Starting phenix.real_space_refine on Sat Aug 23 14:22:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k52_36893/08_2025/8k52_36893.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k52_36893/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8k52_36893/08_2025/8k52_36893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k52_36893/08_2025/8k52_36893.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k52_36893/08_2025/8k52_36893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k52_36893/08_2025/8k52_36893.map" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.49, per 1000 atoms: 0.28 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: 0.97 Conformation dependent library (CDL) restraints added in 808.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.40 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: 2.24 Time building geometry restraints manager: 1.34 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 1002)) selection = (chain 'B' and (resid 23 through 51 or resid 77 through 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: 2.000 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.750 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.080 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:8.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.820 ------------------------------------------------------------------------------- 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 : 15.68 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.015 0.001 ARG A 779 TYR 0.021 0.001 TYR B 207 PHE 0.028 0.002 PHE A 544 TRP 0.023 0.002 TRP B 511 HIS 0.007 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00448 (12831) covalent geometry : angle 0.75711 (17410) hydrogen bonds : bond 0.10161 ( 830) hydrogen bonds : angle 6.01331 ( 2445) *********************** 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 : 0.378 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: 0.4285 time to fit residues: 89.3298 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 : 0.489 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0040 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 0.4530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 535 GLN A 619 GLN B 256 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.100138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.082098 restraints weight = 29011.671| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.25 r_work: 0.3180 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12831 Z= 0.133 Angle : 0.590 13.142 17410 Z= 0.299 Chirality : 0.040 0.159 1908 Planarity : 0.004 0.054 2192 Dihedral : 7.108 82.282 1801 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.68 % Allowed : 25.34 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.22), residues: 1525 helix: 1.67 (0.17), residues: 975 sheet: -0.31 (0.45), residues: 144 loop : -0.80 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 779 TYR 0.018 0.001 TYR A 492 PHE 0.034 0.001 PHE A 487 TRP 0.012 0.001 TRP B 511 HIS 0.004 0.001 HIS B 846 Details of bonding type rmsd covalent geometry : bond 0.00289 (12831) covalent geometry : angle 0.59036 (17410) hydrogen bonds : bond 0.03722 ( 830) hydrogen bonds : angle 5.19956 ( 2445) *********************** 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 212 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 150 time to evaluate : 0.609 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: 0.8932 (tppt) cc_final: 0.8660 (mmtt) REVERT: A 143 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8534 (mm) REVERT: A 148 PHE cc_start: 0.7457 (t80) cc_final: 0.6698 (t80) REVERT: A 325 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8350 (mt0) REVERT: A 403 HIS cc_start: 0.7789 (OUTLIER) cc_final: 0.7466 (m-70) REVERT: A 491 MET cc_start: 0.8142 (ttm) cc_final: 0.7834 (ttm) REVERT: A 493 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.5797 (mm) REVERT: A 495 GLU cc_start: 0.8503 (mp0) cc_final: 0.8260 (mp0) REVERT: A 528 ASP cc_start: 0.8197 (t0) cc_final: 0.7855 (t0) REVERT: B 114 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8368 (mmm160) REVERT: B 208 CYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8078 (t) REVERT: B 491 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.6831 (tmm) REVERT: B 528 ASP cc_start: 0.8076 (t0) cc_final: 0.7788 (t0) REVERT: B 725 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8084 (t80) REVERT: B 780 ARG cc_start: 0.9176 (ttm110) cc_final: 0.8565 (mpt-90) REVERT: B 814 PHE cc_start: 0.9039 (m-10) cc_final: 0.7960 (t80) outliers start: 62 outliers final: 28 residues processed: 197 average time/residue: 0.3608 time to fit residues: 80.6964 Evaluate side-chains 165 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 289 VAL Chi-restraints excluded: chain A residue 317 ILE 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 493 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 615 SER 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 733 SER Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 114 ARG 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 359 LEU Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 PHE 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 38 optimal weight: 0.0980 chunk 49 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 98 optimal weight: 0.3980 chunk 6 optimal weight: 0.4980 chunk 104 optimal weight: 5.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.099449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.081225 restraints weight = 29327.156| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.27 r_work: 0.3162 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12831 Z= 0.126 Angle : 0.569 11.388 17410 Z= 0.286 Chirality : 0.039 0.182 1908 Planarity : 0.004 0.035 2192 Dihedral : 6.850 84.964 1787 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.05 % Allowed : 24.51 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.22), residues: 1525 helix: 1.81 (0.17), residues: 970 sheet: -0.33 (0.46), residues: 138 loop : -0.82 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 779 TYR 0.015 0.001 TYR B 473 PHE 0.017 0.001 PHE A 487 TRP 0.013 0.001 TRP B 511 HIS 0.004 0.001 HIS B 846 Details of bonding type rmsd covalent geometry : bond 0.00268 (12831) covalent geometry : angle 0.56918 (17410) hydrogen bonds : bond 0.03587 ( 830) hydrogen bonds : angle 5.09912 ( 2445) *********************** 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 213 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 146 time to evaluate : 0.464 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 143 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8473 (mm) REVERT: A 184 TRP cc_start: 0.7610 (OUTLIER) cc_final: 0.7296 (t60) REVERT: A 325 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8690 (mm110) REVERT: A 403 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7506 (m-70) REVERT: A 528 ASP cc_start: 0.8154 (t0) cc_final: 0.7818 (t0) REVERT: A 537 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8425 (tptp) REVERT: B 114 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8432 (mmm160) REVERT: B 148 PHE cc_start: 0.7014 (m-10) cc_final: 0.6777 (t80) REVERT: B 208 CYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8047 (t) REVERT: B 330 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7848 (mp0) REVERT: B 381 MET cc_start: 0.9172 (ptt) cc_final: 0.8875 (ptt) REVERT: B 491 MET cc_start: 0.7759 (ttp) cc_final: 0.6782 (tmm) REVERT: B 528 ASP cc_start: 0.8006 (t0) cc_final: 0.7721 (t0) REVERT: B 725 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7940 (t80) REVERT: B 780 ARG cc_start: 0.9159 (ttm110) cc_final: 0.8623 (mmt90) REVERT: B 814 PHE cc_start: 0.9022 (m-10) cc_final: 0.7665 (t80) outliers start: 67 outliers final: 31 residues processed: 197 average time/residue: 0.3373 time to fit residues: 75.4131 Evaluate side-chains 169 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 201 MET 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 516 VAL 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 712 PHE Chi-restraints excluded: chain A residue 713 MET 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 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 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 297 HIS 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 359 LEU Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 PHE 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 90 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 132 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 GLN B 836 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.089475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.070990 restraints weight = 29000.429| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.11 r_work: 0.2949 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12831 Z= 0.185 Angle : 0.628 10.548 17410 Z= 0.320 Chirality : 0.042 0.173 1908 Planarity : 0.004 0.034 2192 Dihedral : 7.032 84.905 1784 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 6.71 % Allowed : 22.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.22), residues: 1525 helix: 1.57 (0.16), residues: 976 sheet: -0.93 (0.44), residues: 154 loop : -0.78 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 779 TYR 0.015 0.002 TYR B 473 PHE 0.023 0.002 PHE B 549 TRP 0.020 0.001 TRP A 511 HIS 0.007 0.001 HIS B 846 Details of bonding type rmsd covalent geometry : bond 0.00408 (12831) covalent geometry : angle 0.62754 (17410) hydrogen bonds : bond 0.03898 ( 830) hydrogen bonds : angle 5.20630 ( 2445) *********************** 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 223 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 134 time to evaluate : 0.336 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 493 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 102 ASP cc_start: 0.9315 (t0) cc_final: 0.9041 (m-30) REVERT: A 264 MET cc_start: 0.8466 (pmm) cc_final: 0.8247 (pmm) REVERT: A 312 GLU cc_start: 0.8370 (tp30) cc_final: 0.8158 (pm20) REVERT: A 325 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8677 (mm110) REVERT: A 403 HIS cc_start: 0.8189 (OUTLIER) cc_final: 0.7953 (m-70) REVERT: A 493 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6555 (mt) REVERT: A 528 ASP cc_start: 0.8344 (t0) cc_final: 0.8004 (t0) REVERT: A 537 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8608 (tptp) REVERT: A 565 PHE cc_start: 0.7750 (t80) cc_final: 0.7477 (t80) REVERT: B 29 MET cc_start: 0.6181 (ttt) cc_final: 0.5761 (ttt) REVERT: B 114 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8416 (mmm160) REVERT: B 208 CYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8351 (t) REVERT: B 210 HIS cc_start: 0.8279 (m-70) cc_final: 0.8069 (m-70) REVERT: B 491 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7380 (tmm) REVERT: B 528 ASP cc_start: 0.8210 (t0) cc_final: 0.7921 (t0) REVERT: B 565 PHE cc_start: 0.7639 (t80) cc_final: 0.7410 (t80) REVERT: B 641 ILE cc_start: 0.9030 (pp) cc_final: 0.8751 (mt) REVERT: B 672 LEU cc_start: 0.9198 (mm) cc_final: 0.8979 (mt) REVERT: B 725 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.8074 (t80) REVERT: B 776 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8653 (pm20) REVERT: B 780 ARG cc_start: 0.9126 (ttm110) cc_final: 0.8651 (mmt90) outliers start: 89 outliers final: 35 residues processed: 200 average time/residue: 0.3384 time to fit residues: 75.9255 Evaluate side-chains 164 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 359 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 511 TRP 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 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 816 VAL Chi-restraints excluded: chain A residue 823 THR 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 206 VAL 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 333 LEU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 712 PHE 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 776 GLU Chi-restraints excluded: chain B residue 823 THR 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 58 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 420 ASN ** A 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.087025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.068650 restraints weight = 29424.249| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.04 r_work: 0.2901 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12831 Z= 0.187 Angle : 0.626 13.786 17410 Z= 0.315 Chirality : 0.041 0.174 1908 Planarity : 0.004 0.043 2192 Dihedral : 6.802 75.288 1780 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.20 % Allowed : 25.11 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.22), residues: 1525 helix: 1.57 (0.16), residues: 982 sheet: -1.30 (0.44), residues: 150 loop : -0.74 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 779 TYR 0.013 0.001 TYR A 492 PHE 0.027 0.001 PHE A 487 TRP 0.017 0.001 TRP B 511 HIS 0.006 0.001 HIS B 846 Details of bonding type rmsd covalent geometry : bond 0.00415 (12831) covalent geometry : angle 0.62556 (17410) hydrogen bonds : bond 0.03745 ( 830) hydrogen bonds : angle 5.26011 ( 2445) *********************** 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 197 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 128 time to evaluate : 0.407 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 102 ASP cc_start: 0.9307 (t0) cc_final: 0.9042 (m-30) REVERT: A 325 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8734 (mm110) REVERT: A 403 HIS cc_start: 0.8248 (OUTLIER) cc_final: 0.8028 (m-70) REVERT: A 528 ASP cc_start: 0.8291 (t0) cc_final: 0.7928 (t0) REVERT: A 537 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8691 (tptp) REVERT: A 725 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7952 (t80) REVERT: A 779 ARG cc_start: 0.9089 (mtp-110) cc_final: 0.8881 (mtp-110) REVERT: B 114 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8330 (mmm160) REVERT: B 138 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7937 (pptt) REVERT: B 325 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8769 (mm110) REVERT: B 491 MET cc_start: 0.7881 (ttp) cc_final: 0.7547 (tmm) REVERT: B 528 ASP cc_start: 0.8237 (t0) cc_final: 0.7936 (t0) REVERT: B 641 ILE cc_start: 0.9022 (pp) cc_final: 0.8703 (mt) REVERT: B 725 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.8060 (t80) REVERT: B 780 ARG cc_start: 0.9203 (ttm110) cc_final: 0.8704 (mmt90) REVERT: B 797 ARG cc_start: 0.8035 (tmm-80) cc_final: 0.7708 (ttp-170) outliers start: 69 outliers final: 35 residues processed: 180 average time/residue: 0.3776 time to fit residues: 76.1794 Evaluate side-chains 151 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 215 SER 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 403 HIS Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 615 SER 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 695 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 823 THR 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 345 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 509 CYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 104 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 134 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 126 optimal weight: 0.4980 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 183 ASN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 ASN A 851 HIS B 175 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 = 0.3415 r_free = 0.3415 target = 0.087576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.069150 restraints weight = 29185.127| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.07 r_work: 0.2905 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12831 Z= 0.145 Angle : 0.609 14.097 17410 Z= 0.304 Chirality : 0.040 0.180 1908 Planarity : 0.004 0.031 2192 Dihedral : 6.707 73.434 1780 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.28 % Allowed : 23.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.22), residues: 1525 helix: 1.65 (0.16), residues: 983 sheet: -1.19 (0.45), residues: 148 loop : -0.72 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 779 TYR 0.010 0.001 TYR A 239 PHE 0.016 0.001 PHE A 545 TRP 0.018 0.001 TRP B 511 HIS 0.005 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00318 (12831) covalent geometry : angle 0.60851 (17410) hydrogen bonds : bond 0.03655 ( 830) hydrogen bonds : angle 5.22114 ( 2445) *********************** 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 185 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 115 time to evaluate : 0.362 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: 0.8299 (mmp80) cc_final: 0.7040 (mpt180) REVERT: A 102 ASP cc_start: 0.9323 (t0) cc_final: 0.9053 (m-30) REVERT: A 264 MET cc_start: 0.8340 (pmm) cc_final: 0.8140 (pmm) REVERT: A 325 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8778 (mm110) REVERT: A 403 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7970 (m-70) REVERT: A 528 ASP cc_start: 0.8277 (t0) cc_final: 0.7912 (t0) REVERT: A 692 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8226 (tp) REVERT: B 114 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8338 (mmm160) REVERT: B 325 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8717 (mm110) REVERT: B 491 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7512 (tmm) REVERT: B 528 ASP cc_start: 0.8221 (t0) cc_final: 0.7914 (t0) REVERT: B 641 ILE cc_start: 0.9015 (pp) cc_final: 0.8684 (mt) REVERT: B 692 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7683 (tp) REVERT: B 780 ARG cc_start: 0.9200 (ttm110) cc_final: 0.8701 (mmt90) outliers start: 70 outliers final: 37 residues processed: 170 average time/residue: 0.3683 time to fit residues: 70.2533 Evaluate side-chains 149 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 107 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 476 THR Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 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 823 THR Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 333 LEU 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 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 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 Chi-restraints excluded: chain B residue 823 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 119 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 112 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 846 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.085767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.067622 restraints weight = 29079.980| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.99 r_work: 0.2877 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12831 Z= 0.164 Angle : 0.642 13.851 17410 Z= 0.319 Chirality : 0.041 0.208 1908 Planarity : 0.004 0.045 2192 Dihedral : 6.642 69.463 1780 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.98 % Allowed : 24.43 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.22), residues: 1525 helix: 1.65 (0.16), residues: 985 sheet: -1.13 (0.44), residues: 149 loop : -0.68 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 779 TYR 0.011 0.001 TYR B 207 PHE 0.017 0.001 PHE A 545 TRP 0.024 0.001 TRP A 511 HIS 0.005 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00364 (12831) covalent geometry : angle 0.64193 (17410) hydrogen bonds : bond 0.03701 ( 830) hydrogen bonds : angle 5.25327 ( 2445) *********************** 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 189 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 123 time to evaluate : 0.392 Fit side-chains TARDY: cannot create tardy model for: "LEU B 493 " (corrupted residue). Skipping it. REVERT: A 26 ARG cc_start: 0.8244 (mmp80) cc_final: 0.7348 (mpt180) REVERT: A 102 ASP cc_start: 0.9330 (t0) cc_final: 0.9067 (m-30) REVERT: A 264 MET cc_start: 0.8479 (pmm) cc_final: 0.8254 (pmm) REVERT: A 325 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8794 (mm110) REVERT: A 381 MET cc_start: 0.9106 (ptp) cc_final: 0.8849 (ptm) REVERT: A 403 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.8002 (m-70) REVERT: A 528 ASP cc_start: 0.8287 (t0) cc_final: 0.7940 (t0) REVERT: A 652 MET cc_start: 0.8305 (mmm) cc_final: 0.7866 (mtt) REVERT: A 725 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8062 (t80) REVERT: A 777 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8112 (tm-30) REVERT: A 781 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8704 (mm-30) REVERT: B 26 ARG cc_start: 0.7930 (mmp80) cc_final: 0.7729 (mpt180) REVERT: B 193 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7980 (ttp) REVERT: B 262 GLU cc_start: 0.8263 (pp20) cc_final: 0.8041 (pp20) REVERT: B 491 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7397 (tmm) REVERT: B 528 ASP cc_start: 0.8286 (t0) cc_final: 0.7996 (t0) REVERT: B 641 ILE cc_start: 0.9010 (pp) cc_final: 0.8719 (mt) REVERT: B 692 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7650 (tp) REVERT: B 780 ARG cc_start: 0.9208 (ttm110) cc_final: 0.8684 (mmt90) outliers start: 66 outliers final: 34 residues processed: 174 average time/residue: 0.3805 time to fit residues: 74.1378 Evaluate side-chains 151 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 385 THR Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 476 THR 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 778 LEU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 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 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 Chi-restraints excluded: chain B residue 823 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 35 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 295 GLN B 346 GLN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.085417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.067594 restraints weight = 28753.009| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.95 r_work: 0.2878 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12831 Z= 0.156 Angle : 0.641 14.129 17410 Z= 0.317 Chirality : 0.041 0.250 1908 Planarity : 0.004 0.035 2192 Dihedral : 6.528 67.551 1776 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.77 % Allowed : 25.57 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.22), residues: 1525 helix: 1.67 (0.16), residues: 985 sheet: -0.99 (0.43), residues: 153 loop : -0.77 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 779 TYR 0.013 0.001 TYR B 207 PHE 0.017 0.001 PHE A 545 TRP 0.030 0.001 TRP A 511 HIS 0.005 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00348 (12831) covalent geometry : angle 0.64097 (17410) hydrogen bonds : bond 0.03676 ( 830) hydrogen bonds : angle 5.26282 ( 2445) *********************** 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: 50 poor density : 115 time to evaluate : 0.341 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: 0.8183 (mmp80) cc_final: 0.7549 (mpt180) REVERT: A 102 ASP cc_start: 0.9301 (t0) cc_final: 0.9037 (m-30) REVERT: A 264 MET cc_start: 0.8508 (pmm) cc_final: 0.8297 (pmm) REVERT: A 325 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8815 (mm110) REVERT: A 403 HIS cc_start: 0.8217 (OUTLIER) cc_final: 0.7844 (m170) REVERT: A 491 MET cc_start: 0.7391 (ttm) cc_final: 0.7091 (tpp) REVERT: A 511 TRP cc_start: 0.7767 (OUTLIER) cc_final: 0.7414 (m-10) REVERT: A 528 ASP cc_start: 0.8287 (t0) cc_final: 0.7943 (t0) REVERT: A 652 MET cc_start: 0.8210 (mmm) cc_final: 0.7829 (mtt) REVERT: A 777 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8043 (tm-30) REVERT: A 781 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8631 (mm-30) REVERT: B 325 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8231 (mt0) REVERT: B 491 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7411 (tmm) REVERT: B 528 ASP cc_start: 0.8288 (t0) cc_final: 0.8000 (t0) REVERT: B 641 ILE cc_start: 0.9034 (pp) cc_final: 0.8747 (mt) REVERT: B 692 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7629 (tp) REVERT: B 780 ARG cc_start: 0.9230 (ttm110) cc_final: 0.8677 (mmt90) outliers start: 50 outliers final: 30 residues processed: 154 average time/residue: 0.3650 time to fit residues: 63.2705 Evaluate side-chains 146 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 452 VAL Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 511 TRP 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 726 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 823 THR 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 288 ILE Chi-restraints excluded: chain B residue 289 VAL 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 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 Chi-restraints excluded: chain B residue 823 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 76 optimal weight: 3.9990 chunk 132 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 263 GLN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.086024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.068238 restraints weight = 28706.355| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.99 r_work: 0.2892 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12831 Z= 0.144 Angle : 0.642 14.263 17410 Z= 0.317 Chirality : 0.041 0.267 1908 Planarity : 0.004 0.030 2192 Dihedral : 6.495 66.430 1776 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.54 % Allowed : 25.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.22), residues: 1525 helix: 1.71 (0.16), residues: 985 sheet: -1.09 (0.44), residues: 146 loop : -0.70 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 779 TYR 0.015 0.001 TYR B 259 PHE 0.017 0.001 PHE A 545 TRP 0.027 0.001 TRP A 511 HIS 0.006 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00320 (12831) covalent geometry : angle 0.64184 (17410) hydrogen bonds : bond 0.03654 ( 830) hydrogen bonds : angle 5.24255 ( 2445) *********************** 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: 47 poor density : 115 time to evaluate : 0.346 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: 0.8130 (mmp80) cc_final: 0.7623 (mpt180) REVERT: A 102 ASP cc_start: 0.9282 (t0) cc_final: 0.8879 (p0) REVERT: A 264 MET cc_start: 0.8525 (pmm) cc_final: 0.8311 (pmm) REVERT: A 325 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8817 (mm110) REVERT: A 403 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7835 (m170) REVERT: A 511 TRP cc_start: 0.7635 (OUTLIER) cc_final: 0.7361 (m-10) REVERT: A 528 ASP cc_start: 0.8283 (t0) cc_final: 0.7934 (t0) REVERT: A 652 MET cc_start: 0.8184 (mmm) cc_final: 0.7885 (mtt) REVERT: A 777 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8065 (tm-30) REVERT: A 781 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8637 (mm-30) REVERT: B 325 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8296 (mt0) REVERT: B 381 MET cc_start: 0.9139 (ptt) cc_final: 0.8747 (ptt) REVERT: B 491 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7372 (tmm) REVERT: B 528 ASP cc_start: 0.8265 (t0) cc_final: 0.7975 (t0) REVERT: B 641 ILE cc_start: 0.9024 (pp) cc_final: 0.8721 (mt) REVERT: B 692 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7549 (tp) REVERT: B 780 ARG cc_start: 0.9249 (ttm110) cc_final: 0.8702 (mmt90) outliers start: 47 outliers final: 29 residues processed: 152 average time/residue: 0.3656 time to fit residues: 62.4538 Evaluate side-chains 141 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 403 HIS 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 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 726 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 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 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 Chi-restraints excluded: chain B residue 823 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 12 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 150 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 295 GLN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.085018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.067346 restraints weight = 28957.544| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.94 r_work: 0.2865 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12831 Z= 0.165 Angle : 0.668 14.374 17410 Z= 0.330 Chirality : 0.042 0.283 1908 Planarity : 0.004 0.031 2192 Dihedral : 6.473 65.412 1773 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.87 % Allowed : 26.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.22), residues: 1525 helix: 1.71 (0.16), residues: 985 sheet: -1.00 (0.42), residues: 155 loop : -0.73 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 779 TYR 0.012 0.001 TYR B 492 PHE 0.034 0.001 PHE A 192 TRP 0.028 0.001 TRP A 511 HIS 0.006 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00372 (12831) covalent geometry : angle 0.66820 (17410) hydrogen bonds : bond 0.03701 ( 830) hydrogen bonds : angle 5.26341 ( 2445) ********************** 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 148 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.372 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: 0.8131 (mmp80) cc_final: 0.7677 (mpt180) REVERT: A 102 ASP cc_start: 0.9273 (t0) cc_final: 0.9008 (m-30) REVERT: A 264 MET cc_start: 0.8544 (pmm) cc_final: 0.8334 (pmm) REVERT: A 325 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8795 (mm110) REVERT: A 403 HIS cc_start: 0.8219 (OUTLIER) cc_final: 0.7867 (m170) REVERT: A 511 TRP cc_start: 0.7714 (OUTLIER) cc_final: 0.7365 (m-10) REVERT: A 528 ASP cc_start: 0.8311 (t0) cc_final: 0.7948 (t0) REVERT: A 654 LEU cc_start: 0.8248 (pt) cc_final: 0.7893 (mm) REVERT: A 777 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8053 (tm-30) REVERT: A 781 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8632 (mm-30) REVERT: B 381 MET cc_start: 0.9154 (ptt) cc_final: 0.8800 (ptt) REVERT: B 491 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7382 (tmm) REVERT: B 528 ASP cc_start: 0.8298 (t0) cc_final: 0.8002 (t0) REVERT: B 641 ILE cc_start: 0.9030 (pp) cc_final: 0.8732 (mt) REVERT: B 692 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7552 (tp) REVERT: B 780 ARG cc_start: 0.9256 (ttm110) cc_final: 0.8696 (mmt90) outliers start: 38 outliers final: 29 residues processed: 138 average time/residue: 0.3422 time to fit residues: 53.6145 Evaluate side-chains 141 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 511 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 665 LEU 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 726 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 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 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 Chi-restraints excluded: chain B residue 823 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 7 optimal weight: 0.0170 chunk 2 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN B 836 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.085930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.068299 restraints weight = 28839.242| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.94 r_work: 0.2892 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12831 Z= 0.137 Angle : 0.661 14.778 17410 Z= 0.325 Chirality : 0.041 0.224 1908 Planarity : 0.004 0.032 2192 Dihedral : 6.390 64.881 1771 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.17 % Allowed : 26.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.22), residues: 1525 helix: 1.74 (0.16), residues: 984 sheet: -1.09 (0.44), residues: 151 loop : -0.77 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 779 TYR 0.013 0.001 TYR B 492 PHE 0.016 0.001 PHE A 545 TRP 0.025 0.001 TRP A 511 HIS 0.006 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00305 (12831) covalent geometry : angle 0.66146 (17410) hydrogen bonds : bond 0.03653 ( 830) hydrogen bonds : angle 5.24442 ( 2445) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2746.34 seconds wall clock time: 48 minutes 0.28 seconds (2880.28 seconds total)