Starting phenix.real_space_refine on Thu Jul 2 13:05:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8wam_37397/07_2026/8wam_37397.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wam_37397/07_2026/8wam_37397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8wam_37397/07_2026/8wam_37397.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8wam_37397/07_2026/8wam_37397.cif" model { file = "/net/cci-nas-00/data/ceres_data/8wam_37397/07_2026/8wam_37397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wam_37397/07_2026/8wam_37397.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wam_37397/07_2026/8wam_37397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wam_37397/07_2026/8wam_37397.map" } resolution = 3.23 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= -0.002 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 5612 2.51 5 N 1448 2.21 5 O 1528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8650 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4293 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain breaks: 4 Chain: "B" Number of atoms: 4293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4293 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain breaks: 4 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.05, per 1000 atoms: 0.24 Number of scatterers: 8650 At special positions: 0 Unit cell: (97.455, 77.745, 124.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 6 15.00 Mg 2 11.99 O 1528 8.00 N 1448 7.00 C 5612 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: 0.72 Conformation dependent library (CDL) restraints added in 405.2 milliseconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 65.1% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 174 through 189 removed outlier: 3.511A pdb=" N LYS A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.671A pdb=" N LYS A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 255 Processing helix chain 'A' and resid 268 through 274 removed outlier: 3.810A pdb=" N MET A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 4.474A pdb=" N ALA A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 338 through 357 removed outlier: 4.228A pdb=" N ALA A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Proline residue: A 351 - end of helix Processing helix chain 'A' and resid 379 through 402 removed outlier: 3.577A pdb=" N ILE A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 4.106A pdb=" N ILE A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 456 removed outlier: 3.790A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.671A pdb=" N VAL A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 473 removed outlier: 3.551A pdb=" N GLU A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILE A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 493 removed outlier: 3.665A pdb=" N TYR A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N MET A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 removed outlier: 3.844A pdb=" N ALA A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 541 removed outlier: 3.593A pdb=" N ILE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 562 removed outlier: 3.945A pdb=" N THR A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 579 removed outlier: 3.973A pdb=" N VAL A 574 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N TRP A 575 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N MET A 576 " --> pdb=" O MET A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 595 removed outlier: 4.223A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 removed outlier: 4.004A pdb=" N MET A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 634 through 660 removed outlier: 3.590A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 174 through 189 Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.724A pdb=" N LYS B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 255 Processing helix chain 'B' and resid 268 through 274 removed outlier: 3.854A pdb=" N MET B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.619A pdb=" N PHE B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.525A pdb=" N PHE B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 358 removed outlier: 4.391A pdb=" N ALA B 350 " --> pdb=" O ASP B 346 " (cutoff:3.500A) Proline residue: B 351 - end of helix removed outlier: 3.942A pdb=" N GLU B 358 " --> pdb=" O LYS B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 402 removed outlier: 3.656A pdb=" N ILE B 383 " --> pdb=" O ILE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 removed outlier: 4.468A pdb=" N ILE B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 455 removed outlier: 3.754A pdb=" N GLY B 438 " --> pdb=" O HIS B 434 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU B 439 " --> pdb=" O ASP B 435 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 440 " --> pdb=" O ARG B 436 " (cutoff:3.500A) Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 457 through 473 removed outlier: 3.854A pdb=" N GLU B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA B 464 " --> pdb=" O PRO B 460 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE B 465 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 467 " --> pdb=" O ARG B 463 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 493 removed outlier: 3.719A pdb=" N TYR B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 489 " --> pdb=" O VAL B 485 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 493 " --> pdb=" O LEU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 507 removed outlier: 3.838A pdb=" N ALA B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TRP B 505 " --> pdb=" O THR B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 541 removed outlier: 3.513A pdb=" N ILE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 561 removed outlier: 3.717A pdb=" N THR B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 579 Processing helix chain 'B' and resid 580 through 595 removed outlier: 4.015A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 621 through 630 Processing helix chain 'B' and resid 634 through 660 removed outlier: 3.614A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 91 removed outlier: 3.599A pdb=" N LEU A 84 " --> pdb=" O TYR A 47 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL A 45 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR A 88 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 43 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET A 90 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS A 41 " --> pdb=" O MET A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.124A pdb=" N MET A 97 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 280 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 91 removed outlier: 3.567A pdb=" N LEU B 84 " --> pdb=" O TYR B 47 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 86 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL B 45 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR B 88 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 43 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET B 90 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS B 41 " --> pdb=" O MET B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.271A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N MET B 97 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 278 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL B 289 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 280 " --> pdb=" O LEU B 287 " (cutoff:3.500A) 481 hydrogen bonds defined for protein. 1410 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: 1.31 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2689 1.34 - 1.46: 1657 1.46 - 1.58: 4386 1.58 - 1.69: 10 1.69 - 1.81: 88 Bond restraints: 8830 Sorted by residual: bond pdb=" CA PHE A 646 " pdb=" C PHE A 646 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.30e-02 5.92e+03 1.13e+00 bond pdb=" CA PHE A 647 " pdb=" C PHE A 647 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.27e-02 6.20e+03 8.79e-01 bond pdb=" C GLU B 599 " pdb=" O GLU B 599 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.26e-02 6.30e+03 7.70e-01 bond pdb=" C ILE B 383 " pdb=" O ILE B 383 " ideal model delta sigma weight residual 1.237 1.246 -0.009 1.13e-02 7.83e+03 6.73e-01 bond pdb=" CE1 PHE A 646 " pdb=" CZ PHE A 646 " ideal model delta sigma weight residual 1.382 1.404 -0.022 3.00e-02 1.11e+03 5.17e-01 ... (remaining 8825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 11759 1.28 - 2.55: 155 2.55 - 3.83: 43 3.83 - 5.10: 19 5.10 - 6.38: 4 Bond angle restraints: 11980 Sorted by residual: angle pdb=" CA GLU B 492 " pdb=" CB GLU B 492 " pdb=" CG GLU B 492 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" C VAL B 43 " pdb=" N ASP B 44 " pdb=" CA ASP B 44 " ideal model delta sigma weight residual 122.46 125.78 -3.32 1.41e+00 5.03e-01 5.56e+00 angle pdb=" C VAL A 43 " pdb=" N ASP A 44 " pdb=" CA ASP A 44 " ideal model delta sigma weight residual 122.46 125.72 -3.26 1.41e+00 5.03e-01 5.35e+00 angle pdb=" N PHE A 647 " pdb=" CA PHE A 647 " pdb=" C PHE A 647 " ideal model delta sigma weight residual 111.07 112.96 -1.89 1.07e+00 8.73e-01 3.12e+00 angle pdb=" C PHE A 646 " pdb=" CA PHE A 646 " pdb=" CB PHE A 646 " ideal model delta sigma weight residual 110.79 113.68 -2.89 1.66e+00 3.63e-01 3.04e+00 ... (remaining 11975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 4344 17.63 - 35.26: 622 35.26 - 52.90: 169 52.90 - 70.53: 23 70.53 - 88.16: 4 Dihedral angle restraints: 5162 sinusoidal: 2010 harmonic: 3152 Sorted by residual: dihedral pdb=" CA TRP B 447 " pdb=" C TRP B 447 " pdb=" N GLY B 448 " pdb=" CA GLY B 448 " ideal model delta harmonic sigma weight residual 180.00 163.29 16.71 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CG ARG A 171 " pdb=" CD ARG A 171 " pdb=" NE ARG A 171 " pdb=" CZ ARG A 171 " ideal model delta sinusoidal sigma weight residual 180.00 135.33 44.67 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA ASP A 44 " pdb=" CB ASP A 44 " pdb=" CG ASP A 44 " pdb=" OD1 ASP A 44 " ideal model delta sinusoidal sigma weight residual -30.00 -85.64 55.64 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 5159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 898 0.026 - 0.052: 303 0.052 - 0.078: 145 0.078 - 0.104: 56 0.104 - 0.130: 18 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA ILE B 129 " pdb=" N ILE B 129 " pdb=" C ILE B 129 " pdb=" CB ILE B 129 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE A 129 " pdb=" N ILE A 129 " pdb=" C ILE A 129 " pdb=" CB ILE A 129 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA VAL A 261 " pdb=" N VAL A 261 " pdb=" C VAL A 261 " pdb=" CB VAL A 261 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1417 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 646 " 0.014 2.00e-02 2.50e+03 1.53e-02 4.08e+00 pdb=" CG PHE A 646 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE A 646 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 646 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 646 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 646 " -0.021 2.00e-02 2.50e+03 pdb=" CZ PHE A 646 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 492 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.60e+00 pdb=" C GLU B 492 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU B 492 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU B 493 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 305 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO A 306 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 306 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 306 " -0.026 5.00e-02 4.00e+02 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 899 2.75 - 3.29: 8168 3.29 - 3.82: 14286 3.82 - 4.36: 15239 4.36 - 4.90: 27932 Nonbonded interactions: 66524 Sorted by model distance: nonbonded pdb=" OG SER A 108 " pdb=" OD2 ASP A 231 " model vdw 2.211 3.040 nonbonded pdb=" O GLU B 599 " pdb=" NE ARG B 602 " model vdw 2.232 3.120 nonbonded pdb=" O SER B 596 " pdb=" OG SER B 596 " model vdw 2.395 3.040 nonbonded pdb=" OG1 THR A 240 " pdb=" OD1 ASN B 321 " model vdw 2.400 3.040 nonbonded pdb=" O SER B 548 " pdb=" OG1 THR B 552 " model vdw 2.405 3.040 ... (remaining 66519 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.270 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.002 0.022 8830 Z= 0.095 Angle : 0.450 6.377 11980 Z= 0.230 Chirality : 0.036 0.130 1420 Planarity : 0.003 0.047 1460 Dihedral : 17.164 88.161 3138 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.11 % Allowed : 27.09 % Favored : 72.81 % 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 are not related in a simple way. whole: 1.70 (0.26), residues: 1082 helix: 2.22 (0.21), residues: 638 sheet: 1.47 (0.62), residues: 80 loop : -1.00 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 293 TYR 0.004 0.001 TYR A 430 PHE 0.021 0.001 PHE A 647 TRP 0.015 0.001 TRP B 505 HIS 0.002 0.000 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.09 ( 8830) covalent geometry : angle 0.45025 / 0.23 (11980) hydrogen bonds : bond 0.12619 / 8.89 ( 481) hydrogen bonds : angle 4.72009 / 3.18 ( 1410) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.323 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.1059 time to fit residues: 16.2259 Evaluate side-chains 110 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 GLN B 484 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.185201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.147311 restraints weight = 10806.750| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.42 r_work: 0.3590 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8830 Z= 0.213 Angle : 0.602 6.743 11980 Z= 0.303 Chirality : 0.043 0.154 1420 Planarity : 0.004 0.042 1460 Dihedral : 6.739 89.856 1203 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.89 % Allowed : 25.05 % Favored : 72.06 % 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 are not related in a simple way. whole: 1.17 (0.26), residues: 1082 helix: 1.63 (0.20), residues: 662 sheet: 1.03 (0.59), residues: 80 loop : -0.99 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 602 TYR 0.017 0.002 TYR B 594 PHE 0.022 0.002 PHE A 499 TRP 0.013 0.002 TRP A 447 HIS 0.005 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.21 ( 8830) covalent geometry : angle 0.60229 / 0.30 (11980) hydrogen bonds : bond 0.05183 / 3.57 ( 481) hydrogen bonds : angle 3.85785 / 2.63 ( 1410) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.322 Fit side-chains REVERT: A 97 MET cc_start: 0.7625 (tpt) cc_final: 0.7076 (tpt) REVERT: A 170 PRO cc_start: 0.6729 (Cg_exo) cc_final: 0.6520 (Cg_endo) REVERT: A 310 MET cc_start: 0.4396 (ppp) cc_final: 0.3496 (ppp) REVERT: A 573 MET cc_start: 0.7607 (mmt) cc_final: 0.7167 (mmt) REVERT: B 265 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.6732 (t-170) outliers start: 27 outliers final: 16 residues processed: 132 average time/residue: 0.1184 time to fit residues: 20.7733 Evaluate side-chains 125 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.189336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.151408 restraints weight = 10868.997| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.43 r_work: 0.3632 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8830 Z= 0.110 Angle : 0.470 5.722 11980 Z= 0.236 Chirality : 0.038 0.131 1420 Planarity : 0.003 0.039 1460 Dihedral : 6.402 88.758 1200 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.71 % Allowed : 25.37 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.26), residues: 1082 helix: 1.89 (0.21), residues: 660 sheet: 1.03 (0.57), residues: 80 loop : -0.99 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 168 TYR 0.008 0.001 TYR B 594 PHE 0.011 0.001 PHE A 499 TRP 0.011 0.001 TRP A 447 HIS 0.003 0.001 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8830) covalent geometry : angle 0.47001 / 0.24 (11980) hydrogen bonds : bond 0.03938 / 2.71 ( 481) hydrogen bonds : angle 3.61289 / 2.46 ( 1410) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.339 Fit side-chains REVERT: A 97 MET cc_start: 0.7603 (tpt) cc_final: 0.7098 (tpt) REVERT: A 310 MET cc_start: 0.4527 (ppp) cc_final: 0.3628 (ppp) REVERT: A 573 MET cc_start: 0.7582 (mmt) cc_final: 0.7096 (mmt) REVERT: A 603 MET cc_start: 0.5077 (mpp) cc_final: 0.4013 (mtt) REVERT: B 196 ASN cc_start: 0.8220 (t0) cc_final: 0.7851 (t0) REVERT: B 265 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.6684 (t-170) outliers start: 16 outliers final: 10 residues processed: 128 average time/residue: 0.1220 time to fit residues: 20.5728 Evaluate side-chains 117 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.183414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.145548 restraints weight = 10962.717| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.40 r_work: 0.3566 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8830 Z= 0.189 Angle : 0.565 6.661 11980 Z= 0.282 Chirality : 0.041 0.144 1420 Planarity : 0.004 0.039 1460 Dihedral : 6.349 83.855 1200 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.75 % Allowed : 24.41 % Favored : 71.84 % 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 are not related in a simple way. whole: 1.04 (0.26), residues: 1082 helix: 1.54 (0.20), residues: 662 sheet: 0.53 (0.57), residues: 82 loop : -0.95 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 293 TYR 0.021 0.002 TYR B 594 PHE 0.019 0.002 PHE A 499 TRP 0.014 0.002 TRP B 505 HIS 0.004 0.001 HIS B 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.19 ( 8830) covalent geometry : angle 0.56512 / 0.28 (11980) hydrogen bonds : bond 0.04933 / 3.39 ( 481) hydrogen bonds : angle 3.69895 / 2.52 ( 1410) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.332 Fit side-chains REVERT: A 97 MET cc_start: 0.7757 (tpt) cc_final: 0.7363 (ttm) REVERT: A 196 ASN cc_start: 0.8149 (t0) cc_final: 0.7843 (t0) REVERT: A 265 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.6938 (t-170) REVERT: A 310 MET cc_start: 0.4656 (ppp) cc_final: 0.3707 (ppp) REVERT: A 603 MET cc_start: 0.5237 (mpp) cc_final: 0.4091 (mtt) REVERT: A 623 ARG cc_start: 0.5555 (OUTLIER) cc_final: 0.5273 (ptp-170) REVERT: B 196 ASN cc_start: 0.8247 (t0) cc_final: 0.7894 (t0) REVERT: B 224 ASN cc_start: 0.7567 (m-40) cc_final: 0.7277 (p0) REVERT: B 265 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.6852 (t-170) REVERT: B 310 MET cc_start: 0.4093 (ppp) cc_final: 0.3336 (ppp) REVERT: B 528 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7853 (mp) outliers start: 35 outliers final: 24 residues processed: 146 average time/residue: 0.1125 time to fit residues: 21.4183 Evaluate side-chains 139 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 ASN A 484 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.185114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.146918 restraints weight = 11039.450| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.44 r_work: 0.3570 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8830 Z= 0.171 Angle : 0.536 6.333 11980 Z= 0.269 Chirality : 0.040 0.137 1420 Planarity : 0.004 0.040 1460 Dihedral : 6.264 81.834 1200 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.07 % Allowed : 25.05 % Favored : 70.88 % 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 are not related in a simple way. whole: 0.97 (0.26), residues: 1082 helix: 1.50 (0.20), residues: 662 sheet: 0.46 (0.57), residues: 82 loop : -1.02 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 293 TYR 0.020 0.002 TYR B 594 PHE 0.016 0.001 PHE A 499 TRP 0.014 0.002 TRP A 447 HIS 0.006 0.001 HIS A 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 ( 8830) covalent geometry : angle 0.53643 / 0.27 (11980) hydrogen bonds : bond 0.04609 / 3.17 ( 481) hydrogen bonds : angle 3.64650 / 2.48 ( 1410) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.323 Fit side-chains REVERT: A 97 MET cc_start: 0.7669 (tpt) cc_final: 0.7289 (ttm) REVERT: A 196 ASN cc_start: 0.8151 (t0) cc_final: 0.7813 (t0) REVERT: A 310 MET cc_start: 0.4636 (ppp) cc_final: 0.3686 (ppp) REVERT: A 397 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.7036 (mp) REVERT: A 492 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6744 (tp30) REVERT: A 603 MET cc_start: 0.5330 (mpp) cc_final: 0.4774 (tmm) REVERT: B 196 ASN cc_start: 0.8289 (t0) cc_final: 0.7946 (t0) REVERT: B 224 ASN cc_start: 0.7883 (m-40) cc_final: 0.7425 (p0) REVERT: B 265 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.6747 (t-170) REVERT: B 310 MET cc_start: 0.4290 (ppp) cc_final: 0.3462 (ppp) REVERT: B 462 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: B 528 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7841 (mp) outliers start: 38 outliers final: 22 residues processed: 147 average time/residue: 0.1017 time to fit residues: 19.8585 Evaluate side-chains 141 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.184725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.146480 restraints weight = 10843.833| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.43 r_work: 0.3567 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8830 Z= 0.151 Angle : 0.526 7.094 11980 Z= 0.264 Chirality : 0.040 0.147 1420 Planarity : 0.004 0.040 1460 Dihedral : 6.227 81.840 1200 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.21 % Allowed : 25.59 % Favored : 71.20 % 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 are not related in a simple way. whole: 0.98 (0.26), residues: 1082 helix: 1.55 (0.20), residues: 662 sheet: 0.28 (0.56), residues: 82 loop : -1.04 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 293 TYR 0.015 0.001 TYR B 594 PHE 0.015 0.001 PHE A 499 TRP 0.015 0.001 TRP A 447 HIS 0.003 0.001 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 8830) covalent geometry : angle 0.52619 / 0.26 (11980) hydrogen bonds : bond 0.04367 / 3.01 ( 481) hydrogen bonds : angle 3.62260 / 2.46 ( 1410) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.335 Fit side-chains REVERT: A 97 MET cc_start: 0.7697 (tpt) cc_final: 0.7351 (ttm) REVERT: A 196 ASN cc_start: 0.8115 (t0) cc_final: 0.7758 (t0) REVERT: A 310 MET cc_start: 0.4673 (ppp) cc_final: 0.3691 (ppp) REVERT: A 492 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6736 (tp30) REVERT: A 573 MET cc_start: 0.7538 (mmt) cc_final: 0.7026 (mmt) REVERT: A 603 MET cc_start: 0.5573 (mpp) cc_final: 0.4982 (tmm) REVERT: B 196 ASN cc_start: 0.8297 (t0) cc_final: 0.7947 (t0) REVERT: B 224 ASN cc_start: 0.7621 (m-40) cc_final: 0.7280 (p0) REVERT: B 265 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.6725 (t-170) REVERT: B 310 MET cc_start: 0.4517 (ppp) cc_final: 0.3686 (ppp) REVERT: B 462 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: B 528 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7841 (mp) REVERT: B 573 MET cc_start: 0.8436 (tpt) cc_final: 0.8076 (tpt) outliers start: 30 outliers final: 23 residues processed: 139 average time/residue: 0.1105 time to fit residues: 20.3936 Evaluate side-chains 137 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 93 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.185539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.147205 restraints weight = 11040.897| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.46 r_work: 0.3577 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8830 Z= 0.140 Angle : 0.510 5.946 11980 Z= 0.256 Chirality : 0.039 0.132 1420 Planarity : 0.003 0.042 1460 Dihedral : 6.189 82.683 1200 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.96 % Allowed : 24.41 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.26), residues: 1082 helix: 1.61 (0.20), residues: 662 sheet: 0.31 (0.56), residues: 82 loop : -1.03 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 293 TYR 0.014 0.001 TYR B 594 PHE 0.014 0.001 PHE B 275 TRP 0.014 0.001 TRP A 447 HIS 0.003 0.001 HIS B 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 8830) covalent geometry : angle 0.51009 / 0.26 (11980) hydrogen bonds : bond 0.04144 / 2.86 ( 481) hydrogen bonds : angle 3.58219 / 2.43 ( 1410) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.231 Fit side-chains REVERT: A 97 MET cc_start: 0.7707 (tpt) cc_final: 0.7377 (ttm) REVERT: A 196 ASN cc_start: 0.8191 (t0) cc_final: 0.7876 (t0) REVERT: A 265 HIS cc_start: 0.7305 (OUTLIER) cc_final: 0.6849 (t-90) REVERT: A 310 MET cc_start: 0.4859 (ppp) cc_final: 0.3907 (ppp) REVERT: A 397 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7099 (tp) REVERT: A 492 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6700 (tp30) REVERT: A 573 MET cc_start: 0.7555 (mmt) cc_final: 0.7084 (mmt) REVERT: A 603 MET cc_start: 0.5711 (mpp) cc_final: 0.5137 (tmm) REVERT: A 623 ARG cc_start: 0.5869 (OUTLIER) cc_final: 0.5498 (ptp-170) REVERT: B 196 ASN cc_start: 0.8311 (t0) cc_final: 0.7960 (t0) REVERT: B 224 ASN cc_start: 0.7612 (m-40) cc_final: 0.7200 (p0) REVERT: B 265 HIS cc_start: 0.7791 (OUTLIER) cc_final: 0.6598 (t-170) REVERT: B 310 MET cc_start: 0.4600 (ppp) cc_final: 0.3768 (ppp) REVERT: B 462 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: B 528 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7749 (mp) REVERT: B 573 MET cc_start: 0.8421 (tpt) cc_final: 0.8121 (tpt) outliers start: 37 outliers final: 25 residues processed: 148 average time/residue: 0.1117 time to fit residues: 21.8990 Evaluate side-chains 145 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 60 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 99 optimal weight: 0.0470 chunk 41 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 ASN B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.186320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.146227 restraints weight = 10747.449| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.51 r_work: 0.3597 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8830 Z= 0.111 Angle : 0.486 6.535 11980 Z= 0.244 Chirality : 0.038 0.132 1420 Planarity : 0.003 0.044 1460 Dihedral : 6.128 83.693 1200 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.10 % Allowed : 25.48 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.26), residues: 1082 helix: 1.78 (0.21), residues: 660 sheet: 0.40 (0.55), residues: 82 loop : -1.03 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 168 TYR 0.010 0.001 TYR B 594 PHE 0.011 0.001 PHE B 275 TRP 0.014 0.001 TRP A 447 HIS 0.002 0.001 HIS B 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 8830) covalent geometry : angle 0.48645 / 0.24 (11980) hydrogen bonds : bond 0.03725 / 2.57 ( 481) hydrogen bonds : angle 3.49129 / 2.37 ( 1410) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.231 Fit side-chains REVERT: A 97 MET cc_start: 0.7684 (tpt) cc_final: 0.7390 (ttm) REVERT: A 196 ASN cc_start: 0.8189 (t0) cc_final: 0.7885 (t0) REVERT: A 265 HIS cc_start: 0.7147 (OUTLIER) cc_final: 0.6871 (t-90) REVERT: A 310 MET cc_start: 0.4801 (ppp) cc_final: 0.3851 (ppp) REVERT: A 397 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7099 (tp) REVERT: A 492 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6677 (tp30) REVERT: A 573 MET cc_start: 0.7551 (mmt) cc_final: 0.6998 (mmt) REVERT: A 603 MET cc_start: 0.5797 (mpp) cc_final: 0.5182 (tmm) REVERT: B 196 ASN cc_start: 0.8287 (t0) cc_final: 0.7949 (t0) REVERT: B 265 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.6805 (t-170) REVERT: B 310 MET cc_start: 0.4543 (ppp) cc_final: 0.3690 (ppp) REVERT: B 462 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6817 (mp0) REVERT: B 528 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7774 (mp) REVERT: B 573 MET cc_start: 0.8433 (tpt) cc_final: 0.8226 (tpt) outliers start: 29 outliers final: 21 residues processed: 140 average time/residue: 0.0993 time to fit residues: 18.3654 Evaluate side-chains 136 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 47 optimal weight: 0.0000 chunk 96 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.187989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.149861 restraints weight = 10936.179| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.47 r_work: 0.3599 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8830 Z= 0.105 Angle : 0.478 6.539 11980 Z= 0.239 Chirality : 0.038 0.126 1420 Planarity : 0.003 0.044 1460 Dihedral : 6.081 84.056 1200 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.10 % Allowed : 25.70 % Favored : 71.20 % 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 are not related in a simple way. whole: 1.29 (0.26), residues: 1082 helix: 1.85 (0.21), residues: 660 sheet: 0.38 (0.55), residues: 82 loop : -1.02 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 168 TYR 0.009 0.001 TYR B 594 PHE 0.010 0.001 PHE A 441 TRP 0.019 0.001 TRP B 505 HIS 0.002 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 ( 8830) covalent geometry : angle 0.47785 / 0.24 (11980) hydrogen bonds : bond 0.03492 / 2.41 ( 481) hydrogen bonds : angle 3.44864 / 2.35 ( 1410) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.337 Fit side-chains REVERT: A 97 MET cc_start: 0.7674 (tpt) cc_final: 0.7366 (ttm) REVERT: A 171 ARG cc_start: 0.5650 (mmm160) cc_final: 0.5327 (mmm160) REVERT: A 196 ASN cc_start: 0.8166 (t0) cc_final: 0.7713 (t0) REVERT: A 265 HIS cc_start: 0.7133 (OUTLIER) cc_final: 0.6852 (t-90) REVERT: A 310 MET cc_start: 0.4779 (ppp) cc_final: 0.3841 (ppp) REVERT: A 397 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7036 (tp) REVERT: A 492 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6682 (tp30) REVERT: A 603 MET cc_start: 0.5734 (mpp) cc_final: 0.5117 (tmm) REVERT: B 168 ARG cc_start: 0.8183 (tpp80) cc_final: 0.7950 (tpp80) REVERT: B 196 ASN cc_start: 0.8288 (t0) cc_final: 0.7921 (t0) REVERT: B 265 HIS cc_start: 0.7726 (OUTLIER) cc_final: 0.6748 (t-170) REVERT: B 310 MET cc_start: 0.4549 (ppp) cc_final: 0.3679 (ppp) REVERT: B 462 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: B 528 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7766 (mp) outliers start: 29 outliers final: 21 residues processed: 143 average time/residue: 0.1080 time to fit residues: 20.5544 Evaluate side-chains 137 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 78 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.187910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.150450 restraints weight = 10774.080| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.38 r_work: 0.3609 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8830 Z= 0.102 Angle : 0.478 6.647 11980 Z= 0.238 Chirality : 0.038 0.139 1420 Planarity : 0.003 0.045 1460 Dihedral : 6.058 84.241 1200 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.78 % Allowed : 26.02 % Favored : 71.20 % 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 are not related in a simple way. whole: 1.31 (0.26), residues: 1082 helix: 1.91 (0.21), residues: 660 sheet: 0.21 (0.55), residues: 80 loop : -1.06 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 270 TYR 0.009 0.001 TYR B 594 PHE 0.012 0.001 PHE B 275 TRP 0.016 0.001 TRP B 505 HIS 0.002 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 8830) covalent geometry : angle 0.47848 / 0.24 (11980) hydrogen bonds : bond 0.03389 / 2.34 ( 481) hydrogen bonds : angle 3.40518 / 2.32 ( 1410) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.323 Fit side-chains REVERT: A 97 MET cc_start: 0.7676 (tpt) cc_final: 0.7371 (ttm) REVERT: A 171 ARG cc_start: 0.5447 (mmm160) cc_final: 0.5183 (mmm160) REVERT: A 196 ASN cc_start: 0.8121 (t0) cc_final: 0.7784 (t0) REVERT: A 265 HIS cc_start: 0.7113 (OUTLIER) cc_final: 0.6844 (t-90) REVERT: A 310 MET cc_start: 0.4794 (ppp) cc_final: 0.3877 (ppp) REVERT: A 397 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7046 (tp) REVERT: A 492 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6676 (tp30) REVERT: A 603 MET cc_start: 0.5729 (mpp) cc_final: 0.5086 (tmm) REVERT: B 168 ARG cc_start: 0.8208 (tpp80) cc_final: 0.7977 (tpp80) REVERT: B 196 ASN cc_start: 0.8276 (t0) cc_final: 0.7914 (t0) REVERT: B 265 HIS cc_start: 0.7697 (OUTLIER) cc_final: 0.6809 (t-170) REVERT: B 310 MET cc_start: 0.4626 (ppp) cc_final: 0.3787 (ppp) REVERT: B 462 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: B 528 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7776 (mp) outliers start: 26 outliers final: 19 residues processed: 135 average time/residue: 0.1162 time to fit residues: 20.9073 Evaluate side-chains 134 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 0.0370 chunk 88 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.185942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.147886 restraints weight = 10864.796| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.44 r_work: 0.3585 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8830 Z= 0.140 Angle : 0.516 6.472 11980 Z= 0.257 Chirality : 0.039 0.142 1420 Planarity : 0.004 0.045 1460 Dihedral : 6.108 83.289 1200 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.00 % Allowed : 26.02 % Favored : 70.99 % 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 are not related in a simple way. whole: 1.21 (0.26), residues: 1082 helix: 1.79 (0.20), residues: 660 sheet: 0.35 (0.55), residues: 82 loop : -1.07 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 270 TYR 0.012 0.001 TYR B 594 PHE 0.015 0.001 PHE B 275 TRP 0.024 0.002 TRP A 505 HIS 0.003 0.001 HIS B 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 8830) covalent geometry : angle 0.51590 / 0.26 (11980) hydrogen bonds : bond 0.03971 / 2.74 ( 481) hydrogen bonds : angle 3.46624 / 2.36 ( 1410) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1972.33 seconds wall clock time: 34 minutes 37.12 seconds (2077.12 seconds total)