 543 " pdb=" CB ALA A 543 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C1' UDP A1001 " pdb=" O4' UDP A1001 " pdb=" C2' UDP A1001 " pdb=" N1 UDP A1001 " both_signs ideal model delta sigma weight residual False 2.45 2.23 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1905 not shown) Planarity restraints: 2192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 541 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ASN A 541 " -0.062 2.00e-02 2.50e+03 pdb=" O ASN A 541 " 0.023 2.00e-02 2.50e+03 pdb=" N GLY A 542 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 264 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.10e+00 pdb=" N PRO A 265 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 598 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C PHE B 598 " -0.039 2.00e-02 2.50e+03 pdb=" O PHE B 598 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE B 599 " 0.013 2.00e-02 2.50e+03 ... (remaining 2189 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 250 2.68 - 3.24: 12521 3.24 - 3.79: 20812 3.79 - 4.35: 26071 4.35 - 4.90: 43913 Nonbonded interactions: 103567 Sorted by model distance: nonbonded pdb=" O2B UDP B1001 " pdb="MN MN B1002 " model vdw 2.130 2.320 nonbonded pdb=" N GLU B 353 " pdb=" OE1 GLU B 353 " model vdw 2.170 3.120 nonbonded pdb=" O GLU A 241 " pdb=" OG1 THR A 300 " model vdw 2.222 3.040 nonbonded pdb=" N GLU A 707 " pdb=" OE1 GLU A 707 " model vdw 2.242 3.120 nonbonded pdb=" OD1 ASN B 109 " pdb=" NH2 ARG B 171 " model vdw 2.242 3.120 ... (remaining 103562 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 23 through 37 or resid 39 through 85 or resid 91 through 4 \ 92 or (resid 493 and (name N or name CA or name C or name O or name CB or name C \ D1 or name CD2)) or resid 494 through 736 or resid 763 through 859 or resid 1001 \ or resid 1002)) selection = (chain 'B' and (resid 23 through 51 or resid 77 through 859 or resid 1001 or res \ id 1002)) } 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: 1.390 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: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.320 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.050 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:14.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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 : 0.004 0.128 12831 Z= 0.278 Angle : 0.757 11.868 17410 Z= 0.440 Chirality : 0.043 0.286 1908 Planarity : 0.005 0.061 2192 Dihedral : 16.040 87.925 4602 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.44 % Favored : 94.36 % Rotamer: Outliers : 3.32 % Allowed : 28.73 % Favored : 67.95 % 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: 1.07 (0.22), residues: 1525 helix: 1.47 (0.17), residues: 972 sheet: -0.13 (0.44), residues: 152 loop : -0.72 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 511 HIS 0.007 0.001 HIS A 578 PHE 0.028 0.002 PHE A 544 TYR 0.021 0.001 TYR B 207 ARG 0.015 0.001 ARG A 779 Details of bonding type rmsd hydrogen bonds : bond 0.10161 ( 830) hydrogen bonds : angle 6.01331 ( 2445) covalent geometry : bond 0.00448 (12831) covalent geometry : angle 0.75711 (17410) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 493 " (corrupted residue). Skipping it. REVERT: A 26 ARG cc_start: 0.7879 (mmp80) cc_final: 0.6332 (mpt180) REVERT: A 118 LYS cc_start: 0.9002 (tppt) cc_final: 0.8756 (mmtt) REVERT: A 148 PHE cc_start: 0.7463 (t80) cc_final: 0.6745 (t80) REVERT: A 295 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8731 (mm110) REVERT: A 403 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.7393 (m-70) REVERT: A 513 MET cc_start: 0.7727 (mtp) cc_final: 0.7248 (mtt) REVERT: A 528 ASP cc_start: 0.8212 (t0) cc_final: 0.7890 (t0) REVERT: A 667 MET cc_start: 0.7892 (mtp) cc_final: 0.7618 (mtp) REVERT: A 735 CYS cc_start: 0.8168 (m) cc_final: 0.7731 (m) REVERT: B 114 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8448 (mmm160) REVERT: B 208 CYS cc_start: 0.8434 (t) cc_final: 0.8124 (t) REVERT: B 297 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.7989 (t70) REVERT: B 491 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.6870 (tmm) REVERT: B 528 ASP cc_start: 0.8137 (t0) cc_final: 0.7880 (t0) REVERT: B 780 ARG cc_start: 0.9186 (ttm110) cc_final: 0.8470 (mpt-90) REVERT: B 814 PHE cc_start: 0.9028 (m-10) cc_final: 0.7943 (t80) outliers start: 44 outliers final: 21 residues processed: 186 average time/residue: 0.9464 time to fit residues: 198.1702 Evaluate side-chains 159 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 726 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 GLN A 836 ASN B 256 ASN B 836 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.093582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.075436 restraints weight = 28743.309| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.11 r_work: 0.3045 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12831 Z= 0.187 Angle : 0.624 11.782 17410 Z= 0.322 Chirality : 0.042 0.158 1908 Planarity : 0.005 0.051 2192 Dihedral : 7.453 83.112 1801 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 6.18 % Allowed : 23.30 % Favored : 70.51 % 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: 1.03 (0.22), residues: 1525 helix: 1.49 (0.17), residues: 977 sheet: -0.40 (0.45), residues: 140 loop : -0.81 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 539 HIS 0.006 0.001 HIS B 846 PHE 0.032 0.002 PHE A 487 TYR 0.024 0.002 TYR A 492 ARG 0.008 0.001 ARG A 779 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 830) hydrogen bonds : angle 5.29564 ( 2445) covalent geometry : bond 0.00414 (12831) covalent geometry : angle 0.62416 (17410) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 146 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 493 " (corrupted residue). Skipping it. REVERT: A 118 LYS cc_start: 0.8957 (tppt) cc_final: 0.8696 (mmtt) REVERT: A 143 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8459 (mm) REVERT: A 148 PHE cc_start: 0.7536 (t80) cc_final: 0.6732 (t80) REVERT: A 184 TRP cc_start: 0.7692 (OUTLIER) cc_final: 0.7333 (t60) REVERT: A 403 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7886 (m-70) REVERT: A 491 MET cc_start: 0.8299 (ttm) cc_final: 0.8090 (ttm) REVERT: A 495 GLU cc_start: 0.8830 (mp0) cc_final: 0.8521 (mp0) REVERT: A 528 ASP cc_start: 0.8201 (t0) cc_final: 0.7877 (t0) REVERT: A 565 PHE cc_start: 0.7431 (t80) cc_final: 0.7147 (t80) REVERT: A 771 LYS cc_start: 0.9230 (tppp) cc_final: 0.9022 (mmpt) REVERT: B 30 MET cc_start: 0.4375 (OUTLIER) cc_final: 0.4166 (mpt) REVERT: B 114 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8416 (mmm160) REVERT: B 148 PHE cc_start: 0.7244 (m-10) cc_final: 0.7034 (t80) REVERT: B 208 CYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8080 (t) REVERT: B 330 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7953 (mp0) REVERT: B 491 MET cc_start: 0.8312 (ttp) cc_final: 0.7235 (tmm) REVERT: B 528 ASP cc_start: 0.8183 (t0) cc_final: 0.7896 (t0) REVERT: B 565 PHE cc_start: 0.7400 (t80) cc_final: 0.7168 (t80) REVERT: B 695 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8288 (p) REVERT: B 725 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.8099 (t80) REVERT: B 780 ARG cc_start: 0.9149 (ttm110) cc_final: 0.8619 (mpt-90) REVERT: B 814 PHE cc_start: 0.9067 (m-10) cc_final: 0.7719 (t80) outliers start: 82 outliers final: 29 residues processed: 208 average time/residue: 0.8698 time to fit residues: 204.2329 Evaluate side-chains 160 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 PHE Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 834 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 121 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 GLN ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 846 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.082294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.063979 restraints weight = 29417.352| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.02 r_work: 0.2780 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 12831 Z= 0.310 Angle : 0.725 12.768 17410 Z= 0.375 Chirality : 0.045 0.208 1908 Planarity : 0.005 0.034 2192 Dihedral : 7.356 73.231 1783 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 6.86 % Allowed : 22.32 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.22), residues: 1525 helix: 1.24 (0.16), residues: 976 sheet: -1.35 (0.41), residues: 159 loop : -0.82 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 511 HIS 0.009 0.001 HIS B 846 PHE 0.022 0.002 PHE A 449 TYR 0.021 0.002 TYR B 207 ARG 0.011 0.001 ARG A 779 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 830) hydrogen bonds : angle 5.54966 ( 2445) covalent geometry : bond 0.00690 (12831) covalent geometry : angle 0.72502 (17410) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 123 time to evaluate : 1.489 Fit side-chains TARDY: cannot create tardy model for: "LEU B 493 " (corrupted residue). Skipping it. REVERT: A 102 ASP cc_start: 0.9328 (t0) cc_final: 0.9045 (m-30) REVERT: A 118 LYS cc_start: 0.9120 (tppt) cc_final: 0.8865 (tmmm) REVERT: A 264 MET cc_start: 0.8650 (pmm) cc_final: 0.8375 (pmm) REVERT: A 312 GLU cc_start: 0.8443 (tp30) cc_final: 0.8199 (pm20) REVERT: A 491 MET cc_start: 0.8407 (ttm) cc_final: 0.8153 (ttm) REVERT: A 528 ASP cc_start: 0.8517 (t0) cc_final: 0.8174 (t0) REVERT: A 537 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8736 (tptp) REVERT: A 654 LEU cc_start: 0.8550 (pt) cc_final: 0.8157 (mm) REVERT: A 667 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8355 (mtp) REVERT: A 725 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.8233 (t80) REVERT: B 29 MET cc_start: 0.7021 (ttt) cc_final: 0.6584 (ttt) REVERT: B 114 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8597 (tpp80) REVERT: B 138 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8072 (pptt) REVERT: B 148 PHE cc_start: 0.7488 (m-10) cc_final: 0.7248 (t80) REVERT: B 264 MET cc_start: 0.8618 (pmm) cc_final: 0.8350 (pmm) REVERT: B 325 GLN cc_start: 0.9215 (mm-40) cc_final: 0.8983 (mm-40) REVERT: B 491 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7469 (tmm) REVERT: B 509 CYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8510 (m) REVERT: B 528 ASP cc_start: 0.8418 (t0) cc_final: 0.8134 (t0) REVERT: B 721 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9146 (tp) REVERT: B 725 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.8025 (t80) REVERT: B 776 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8578 (pm20) REVERT: B 780 ARG cc_start: 0.9181 (ttm110) cc_final: 0.8771 (mmt90) REVERT: B 794 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8046 (mm-30) REVERT: B 797 ARG cc_start: 0.8159 (tmm-80) cc_final: 0.7909 (tmm-80) outliers start: 91 outliers final: 31 residues processed: 197 average time/residue: 0.9719 time to fit residues: 213.2353 Evaluate side-chains 143 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 725 PHE Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 830 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 101 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 71 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 50 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 346 GLN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.085036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.066889 restraints weight = 28730.295| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.97 r_work: 0.2865 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12831 Z= 0.135 Angle : 0.594 13.540 17410 Z= 0.300 Chirality : 0.041 0.177 1908 Planarity : 0.004 0.031 2192 Dihedral : 6.746 69.414 1779 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.83 % Allowed : 23.76 % Favored : 71.42 % 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: 0.89 (0.22), residues: 1525 helix: 1.54 (0.16), residues: 977 sheet: -1.35 (0.43), residues: 149 loop : -0.92 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 511 HIS 0.005 0.001 HIS B 175 PHE 0.014 0.001 PHE A 601 TYR 0.011 0.001 TYR B 207 ARG 0.005 0.000 ARG B 228 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 830) hydrogen bonds : angle 5.38670 ( 2445) covalent geometry : bond 0.00284 (12831) covalent geometry : angle 0.59409 (17410) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 123 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 493 " (corrupted residue). Skipping it. REVERT: A 102 ASP cc_start: 0.9318 (t0) cc_final: 0.8917 (p0) REVERT: A 118 LYS cc_start: 0.9067 (tppt) cc_final: 0.8850 (mptt) REVERT: A 264 MET cc_start: 0.8547 (pmm) cc_final: 0.8278 (pmm) REVERT: A 325 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8817 (mm110) REVERT: A 511 TRP cc_start: 0.8155 (m-10) cc_final: 0.7942 (m-10) REVERT: A 528 ASP cc_start: 0.8382 (t0) cc_final: 0.8041 (t0) REVERT: A 537 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8691 (tptp) REVERT: A 725 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8132 (t80) REVERT: A 777 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8093 (tm-30) REVERT: B 26 ARG cc_start: 0.8026 (mmp80) cc_final: 0.7592 (mpt180) REVERT: B 114 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8610 (tpp80) REVERT: B 148 PHE cc_start: 0.7404 (m-10) cc_final: 0.7178 (t80) REVERT: B 264 MET cc_start: 0.8525 (pmm) cc_final: 0.8296 (pmm) REVERT: B 325 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8357 (mt0) REVERT: B 528 ASP cc_start: 0.8277 (t0) cc_final: 0.8023 (t0) REVERT: B 692 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7677 (tp) REVERT: B 725 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.8029 (t80) REVERT: B 780 ARG cc_start: 0.9183 (ttm110) cc_final: 0.8765 (mmt90) outliers start: 64 outliers final: 30 residues processed: 170 average time/residue: 0.9757 time to fit residues: 185.5899 Evaluate side-chains 140 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 725 PHE Chi-restraints excluded: chain B residue 830 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN A 619 GLN A 851 HIS B 175 HIS B 346 GLN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.084083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.065957 restraints weight = 28885.901| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.96 r_work: 0.2845 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12831 Z= 0.160 Angle : 0.605 13.461 17410 Z= 0.307 Chirality : 0.041 0.161 1908 Planarity : 0.004 0.033 2192 Dihedral : 6.700 67.259 1779 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.66 % Allowed : 23.30 % Favored : 71.04 % 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: 1.03 (0.22), residues: 1525 helix: 1.66 (0.16), residues: 974 sheet: -1.33 (0.43), residues: 151 loop : -0.86 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 188 HIS 0.005 0.001 HIS B 175 PHE 0.014 0.001 PHE A 601 TYR 0.012 0.001 TYR B 207 ARG 0.004 0.000 ARG B 228 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 830) hydrogen bonds : angle 5.27899 ( 2445) covalent geometry : bond 0.00353 (12831) covalent geometry : angle 0.60484 (17410) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 109 time to evaluate : 1.342 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 493 " (corrupted residue). Skipping it. REVERT: A 26 ARG cc_start: 0.8314 (mmp80) cc_final: 0.7159 (mpt180) REVERT: A 102 ASP cc_start: 0.9319 (t0) cc_final: 0.9029 (m-30) REVERT: A 118 LYS cc_start: 0.9122 (tppt) cc_final: 0.8861 (tmmm) REVERT: A 264 MET cc_start: 0.8522 (pmm) cc_final: 0.8270 (pmm) REVERT: A 325 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8811 (mm110) REVERT: A 528 ASP cc_start: 0.8398 (t0) cc_final: 0.8055 (t0) REVERT: A 537 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8756 (tptp) REVERT: A 725 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7993 (t80) REVERT: B 26 ARG cc_start: 0.8017 (mmp80) cc_final: 0.7724 (mpt180) REVERT: B 114 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8570 (tpp80) REVERT: B 148 PHE cc_start: 0.7486 (m-10) cc_final: 0.7237 (t80) REVERT: B 193 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8145 (ttp) REVERT: B 262 GLU cc_start: 0.8316 (pp20) cc_final: 0.8073 (pp20) REVERT: B 264 MET cc_start: 0.8589 (pmm) cc_final: 0.8341 (pmm) REVERT: B 325 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8898 (mm-40) REVERT: B 528 ASP cc_start: 0.8336 (t0) cc_final: 0.8070 (t0) REVERT: B 634 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9152 (mm) REVERT: B 692 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7674 (tp) REVERT: B 725 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7943 (t80) REVERT: B 780 ARG cc_start: 0.9191 (ttm110) cc_final: 0.8629 (mmt90) outliers start: 75 outliers final: 33 residues processed: 168 average time/residue: 0.9350 time to fit residues: 176.7861 Evaluate side-chains 147 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 PHE Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 830 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 95 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 111 optimal weight: 0.0470 chunk 110 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 98 optimal weight: 0.0170 chunk 66 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN B 175 HIS B 210 HIS B 346 GLN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.085573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.067821 restraints weight = 29164.104| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.95 r_work: 0.2910 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12831 Z= 0.128 Angle : 0.598 13.713 17410 Z= 0.299 Chirality : 0.040 0.166 1908 Planarity : 0.004 0.029 2192 Dihedral : 6.549 64.871 1779 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.37 % Allowed : 24.43 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.14 (0.22), residues: 1525 helix: 1.72 (0.16), residues: 974 sheet: -1.20 (0.44), residues: 144 loop : -0.81 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 511 HIS 0.005 0.001 HIS B 175 PHE 0.014 0.001 PHE A 545 TYR 0.010 0.001 TYR B 207 ARG 0.005 0.000 ARG B 228 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 830) hydrogen bonds : angle 5.22829 ( 2445) covalent geometry : bond 0.00275 (12831) covalent geometry : angle 0.59759 (17410) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 122 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 493 " (corrupted residue). Skipping it. REVERT: A 102 ASP cc_start: 0.9278 (t0) cc_final: 0.8901 (p0) REVERT: A 118 LYS cc_start: 0.9144 (tppt) cc_final: 0.8907 (tmmm) REVERT: A 359 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8687 (mm) REVERT: A 528 ASP cc_start: 0.8301 (t0) cc_final: 0.7994 (t0) REVERT: A 537 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8713 (tptp) REVERT: A 692 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8368 (tp) REVERT: A 725 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7903 (t80) REVERT: B 262 GLU cc_start: 0.8273 (pp20) cc_final: 0.8038 (pp20) REVERT: B 325 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8882 (mm-40) REVERT: B 330 GLU cc_start: 0.8591 (mp0) cc_final: 0.8352 (mp0) REVERT: B 528 ASP cc_start: 0.8211 (t0) cc_final: 0.7988 (t0) REVERT: B 634 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9240 (mm) REVERT: B 692 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7710 (tp) REVERT: B 780 ARG cc_start: 0.9212 (ttm110) cc_final: 0.8637 (mtt90) REVERT: B 856 ARG cc_start: 0.6538 (ppp-140) cc_final: 0.6181 (ttp80) outliers start: 58 outliers final: 29 residues processed: 169 average time/residue: 1.0595 time to fit residues: 201.8268 Evaluate side-chains 141 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 511 TRP Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 716 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 132 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 0.0370 chunk 136 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 6 optimal weight: 0.1980 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 295 GLN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.083495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.065755 restraints weight = 28972.822| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.92 r_work: 0.2834 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12831 Z= 0.172 Angle : 0.626 13.914 17410 Z= 0.313 Chirality : 0.041 0.184 1908 Planarity : 0.004 0.030 2192 Dihedral : 6.475 63.401 1773 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.52 % Allowed : 24.96 % Favored : 70.51 % 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: 1.13 (0.22), residues: 1525 helix: 1.68 (0.16), residues: 980 sheet: -1.09 (0.42), residues: 156 loop : -0.74 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 511 HIS 0.005 0.001 HIS B 175 PHE 0.025 0.001 PHE A 192 TYR 0.011 0.001 TYR B 207 ARG 0.005 0.000 ARG B 228 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 830) hydrogen bonds : angle 5.26165 ( 2445) covalent geometry : bond 0.00385 (12831) covalent geometry : angle 0.62599 (17410) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 110 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 493 " (corrupted residue). Skipping it. REVERT: A 26 ARG cc_start: 0.8414 (mmp80) cc_final: 0.7329 (mpt180) REVERT: A 102 ASP cc_start: 0.9274 (t0) cc_final: 0.8872 (p0) REVERT: A 118 LYS cc_start: 0.9118 (tppt) cc_final: 0.8881 (tmmm) REVERT: A 264 MET cc_start: 0.8519 (pmm) cc_final: 0.8292 (pmm) REVERT: A 528 ASP cc_start: 0.8376 (t0) cc_final: 0.8019 (t0) REVERT: A 537 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8682 (tptp) REVERT: A 725 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7872 (t80) REVERT: B 117 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8582 (tp) REVERT: B 210 HIS cc_start: 0.8526 (t70) cc_final: 0.8323 (t70) REVERT: B 262 GLU cc_start: 0.8307 (pp20) cc_final: 0.8059 (pp20) REVERT: B 330 GLU cc_start: 0.8632 (mp0) cc_final: 0.8339 (mp0) REVERT: B 528 ASP cc_start: 0.8335 (t0) cc_final: 0.8054 (t0) REVERT: B 634 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9146 (mm) REVERT: B 692 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7659 (tp) REVERT: B 721 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9096 (tp) REVERT: B 780 ARG cc_start: 0.9221 (ttm110) cc_final: 0.8624 (mtt90) REVERT: B 856 ARG cc_start: 0.6736 (ppp-140) cc_final: 0.6359 (ttp80) outliers start: 60 outliers final: 37 residues processed: 156 average time/residue: 0.9114 time to fit residues: 160.4697 Evaluate side-chains 148 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 511 TRP Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 733 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 18 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 132 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** 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 = 0.3358 r_free = 0.3358 target = 0.083752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.066041 restraints weight = 29018.379| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.92 r_work: 0.2835 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12831 Z= 0.154 Angle : 0.621 14.291 17410 Z= 0.310 Chirality : 0.041 0.224 1908 Planarity : 0.004 0.031 2192 Dihedral : 6.413 61.804 1773 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.45 % Allowed : 25.26 % Favored : 70.29 % 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: 1.13 (0.22), residues: 1525 helix: 1.66 (0.16), residues: 981 sheet: -1.12 (0.42), residues: 155 loop : -0.70 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 511 HIS 0.005 0.001 HIS B 175 PHE 0.020 0.001 PHE B 725 TYR 0.012 0.001 TYR B 207 ARG 0.005 0.000 ARG B 228 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 830) hydrogen bonds : angle 5.28790 ( 2445) covalent geometry : bond 0.00343 (12831) covalent geometry : angle 0.62149 (17410) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 114 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 493 " (corrupted residue). Skipping it. REVERT: A 26 ARG cc_start: 0.8374 (mmp80) cc_final: 0.7502 (mpt180) REVERT: A 102 ASP cc_start: 0.9269 (t0) cc_final: 0.8869 (p0) REVERT: A 118 LYS cc_start: 0.9133 (tppt) cc_final: 0.8917 (tmmm) REVERT: A 528 ASP cc_start: 0.8383 (t0) cc_final: 0.8019 (t0) REVERT: A 537 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8670 (tptp) REVERT: A 725 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7832 (t80) REVERT: B 102 ASP cc_start: 0.9309 (t0) cc_final: 0.8981 (m-30) REVERT: B 262 GLU cc_start: 0.8350 (pp20) cc_final: 0.8054 (pp20) REVERT: B 330 GLU cc_start: 0.8641 (mp0) cc_final: 0.8321 (mp0) REVERT: B 528 ASP cc_start: 0.8319 (t0) cc_final: 0.8047 (t0) REVERT: B 634 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9161 (mm) REVERT: B 692 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7636 (tp) REVERT: B 721 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9111 (tp) REVERT: B 780 ARG cc_start: 0.9256 (ttm110) cc_final: 0.8628 (mtt90) REVERT: B 856 ARG cc_start: 0.6800 (ppp-140) cc_final: 0.6432 (ttp80) outliers start: 59 outliers final: 36 residues processed: 164 average time/residue: 0.9188 time to fit residues: 170.8402 Evaluate side-chains 144 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 103 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 511 TRP Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 733 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 149 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 338 ASN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.083142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.065789 restraints weight = 28939.602| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.86 r_work: 0.2859 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12831 Z= 0.143 Angle : 0.631 14.487 17410 Z= 0.312 Chirality : 0.041 0.266 1908 Planarity : 0.004 0.031 2192 Dihedral : 6.393 61.292 1773 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.85 % Allowed : 26.24 % Favored : 69.91 % 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: 1.09 (0.22), residues: 1525 helix: 1.66 (0.16), residues: 984 sheet: -1.23 (0.41), residues: 157 loop : -0.76 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 511 HIS 0.006 0.001 HIS B 175 PHE 0.025 0.001 PHE A 192 TYR 0.012 0.001 TYR B 207 ARG 0.004 0.000 ARG B 228 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 830) hydrogen bonds : angle 5.27114 ( 2445) covalent geometry : bond 0.00316 (12831) covalent geometry : angle 0.63095 (17410) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 113 time to evaluate : 1.354 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 493 " (corrupted residue). Skipping it. REVERT: A 26 ARG cc_start: 0.8242 (mmp80) cc_final: 0.7603 (mpt180) REVERT: A 102 ASP cc_start: 0.9269 (t0) cc_final: 0.8902 (p0) REVERT: A 118 LYS cc_start: 0.9168 (tppt) cc_final: 0.8957 (tmmm) REVERT: A 490 ASN cc_start: 0.8276 (m110) cc_final: 0.7579 (m110) REVERT: A 528 ASP cc_start: 0.8307 (t0) cc_final: 0.7987 (t0) REVERT: A 537 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8734 (tptp) REVERT: A 652 MET cc_start: 0.8128 (mmm) cc_final: 0.7918 (mtt) REVERT: A 725 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7867 (t80) REVERT: B 102 ASP cc_start: 0.9290 (t0) cc_final: 0.8982 (m-30) REVERT: B 262 GLU cc_start: 0.8265 (pp20) cc_final: 0.7999 (pp20) REVERT: B 330 GLU cc_start: 0.8602 (mp0) cc_final: 0.8314 (mp0) REVERT: B 511 TRP cc_start: 0.7554 (OUTLIER) cc_final: 0.7332 (m-10) REVERT: B 528 ASP cc_start: 0.8261 (t0) cc_final: 0.8019 (t0) REVERT: B 634 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9211 (mm) REVERT: B 692 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7618 (tp) REVERT: B 721 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9177 (tp) REVERT: B 780 ARG cc_start: 0.9260 (ttm110) cc_final: 0.8638 (mtt90) REVERT: B 856 ARG cc_start: 0.6749 (ppp-140) cc_final: 0.6475 (ttp80) outliers start: 51 outliers final: 35 residues processed: 156 average time/residue: 1.0093 time to fit residues: 176.1365 Evaluate side-chains 148 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 TRP Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 733 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 80 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 GLN B 175 HIS ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.082347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.064918 restraints weight = 28864.471| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.87 r_work: 0.2843 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12831 Z= 0.160 Angle : 0.656 14.513 17410 Z= 0.325 Chirality : 0.042 0.285 1908 Planarity : 0.004 0.033 2192 Dihedral : 6.404 61.218 1771 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.54 % Allowed : 26.85 % Favored : 69.61 % 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: 1.09 (0.22), residues: 1525 helix: 1.64 (0.16), residues: 985 sheet: -1.19 (0.42), residues: 157 loop : -0.74 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 511 HIS 0.006 0.001 HIS A 169 PHE 0.019 0.001 PHE B 725 TYR 0.012 0.001 TYR B 207 ARG 0.006 0.000 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 830) hydrogen bonds : angle 5.27899 ( 2445) covalent geometry : bond 0.00360 (12831) covalent geometry : angle 0.65632 (17410) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 108 time to evaluate : 1.528 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 493 " (corrupted residue). Skipping it. REVERT: A 26 ARG cc_start: 0.8209 (mmp80) cc_final: 0.7701 (mpt180) REVERT: A 102 ASP cc_start: 0.9268 (t0) cc_final: 0.8898 (p0) REVERT: A 118 LYS cc_start: 0.9169 (tppt) cc_final: 0.8959 (tmmm) REVERT: A 490 ASN cc_start: 0.8293 (m110) cc_final: 0.7609 (m110) REVERT: A 491 MET cc_start: 0.7734 (ttm) cc_final: 0.7473 (tpt) REVERT: A 528 ASP cc_start: 0.8340 (t0) cc_final: 0.8023 (t0) REVERT: A 537 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8734 (tptp) REVERT: A 692 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8498 (tp) REVERT: A 725 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7869 (t80) REVERT: B 102 ASP cc_start: 0.9294 (t0) cc_final: 0.8989 (m-30) REVERT: B 262 GLU cc_start: 0.8273 (pp20) cc_final: 0.7999 (pp20) REVERT: B 330 GLU cc_start: 0.8627 (mp0) cc_final: 0.8188 (mp0) REVERT: B 528 ASP cc_start: 0.8281 (t0) cc_final: 0.8034 (t0) REVERT: B 634 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9209 (mm) REVERT: B 692 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7640 (tp) REVERT: B 721 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9190 (tp) REVERT: B 780 ARG cc_start: 0.9264 (ttm110) cc_final: 0.8832 (mtt90) REVERT: B 856 ARG cc_start: 0.6812 (ppp-140) cc_final: 0.6530 (ttp80) outliers start: 47 outliers final: 35 residues processed: 148 average time/residue: 0.9659 time to fit residues: 160.1611 Evaluate side-chains 148 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 733 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 79 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 95 optimal weight: 0.2980 chunk 146 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 GLN B 175 HIS ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.082591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.065220 restraints weight = 28808.173| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.87 r_work: 0.2860 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12831 Z= 0.151 Angle : 0.662 14.628 17410 Z= 0.327 Chirality : 0.042 0.224 1908 Planarity : 0.004 0.032 2192 Dihedral : 6.344 60.891 1771 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.77 % Allowed : 26.24 % Favored : 69.98 % 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: 1.06 (0.22), residues: 1525 helix: 1.62 (0.16), residues: 984 sheet: -1.33 (0.41), residues: 161 loop : -0.68 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 511 HIS 0.006 0.001 HIS B 175 PHE 0.027 0.001 PHE A 192 TYR 0.011 0.001 TYR B 207 ARG 0.005 0.000 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 830) hydrogen bonds : angle 5.30577 ( 2445) covalent geometry : bond 0.00338 (12831) covalent geometry : angle 0.66176 (17410) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6731.53 seconds wall clock time: 118 minutes 44.51 seconds (7124.51 seconds total)