Starting phenix.real_space_refine on Thu May 15 03:38:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k52_36893/05_2025/8k52_36893.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k52_36893/05_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_36893/05_2025/8k52_36893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k52_36893/05_2025/8k52_36893.map" model { file = "/net/cci-nas-00/data/ceres_data/8k52_36893/05_2025/8k52_36893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k52_36893/05_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-5687/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: 8.29, per 1000 atoms: 0.66 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: 3.07 Conformation dependent library (CDL) restraints added in 1.6 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: 1.18 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: 3.50 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: 1.870 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: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 30.420 Find NCS groups from input model: 0.760 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: 0.010 Load rotamer database and sin/cos tables:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.280 ------------------------------------------------------------------------------- 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 : 1.351 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: 0.8481 time to fit residues: 178.0802 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 : 1.344 ------------------------------------------------------------------------------- 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 = 0.075437 restraints weight = 28743.295| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.11 r_work: 0.3046 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 83.111 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 : 1.385 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: 0.8956 (tppt) cc_final: 0.8692 (mmtt) REVERT: A 143 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8459 (mm) REVERT: A 148 PHE cc_start: 0.7535 (t80) cc_final: 0.6730 (t80) REVERT: A 184 TRP cc_start: 0.7692 (OUTLIER) cc_final: 0.7333 (t60) REVERT: A 403 HIS cc_start: 0.8088 (OUTLIER) cc_final: 0.7880 (m-70) REVERT: A 491 MET cc_start: 0.8300 (ttm) cc_final: 0.8091 (ttm) REVERT: A 495 GLU cc_start: 0.8833 (mp0) cc_final: 0.8523 (mp0) REVERT: A 528 ASP cc_start: 0.8201 (t0) cc_final: 0.7876 (t0) REVERT: A 565 PHE cc_start: 0.7429 (t80) cc_final: 0.7145 (t80) REVERT: A 771 LYS cc_start: 0.9227 (tppp) cc_final: 0.9020 (mmpt) REVERT: B 30 MET cc_start: 0.4388 (OUTLIER) cc_final: 0.4181 (mpt) REVERT: B 114 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8414 (mmm160) REVERT: B 148 PHE cc_start: 0.7246 (m-10) cc_final: 0.7035 (t80) REVERT: B 208 CYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8083 (t) REVERT: B 330 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7953 (mp0) REVERT: B 491 MET cc_start: 0.8313 (ttp) cc_final: 0.7236 (tmm) REVERT: B 528 ASP cc_start: 0.8183 (t0) cc_final: 0.7895 (t0) REVERT: B 565 PHE cc_start: 0.7398 (t80) cc_final: 0.7166 (t80) REVERT: B 695 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8285 (p) REVERT: B 725 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.8095 (t80) REVERT: B 780 ARG cc_start: 0.9149 (ttm110) cc_final: 0.8619 (mpt-90) REVERT: B 814 PHE cc_start: 0.9062 (m-10) cc_final: 0.7715 (t80) outliers start: 82 outliers final: 29 residues processed: 208 average time/residue: 0.8642 time to fit residues: 202.9841 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 : 1.381 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.9988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.083166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.064854 restraints weight = 29417.350| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.05 r_work: 0.2821 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 12831 Z= 0.287 Angle : 0.695 12.946 17410 Z= 0.358 Chirality : 0.045 0.237 1908 Planarity : 0.005 0.033 2192 Dihedral : 7.276 77.448 1783 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 6.86 % Allowed : 22.02 % Favored : 71.12 % 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: 0.71 (0.22), residues: 1525 helix: 1.34 (0.16), residues: 975 sheet: -1.30 (0.42), residues: 159 loop : -0.82 (0.33), residues: 391 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 0.019 0.002 PHE A 449 TYR 0.020 0.002 TYR B 207 ARG 0.011 0.001 ARG A 779 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 830) hydrogen bonds : angle 5.46881 ( 2445) covalent geometry : bond 0.00643 (12831) covalent geometry : angle 0.69514 (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 218 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 127 time to evaluate : 1.482 Fit side-chains TARDY: cannot create tardy model for: "LEU B 493 " (corrupted residue). Skipping it. REVERT: A 102 ASP cc_start: 0.9325 (t0) cc_final: 0.9038 (m-30) REVERT: A 184 TRP cc_start: 0.7887 (OUTLIER) cc_final: 0.7683 (t60) REVERT: A 264 MET cc_start: 0.8608 (pmm) cc_final: 0.8340 (pmm) REVERT: A 312 GLU cc_start: 0.8420 (tp30) cc_final: 0.8178 (pm20) REVERT: A 528 ASP cc_start: 0.8458 (t0) cc_final: 0.8108 (t0) REVERT: A 537 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8779 (tptp) REVERT: A 654 LEU cc_start: 0.8536 (pt) cc_final: 0.8120 (mm) REVERT: A 725 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8192 (t80) REVERT: B 29 MET cc_start: 0.6742 (ttt) cc_final: 0.6317 (ttt) REVERT: B 114 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8631 (tpp80) REVERT: B 138 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.7923 (pptt) REVERT: B 148 PHE cc_start: 0.7423 (m-10) cc_final: 0.7100 (t80) REVERT: B 264 MET cc_start: 0.8586 (pmm) cc_final: 0.8355 (pmm) REVERT: B 325 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8902 (mm-40) REVERT: B 491 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7553 (tmm) REVERT: B 509 CYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8490 (m) REVERT: B 528 ASP cc_start: 0.8397 (t0) cc_final: 0.8103 (t0) REVERT: B 721 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9160 (tp) REVERT: B 725 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8092 (t80) REVERT: B 776 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8595 (pm20) REVERT: B 780 ARG cc_start: 0.9179 (ttm110) cc_final: 0.8771 (mmt90) outliers start: 91 outliers final: 33 residues processed: 200 average time/residue: 0.9203 time to fit residues: 205.8867 Evaluate side-chains 144 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 101 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 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 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 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 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 830 ILE Chi-restraints excluded: chain B residue 834 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 101 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 50 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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** A 851 HIS B 175 HIS ** B 283 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.085645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.067414 restraints weight = 28595.832| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.99 r_work: 0.2878 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3589 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= 0.141 Angle : 0.596 13.365 17410 Z= 0.302 Chirality : 0.040 0.170 1908 Planarity : 0.004 0.030 2192 Dihedral : 6.799 72.363 1781 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.73 % Allowed : 22.70 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.22), residues: 1525 helix: 1.59 (0.16), residues: 976 sheet: -1.26 (0.45), residues: 147 loop : -0.92 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 511 HIS 0.004 0.001 HIS B 175 PHE 0.015 0.001 PHE A 487 TYR 0.009 0.001 TYR B 207 ARG 0.005 0.000 ARG B 228 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 830) hydrogen bonds : angle 5.32725 ( 2445) covalent geometry : bond 0.00305 (12831) covalent geometry : angle 0.59557 (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 193 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 117 time to evaluate : 1.367 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: 0.9314 (t0) cc_final: 0.9037 (m-30) REVERT: A 264 MET cc_start: 0.8482 (pmm) cc_final: 0.8172 (pmm) REVERT: A 325 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8804 (mm110) REVERT: A 528 ASP cc_start: 0.8339 (t0) cc_final: 0.7996 (t0) REVERT: A 537 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8742 (tptp) REVERT: A 692 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8338 (tp) REVERT: A 725 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.8085 (t80) REVERT: A 777 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8097 (tm-30) REVERT: B 114 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8612 (tpp80) REVERT: B 138 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.7999 (pptt) REVERT: B 148 PHE cc_start: 0.7383 (m-10) cc_final: 0.7096 (t80) REVERT: B 264 MET cc_start: 0.8484 (pmm) cc_final: 0.8230 (pmm) REVERT: B 325 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8393 (mt0) REVERT: B 360 ASP cc_start: 0.9392 (t0) cc_final: 0.9188 (t0) REVERT: B 528 ASP cc_start: 0.8247 (t0) cc_final: 0.7985 (t0) REVERT: B 692 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7717 (tp) REVERT: B 725 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.8006 (t80) REVERT: B 780 ARG cc_start: 0.9186 (ttm110) cc_final: 0.8685 (mmt90) outliers start: 76 outliers final: 34 residues processed: 172 average time/residue: 0.8955 time to fit residues: 173.6363 Evaluate side-chains 146 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 385 THR 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 692 ILE 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 778 LEU 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 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 527 HIS 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 Chi-restraints excluded: chain B residue 834 SER 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: 1.9990 chunk 14 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 113 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 B 175 HIS B 210 HIS B 346 GLN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** 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 = 0.3369 r_free = 0.3369 target = 0.084393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.066229 restraints weight = 28893.498| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.96 r_work: 0.2849 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12831 Z= 0.169 Angle : 0.600 13.482 17410 Z= 0.304 Chirality : 0.041 0.153 1908 Planarity : 0.004 0.034 2192 Dihedral : 6.694 69.936 1779 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 6.11 % Allowed : 22.55 % Favored : 71.34 % 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: 1.67 (0.16), residues: 974 sheet: -1.30 (0.43), residues: 151 loop : -0.88 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 184 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 0.005 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 830) hydrogen bonds : angle 5.28167 ( 2445) covalent geometry : bond 0.00374 (12831) covalent geometry : angle 0.59952 (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 196 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 115 time to evaluate : 1.418 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: 0.8304 (mmp80) cc_final: 0.7075 (mpt180) REVERT: A 102 ASP cc_start: 0.9320 (t0) cc_final: 0.9047 (m-30) REVERT: A 264 MET cc_start: 0.8512 (pmm) cc_final: 0.8233 (pmm) REVERT: A 325 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8799 (mm110) REVERT: A 528 ASP cc_start: 0.8370 (t0) cc_final: 0.8029 (t0) REVERT: A 537 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8745 (tptp) REVERT: A 725 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7982 (t80) REVERT: B 26 ARG cc_start: 0.7979 (mmp80) cc_final: 0.7591 (mpt180) REVERT: B 114 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8598 (tpp80) REVERT: B 138 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8029 (pptt) REVERT: B 148 PHE cc_start: 0.7420 (m-10) cc_final: 0.7195 (t80) REVERT: B 262 GLU cc_start: 0.8331 (pp20) cc_final: 0.8098 (pp20) REVERT: B 264 MET cc_start: 0.8537 (pmm) cc_final: 0.8296 (pmm) REVERT: B 325 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8895 (mm-40) REVERT: B 528 ASP cc_start: 0.8322 (t0) cc_final: 0.8051 (t0) REVERT: B 692 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7731 (tp) REVERT: B 725 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7963 (t80) REVERT: B 780 ARG cc_start: 0.9193 (ttm110) cc_final: 0.8712 (mmt90) outliers start: 81 outliers final: 38 residues processed: 178 average time/residue: 0.8869 time to fit residues: 179.5318 Evaluate side-chains 152 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TRP 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 359 LEU Chi-restraints excluded: chain A residue 385 THR 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 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 114 ARG Chi-restraints excluded: chain B residue 138 LYS 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 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 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: 0.4980 chunk 84 optimal weight: 0.0970 chunk 111 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 12 optimal weight: 0.0050 chunk 103 optimal weight: 1.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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** B 647 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.085991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.068291 restraints weight = 29125.190| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.96 r_work: 0.2899 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4000 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= 0.125 Angle : 0.594 13.600 17410 Z= 0.298 Chirality : 0.040 0.149 1908 Planarity : 0.004 0.033 2192 Dihedral : 6.547 67.525 1779 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.98 % Allowed : 23.76 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.22), residues: 1525 helix: 1.72 (0.16), residues: 976 sheet: -1.12 (0.45), residues: 144 loop : -0.85 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 184 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 0.004 0.000 ARG B 228 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 830) hydrogen bonds : angle 5.21019 ( 2445) covalent geometry : bond 0.00267 (12831) covalent geometry : angle 0.59406 (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 187 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 121 time to evaluate : 1.375 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 493 " (corrupted residue). Skipping it. REVERT: A 102 ASP cc_start: 0.9315 (t0) cc_final: 0.8917 (p0) REVERT: A 325 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8827 (mm110) REVERT: A 359 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8709 (mm) REVERT: A 528 ASP cc_start: 0.8310 (t0) cc_final: 0.7942 (t0) REVERT: A 537 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8643 (tptp) REVERT: A 725 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7844 (t80) REVERT: B 26 ARG cc_start: 0.7976 (mmp80) cc_final: 0.7728 (mpt180) REVERT: B 114 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8338 (mmm160) REVERT: B 148 PHE cc_start: 0.7470 (m-10) cc_final: 0.7190 (t80) REVERT: B 262 GLU cc_start: 0.8305 (pp20) cc_final: 0.8066 (pp20) REVERT: B 325 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8791 (mm-40) REVERT: B 528 ASP cc_start: 0.8234 (t0) cc_final: 0.7963 (t0) REVERT: B 692 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7661 (tp) REVERT: B 780 ARG cc_start: 0.9198 (ttm110) cc_final: 0.8606 (mtt90) outliers start: 66 outliers final: 29 residues processed: 172 average time/residue: 0.7902 time to fit residues: 154.5947 Evaluate side-chains 143 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 MET 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 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 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 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 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 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: 0.5980 chunk 153 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 59 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.085046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.067293 restraints weight = 28941.673| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.94 r_work: 0.2912 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4144 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= 0.144 Angle : 0.618 13.766 17410 Z= 0.306 Chirality : 0.041 0.173 1908 Planarity : 0.004 0.035 2192 Dihedral : 6.540 65.833 1779 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.37 % Allowed : 25.11 % 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: 1.15 (0.22), residues: 1525 helix: 1.73 (0.16), residues: 976 sheet: -1.12 (0.44), residues: 146 loop : -0.81 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 184 HIS 0.005 0.001 HIS B 175 PHE 0.018 0.001 PHE B 725 TYR 0.010 0.001 TYR B 207 ARG 0.005 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 830) hydrogen bonds : angle 5.20130 ( 2445) covalent geometry : bond 0.00316 (12831) covalent geometry : angle 0.61827 (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 176 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 118 time to evaluate : 1.373 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: 0.8291 (mmp80) cc_final: 0.7199 (mpt180) REVERT: A 102 ASP cc_start: 0.9311 (t0) cc_final: 0.8940 (p0) REVERT: A 325 GLN cc_start: 0.9094 (mm-40) cc_final: 0.8852 (mm-40) REVERT: A 359 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8688 (mm) REVERT: A 528 ASP cc_start: 0.8272 (t0) cc_final: 0.7948 (t0) REVERT: A 537 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8709 (tptp) REVERT: A 652 MET cc_start: 0.8180 (mmm) cc_final: 0.7852 (mtt) REVERT: A 725 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7864 (t80) REVERT: B 148 PHE cc_start: 0.7580 (m-10) cc_final: 0.7335 (t80) REVERT: B 325 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8875 (mm-40) REVERT: B 330 GLU cc_start: 0.8609 (mp0) cc_final: 0.8249 (mp0) REVERT: B 528 ASP cc_start: 0.8276 (t0) cc_final: 0.8025 (t0) REVERT: B 692 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7706 (tp) REVERT: B 780 ARG cc_start: 0.9215 (ttm110) cc_final: 0.8613 (mtt90) outliers start: 58 outliers final: 32 residues processed: 162 average time/residue: 0.8880 time to fit residues: 162.1895 Evaluate side-chains 146 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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 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 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 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 564 THR 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 733 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 18 optimal weight: 0.2980 chunk 131 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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** B 619 GLN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.079254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.061669 restraints weight = 29255.710| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.85 r_work: 0.2767 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12831 Z= 0.243 Angle : 0.688 14.382 17410 Z= 0.346 Chirality : 0.044 0.242 1908 Planarity : 0.004 0.034 2192 Dihedral : 6.636 62.689 1773 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.45 % Allowed : 24.74 % 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: 0.98 (0.22), residues: 1525 helix: 1.56 (0.16), residues: 980 sheet: -1.37 (0.41), residues: 166 loop : -0.66 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 511 HIS 0.005 0.001 HIS B 175 PHE 0.015 0.002 PHE B 501 TYR 0.014 0.002 TYR B 207 ARG 0.005 0.000 ARG B 228 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 830) hydrogen bonds : angle 5.41434 ( 2445) covalent geometry : bond 0.00549 (12831) covalent geometry : angle 0.68773 (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 165 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 106 time to evaluate : 1.549 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: 0.8427 (mmp80) cc_final: 0.7468 (mpt180) REVERT: A 102 ASP cc_start: 0.9246 (t0) cc_final: 0.8905 (p0) REVERT: A 184 TRP cc_start: 0.8371 (OUTLIER) cc_final: 0.7947 (t60) REVERT: A 325 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8887 (mm110) REVERT: A 511 TRP cc_start: 0.8091 (OUTLIER) cc_final: 0.7280 (m-10) REVERT: A 528 ASP cc_start: 0.8477 (t0) cc_final: 0.8148 (t0) REVERT: A 537 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8831 (tptp) REVERT: A 654 LEU cc_start: 0.8571 (pt) cc_final: 0.8245 (mm) REVERT: A 725 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8177 (t80) REVERT: B 511 TRP cc_start: 0.8081 (OUTLIER) cc_final: 0.6312 (m-10) REVERT: B 528 ASP cc_start: 0.8447 (t0) cc_final: 0.8200 (t0) REVERT: B 641 ILE cc_start: 0.9143 (pp) cc_final: 0.8868 (mt) REVERT: B 692 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7778 (tp) REVERT: B 721 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9269 (tp) REVERT: B 780 ARG cc_start: 0.9245 (ttm110) cc_final: 0.8836 (mtt90) outliers start: 59 outliers final: 34 residues processed: 152 average time/residue: 0.8607 time to fit residues: 148.5713 Evaluate side-chains 138 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TRP 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 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 149 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.083122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.065635 restraints weight = 28725.794| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.86 r_work: 0.2829 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12831 Z= 0.149 Angle : 0.649 14.524 17410 Z= 0.321 Chirality : 0.042 0.296 1908 Planarity : 0.004 0.035 2192 Dihedral : 6.497 62.168 1773 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.85 % Allowed : 25.79 % Favored : 70.36 % 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: 979 sheet: -1.21 (0.41), residues: 155 loop : -0.69 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 511 HIS 0.007 0.001 HIS B 175 PHE 0.032 0.001 PHE A 192 TYR 0.013 0.001 TYR B 207 ARG 0.006 0.000 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 830) hydrogen bonds : angle 5.37009 ( 2445) covalent geometry : bond 0.00329 (12831) covalent geometry : angle 0.64869 (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 162 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 111 time to evaluate : 1.461 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: 0.8258 (mmp80) cc_final: 0.7535 (mpt180) REVERT: A 102 ASP cc_start: 0.9252 (t0) cc_final: 0.8899 (p0) REVERT: A 325 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8900 (mm110) REVERT: A 490 ASN cc_start: 0.8638 (m110) cc_final: 0.7940 (m110) REVERT: A 528 ASP cc_start: 0.8410 (t0) cc_final: 0.8084 (t0) REVERT: A 537 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8768 (tptp) REVERT: A 654 LEU cc_start: 0.8519 (pt) cc_final: 0.8197 (mm) REVERT: A 725 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7989 (t80) REVERT: B 23 HIS cc_start: 0.7193 (t70) cc_final: 0.6831 (t-90) REVERT: B 102 ASP cc_start: 0.9311 (t0) cc_final: 0.8990 (m-30) REVERT: B 148 PHE cc_start: 0.7646 (m-10) cc_final: 0.7444 (t80) REVERT: B 528 ASP cc_start: 0.8362 (t0) cc_final: 0.8120 (t0) REVERT: B 641 ILE cc_start: 0.9033 (pp) cc_final: 0.8807 (mt) REVERT: B 692 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7686 (tp) REVERT: B 721 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9150 (tp) REVERT: B 780 ARG cc_start: 0.9260 (ttm110) cc_final: 0.8649 (mtt90) outliers start: 51 outliers final: 32 residues processed: 153 average time/residue: 0.8536 time to fit residues: 147.9499 Evaluate side-chains 141 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 359 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 491 MET 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 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 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 435 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 498 ILE 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 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: 0.7980 chunk 10 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 106 optimal weight: 0.0870 chunk 56 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.081970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.064703 restraints weight = 28795.519| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.86 r_work: 0.2838 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4944 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= 0.148 Angle : 0.651 14.655 17410 Z= 0.322 Chirality : 0.042 0.223 1908 Planarity : 0.004 0.034 2192 Dihedral : 6.446 61.897 1771 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.17 % Allowed : 26.62 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.22), residues: 1525 helix: 1.57 (0.16), residues: 990 sheet: -1.40 (0.41), residues: 149 loop : -0.77 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 511 HIS 0.006 0.001 HIS B 175 PHE 0.018 0.001 PHE B 725 TYR 0.012 0.001 TYR B 207 ARG 0.005 0.000 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 830) hydrogen bonds : angle 5.33025 ( 2445) covalent geometry : bond 0.00328 (12831) covalent geometry : angle 0.65129 (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 158 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 1.360 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: 0.8140 (mmp80) cc_final: 0.7635 (mpt180) REVERT: A 102 ASP cc_start: 0.9254 (t0) cc_final: 0.8888 (p0) REVERT: A 325 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8893 (mm110) REVERT: A 490 ASN cc_start: 0.8649 (m110) cc_final: 0.7932 (m110) REVERT: A 528 ASP cc_start: 0.8374 (t0) cc_final: 0.8064 (t0) REVERT: A 537 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8753 (tptp) REVERT: A 652 MET cc_start: 0.7930 (mtp) cc_final: 0.7439 (mtt) REVERT: A 654 LEU cc_start: 0.8543 (pt) cc_final: 0.8231 (mm) REVERT: A 725 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7907 (t80) REVERT: B 23 HIS cc_start: 0.7166 (t70) cc_final: 0.6793 (t-90) REVERT: B 102 ASP cc_start: 0.9313 (t0) cc_final: 0.8991 (m-30) REVERT: B 491 MET cc_start: 0.8152 (ttp) cc_final: 0.7782 (tpt) REVERT: B 528 ASP cc_start: 0.8375 (t0) cc_final: 0.8121 (t0) REVERT: B 641 ILE cc_start: 0.9061 (pp) cc_final: 0.8786 (mt) REVERT: B 692 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7686 (tp) REVERT: B 721 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9190 (tp) REVERT: B 780 ARG cc_start: 0.9258 (ttm110) cc_final: 0.8843 (mtt90) outliers start: 42 outliers final: 31 residues processed: 150 average time/residue: 0.8843 time to fit residues: 149.6396 Evaluate side-chains 142 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 MET 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 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 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 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 435 ILE 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 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 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: 7.9990 chunk 26 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 119 optimal weight: 0.0970 chunk 137 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 95 optimal weight: 0.0770 chunk 146 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN ** 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** B 619 GLN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.083209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.065976 restraints weight = 28855.443| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.86 r_work: 0.2865 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.5006 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= 0.136 Angle : 0.664 14.603 17410 Z= 0.328 Chirality : 0.042 0.259 1908 Planarity : 0.004 0.031 2192 Dihedral : 6.416 61.321 1771 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.24 % Allowed : 26.62 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.22), residues: 1525 helix: 1.60 (0.16), residues: 990 sheet: -1.60 (0.40), residues: 155 loop : -0.77 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 511 HIS 0.006 0.001 HIS B 175 PHE 0.031 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 0.03728 ( 830) hydrogen bonds : angle 5.31599 ( 2445) covalent geometry : bond 0.00296 (12831) covalent geometry : angle 0.66355 (17410) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6500.06 seconds wall clock time: 113 minutes 34.14 seconds (6814.14 seconds total)