Starting phenix.real_space_refine on Mon May 12 06:51:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wam_37397/05_2025/8wam_37397.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wam_37397/05_2025/8wam_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wam_37397/05_2025/8wam_37397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wam_37397/05_2025/8wam_37397.map" model { file = "/net/cci-nas-00/data/ceres_data/8wam_37397/05_2025/8wam_37397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wam_37397/05_2025/8wam_37397.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.43, per 1000 atoms: 0.63 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: 2.22 Conformation dependent library (CDL) restraints added in 946.6 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: 0.81 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: 2.53 Time building geometry restraints manager: 2.60 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 - 17.92: 4369 17.92 - 35.84: 637 35.84 - 53.77: 186 53.77 - 71.69: 25 71.69 - 89.61: 7 Dihedral angle restraints: 5224 sinusoidal: 2072 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 5221 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: 0.05 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: 0.890 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.080 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 26.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 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 : 17.901 89.612 3200 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (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 TRP 0.015 0.001 TRP B 505 HIS 0.002 0.000 HIS B 219 PHE 0.021 0.001 PHE A 647 TYR 0.004 0.001 TYR A 430 ARG 0.006 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.12619 ( 481) hydrogen bonds : angle 4.72009 ( 1410) covalent geometry : bond 0.00176 ( 8830) covalent geometry : angle 0.45025 (11980) *********************** 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 : 0.939 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.2294 time to fit residues: 34.7269 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 : 0.887 ------------------------------------------------------------------------------- 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 92 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 0.0980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN B 147 GLN B 484 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.187497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.149798 restraints weight = 10668.499| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.42 r_work: 0.3623 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8830 Z= 0.177 Angle : 0.544 6.276 11980 Z= 0.275 Chirality : 0.041 0.143 1420 Planarity : 0.004 0.042 1460 Dihedral : 9.927 88.237 1265 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.36 % Allowed : 25.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.26), residues: 1082 helix: 1.81 (0.20), residues: 662 sheet: 1.17 (0.59), residues: 80 loop : -0.98 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 447 HIS 0.004 0.001 HIS B 154 PHE 0.019 0.001 PHE A 499 TYR 0.013 0.002 TYR B 594 ARG 0.007 0.001 ARG B 602 Details of bonding type rmsd hydrogen bonds : bond 0.05071 ( 481) hydrogen bonds : angle 3.83920 ( 1410) covalent geometry : bond 0.00423 ( 8830) covalent geometry : angle 0.54440 (11980) *********************** 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 131 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.984 Fit side-chains REVERT: A 170 PRO cc_start: 0.6859 (Cg_exo) cc_final: 0.6651 (Cg_endo) REVERT: A 573 MET cc_start: 0.7516 (mmt) cc_final: 0.7114 (mmt) REVERT: B 265 HIS cc_start: 0.7671 (OUTLIER) cc_final: 0.6576 (t-170) outliers start: 22 outliers final: 13 residues processed: 125 average time/residue: 0.2271 time to fit residues: 38.4925 Evaluate side-chains 119 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 145 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 SER 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 21 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 0.0040 chunk 45 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN A 265 HIS A 454 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.189349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.151835 restraints weight = 10837.308| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.43 r_work: 0.3644 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8830 Z= 0.110 Angle : 0.467 5.543 11980 Z= 0.236 Chirality : 0.038 0.128 1420 Planarity : 0.003 0.040 1460 Dihedral : 9.325 89.688 1262 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.03 % Allowed : 25.27 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.26), residues: 1082 helix: 1.96 (0.21), residues: 660 sheet: 1.13 (0.57), residues: 80 loop : -0.99 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.003 0.001 HIS A 265 PHE 0.012 0.001 PHE A 499 TYR 0.008 0.001 TYR B 594 ARG 0.004 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 481) hydrogen bonds : angle 3.60401 ( 1410) covalent geometry : bond 0.00247 ( 8830) covalent geometry : angle 0.46739 (11980) *********************** 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 136 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.914 Fit side-chains REVERT: A 310 MET cc_start: 0.4647 (ppp) cc_final: 0.3718 (ppp) REVERT: A 573 MET cc_start: 0.7535 (mmt) cc_final: 0.7086 (mmt) REVERT: B 265 HIS cc_start: 0.7594 (OUTLIER) cc_final: 0.6619 (t-170) REVERT: B 310 MET cc_start: 0.3864 (ppp) cc_final: 0.3138 (ppp) outliers start: 19 outliers final: 13 residues processed: 132 average time/residue: 0.2491 time to fit residues: 43.6700 Evaluate side-chains 121 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 131 ASP Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 381 THR 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 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 286 CYS 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 99 optimal weight: 2.9990 chunk 27 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4199 r_free = 0.4199 target = 0.188397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.150235 restraints weight = 10959.872| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.46 r_work: 0.3608 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8830 Z= 0.146 Angle : 0.502 5.875 11980 Z= 0.254 Chirality : 0.039 0.131 1420 Planarity : 0.003 0.037 1460 Dihedral : 9.175 89.992 1262 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.68 % Allowed : 24.84 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.26), residues: 1082 helix: 1.83 (0.20), residues: 662 sheet: 0.96 (0.57), residues: 80 loop : -0.97 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 447 HIS 0.004 0.001 HIS A 265 PHE 0.015 0.001 PHE A 499 TYR 0.015 0.001 TYR B 594 ARG 0.005 0.000 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 481) hydrogen bonds : angle 3.58213 ( 1410) covalent geometry : bond 0.00350 ( 8830) covalent geometry : angle 0.50233 (11980) *********************** 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 127 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 1.022 Fit side-chains REVERT: A 97 MET cc_start: 0.7530 (tpt) cc_final: 0.7079 (tpt) REVERT: A 310 MET cc_start: 0.4629 (ppp) cc_final: 0.3644 (ppp) REVERT: A 573 MET cc_start: 0.7532 (mmt) cc_final: 0.7026 (mmt) REVERT: B 265 HIS cc_start: 0.7726 (OUTLIER) cc_final: 0.6637 (t-170) REVERT: B 310 MET cc_start: 0.3954 (ppp) cc_final: 0.3222 (ppp) REVERT: B 528 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7926 (mp) outliers start: 25 outliers final: 17 residues processed: 122 average time/residue: 0.2508 time to fit residues: 40.7771 Evaluate side-chains 120 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 381 THR 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 133 LYS Chi-restraints excluded: chain B residue 145 VAL 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 660 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 0.0000 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 32 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.191353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.153621 restraints weight = 10900.561| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.47 r_work: 0.3652 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8830 Z= 0.093 Angle : 0.449 6.391 11980 Z= 0.226 Chirality : 0.037 0.127 1420 Planarity : 0.003 0.038 1460 Dihedral : 8.765 85.708 1262 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.36 % Allowed : 24.95 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.26), residues: 1082 helix: 2.03 (0.21), residues: 660 sheet: 0.90 (0.56), residues: 78 loop : -0.97 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 505 HIS 0.002 0.000 HIS B 265 PHE 0.009 0.001 PHE A 441 TYR 0.009 0.001 TYR B 594 ARG 0.007 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 481) hydrogen bonds : angle 3.42766 ( 1410) covalent geometry : bond 0.00200 ( 8830) covalent geometry : angle 0.44932 (11980) *********************** 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 135 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.955 Fit side-chains REVERT: A 97 MET cc_start: 0.7570 (tpt) cc_final: 0.7080 (tpt) REVERT: A 310 MET cc_start: 0.4576 (ppp) cc_final: 0.3587 (ppp) REVERT: A 573 MET cc_start: 0.7535 (mmt) cc_final: 0.7019 (mmt) REVERT: B 196 ASN cc_start: 0.8229 (t0) cc_final: 0.7911 (t0) REVERT: B 265 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.6664 (t-170) REVERT: B 310 MET cc_start: 0.4285 (ppp) cc_final: 0.3543 (ppp) REVERT: B 394 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8111 (mm) outliers start: 22 outliers final: 17 residues processed: 132 average time/residue: 0.2344 time to fit residues: 41.7875 Evaluate side-chains 124 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS 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 133 LYS 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 394 LEU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 561 THR 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 35 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.184668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.146616 restraints weight = 10765.056| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.41 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: 0.7586 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8830 Z= 0.184 Angle : 0.552 6.771 11980 Z= 0.278 Chirality : 0.041 0.142 1420 Planarity : 0.004 0.046 1460 Dihedral : 8.960 86.369 1262 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.10 % Allowed : 24.20 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1082 helix: 1.67 (0.20), residues: 662 sheet: 0.64 (0.57), residues: 82 loop : -0.99 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 447 HIS 0.004 0.001 HIS A 484 PHE 0.019 0.002 PHE A 499 TYR 0.020 0.002 TYR B 594 ARG 0.007 0.001 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.04647 ( 481) hydrogen bonds : angle 3.57372 ( 1410) covalent geometry : bond 0.00452 ( 8830) covalent geometry : angle 0.55154 (11980) *********************** 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 139 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.943 Fit side-chains REVERT: A 97 MET cc_start: 0.7663 (tpt) cc_final: 0.7190 (ttm) REVERT: A 196 ASN cc_start: 0.8241 (t0) cc_final: 0.7950 (t0) REVERT: A 265 HIS cc_start: 0.7486 (OUTLIER) cc_final: 0.6809 (t-170) REVERT: A 310 MET cc_start: 0.4637 (ppp) cc_final: 0.3664 (ppp) REVERT: A 573 MET cc_start: 0.7666 (mmt) cc_final: 0.7144 (mmt) REVERT: A 623 ARG cc_start: 0.5665 (OUTLIER) cc_final: 0.5359 (ptp-170) REVERT: B 196 ASN cc_start: 0.8271 (t0) cc_final: 0.7951 (t0) REVERT: B 265 HIS cc_start: 0.7877 (OUTLIER) cc_final: 0.6803 (t-170) REVERT: B 310 MET cc_start: 0.4370 (ppp) cc_final: 0.3612 (ppp) REVERT: B 528 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7822 (mp) outliers start: 29 outliers final: 20 residues processed: 134 average time/residue: 0.2699 time to fit residues: 47.4064 Evaluate side-chains 129 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.182497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143600 restraints weight = 11028.684| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.47 r_work: 0.3536 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8830 Z= 0.235 Angle : 0.622 6.603 11980 Z= 0.315 Chirality : 0.044 0.175 1420 Planarity : 0.004 0.047 1460 Dihedral : 9.213 87.746 1262 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.75 % Allowed : 23.55 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1082 helix: 1.31 (0.20), residues: 660 sheet: 0.46 (0.57), residues: 82 loop : -1.07 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 447 HIS 0.005 0.001 HIS B 484 PHE 0.021 0.002 PHE A 499 TYR 0.024 0.002 TYR B 594 ARG 0.012 0.001 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.05424 ( 481) hydrogen bonds : angle 3.78402 ( 1410) covalent geometry : bond 0.00580 ( 8830) covalent geometry : angle 0.62191 (11980) *********************** 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 153 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.879 Fit side-chains REVERT: A 97 MET cc_start: 0.7678 (tpt) cc_final: 0.7357 (ttm) REVERT: A 196 ASN cc_start: 0.8222 (t0) cc_final: 0.7960 (t0) REVERT: A 265 HIS cc_start: 0.7592 (OUTLIER) cc_final: 0.6850 (t-170) REVERT: A 310 MET cc_start: 0.4662 (ppp) cc_final: 0.3693 (ppp) REVERT: A 492 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6626 (tp30) REVERT: A 573 MET cc_start: 0.7599 (mmt) cc_final: 0.7030 (mmt) REVERT: A 603 MET cc_start: 0.4878 (mpp) cc_final: 0.3922 (tmm) REVERT: A 623 ARG cc_start: 0.5847 (OUTLIER) cc_final: 0.5406 (ptp-170) REVERT: B 196 ASN cc_start: 0.8259 (t0) cc_final: 0.7920 (t0) REVERT: B 224 ASN cc_start: 0.7678 (m-40) cc_final: 0.7205 (p0) REVERT: B 265 HIS cc_start: 0.7978 (OUTLIER) cc_final: 0.6821 (t-170) REVERT: B 310 MET cc_start: 0.4494 (ppp) cc_final: 0.3743 (ppp) REVERT: B 462 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: B 528 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7731 (mp) outliers start: 35 outliers final: 24 residues processed: 147 average time/residue: 0.2531 time to fit residues: 48.3456 Evaluate side-chains 141 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 265 HIS 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 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 462 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.184106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.145433 restraints weight = 11084.979| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.49 r_work: 0.3551 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2450 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= 0.174 Angle : 0.553 6.167 11980 Z= 0.280 Chirality : 0.041 0.144 1420 Planarity : 0.004 0.047 1460 Dihedral : 9.097 86.439 1262 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.00 % Allowed : 24.52 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1082 helix: 1.45 (0.20), residues: 660 sheet: 0.37 (0.56), residues: 82 loop : -1.10 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 505 HIS 0.004 0.001 HIS A 427 PHE 0.018 0.001 PHE B 275 TYR 0.018 0.002 TYR B 594 ARG 0.008 0.001 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 481) hydrogen bonds : angle 3.67332 ( 1410) covalent geometry : bond 0.00424 ( 8830) covalent geometry : angle 0.55328 (11980) *********************** 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 146 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.902 Fit side-chains REVERT: A 97 MET cc_start: 0.7720 (tpt) cc_final: 0.7438 (ttm) REVERT: A 196 ASN cc_start: 0.8184 (t0) cc_final: 0.7750 (t0) REVERT: A 265 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.6807 (t-170) REVERT: A 310 MET cc_start: 0.4881 (ppp) cc_final: 0.3933 (ppp) REVERT: A 492 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6628 (tp30) REVERT: A 573 MET cc_start: 0.7592 (mmt) cc_final: 0.6986 (mmt) REVERT: A 603 MET cc_start: 0.5379 (mpp) cc_final: 0.4296 (tmm) REVERT: B 196 ASN cc_start: 0.8253 (t0) cc_final: 0.7913 (t0) REVERT: B 224 ASN cc_start: 0.7716 (m-40) cc_final: 0.7163 (p0) REVERT: B 265 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.6672 (t-170) REVERT: B 310 MET cc_start: 0.4594 (ppp) cc_final: 0.3831 (ppp) REVERT: B 462 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: B 528 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7770 (mp) outliers start: 28 outliers final: 20 residues processed: 141 average time/residue: 0.2404 time to fit residues: 44.8776 Evaluate side-chains 138 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 248 THR Chi-restraints excluded: chain A residue 265 HIS 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 548 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 133 LYS Chi-restraints excluded: chain B residue 145 VAL 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 652 LEU 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 18 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 107 optimal weight: 0.0040 chunk 33 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.187846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.149688 restraints weight = 10954.246| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.49 r_work: 0.3601 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8830 Z= 0.109 Angle : 0.486 6.418 11980 Z= 0.246 Chirality : 0.038 0.132 1420 Planarity : 0.003 0.046 1460 Dihedral : 8.840 84.740 1262 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.25 % Allowed : 25.59 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1082 helix: 1.77 (0.21), residues: 660 sheet: 0.25 (0.55), residues: 80 loop : -1.10 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 505 HIS 0.003 0.001 HIS A 427 PHE 0.013 0.001 PHE B 275 TYR 0.010 0.001 TYR B 594 ARG 0.007 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 481) hydrogen bonds : angle 3.50718 ( 1410) covalent geometry : bond 0.00248 ( 8830) covalent geometry : angle 0.48630 (11980) *********************** 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 136 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.889 Fit side-chains REVERT: A 97 MET cc_start: 0.7714 (tpt) cc_final: 0.7425 (ttm) REVERT: A 171 ARG cc_start: 0.5753 (mmm160) cc_final: 0.5399 (mmm160) REVERT: A 196 ASN cc_start: 0.8102 (t0) cc_final: 0.7798 (t0) REVERT: A 310 MET cc_start: 0.4824 (ppp) cc_final: 0.3893 (ppp) REVERT: A 603 MET cc_start: 0.5373 (mpp) cc_final: 0.4247 (tmm) REVERT: B 196 ASN cc_start: 0.8224 (t0) cc_final: 0.7920 (t0) REVERT: B 265 HIS cc_start: 0.7546 (OUTLIER) cc_final: 0.6608 (t-170) REVERT: B 310 MET cc_start: 0.4595 (ppp) cc_final: 0.3800 (ppp) REVERT: B 462 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: B 528 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7709 (mp) REVERT: B 573 MET cc_start: 0.8095 (tpt) cc_final: 0.7824 (tpt) outliers start: 21 outliers final: 18 residues processed: 132 average time/residue: 0.2447 time to fit residues: 42.6300 Evaluate side-chains 131 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 248 THR 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 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 660 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 96 optimal weight: 0.0870 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 0.0050 chunk 25 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.184364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.145695 restraints weight = 11045.384| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.50 r_work: 0.3560 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8830 Z= 0.169 Angle : 0.546 6.145 11980 Z= 0.275 Chirality : 0.040 0.138 1420 Planarity : 0.004 0.046 1460 Dihedral : 8.912 86.010 1262 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.46 % Allowed : 25.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1082 helix: 1.59 (0.20), residues: 662 sheet: 0.34 (0.55), residues: 82 loop : -1.11 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 505 HIS 0.004 0.001 HIS B 219 PHE 0.017 0.001 PHE B 275 TYR 0.016 0.002 TYR B 594 ARG 0.007 0.001 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 481) hydrogen bonds : angle 3.58640 ( 1410) covalent geometry : bond 0.00411 ( 8830) covalent geometry : angle 0.54595 (11980) ********************** 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: 23 poor density : 114 time to evaluate : 0.895 Fit side-chains REVERT: A 97 MET cc_start: 0.7735 (tpt) cc_final: 0.7491 (ttm) REVERT: A 196 ASN cc_start: 0.8179 (t0) cc_final: 0.7883 (t0) REVERT: A 265 HIS cc_start: 0.7447 (OUTLIER) cc_final: 0.6789 (t-170) REVERT: A 310 MET cc_start: 0.4802 (ppp) cc_final: 0.3867 (ppp) REVERT: A 397 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7187 (tp) REVERT: A 492 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6664 (tp30) REVERT: A 603 MET cc_start: 0.5379 (mpp) cc_final: 0.4264 (tmm) REVERT: B 196 ASN cc_start: 0.8281 (t0) cc_final: 0.7983 (t0) REVERT: B 224 ASN cc_start: 0.7754 (t0) cc_final: 0.7022 (p0) REVERT: B 265 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.6801 (t-170) REVERT: B 310 MET cc_start: 0.4640 (ppp) cc_final: 0.3830 (ppp) REVERT: B 462 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: B 528 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7804 (mp) REVERT: B 573 MET cc_start: 0.8148 (tpt) cc_final: 0.7863 (tpt) outliers start: 23 outliers final: 17 residues processed: 133 average time/residue: 0.2481 time to fit residues: 43.7368 Evaluate side-chains 135 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 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 660 ILE 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 660 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.184591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.146027 restraints weight = 11029.572| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.50 r_work: 0.3555 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8830 Z= 0.161 Angle : 0.539 6.318 11980 Z= 0.272 Chirality : 0.040 0.140 1420 Planarity : 0.004 0.047 1460 Dihedral : 8.959 86.633 1262 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.78 % Allowed : 25.48 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1082 helix: 1.59 (0.20), residues: 660 sheet: 0.31 (0.55), residues: 82 loop : -1.09 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 505 HIS 0.003 0.001 HIS B 427 PHE 0.016 0.001 PHE B 275 TYR 0.016 0.001 TYR B 594 ARG 0.007 0.001 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 481) hydrogen bonds : angle 3.58796 ( 1410) covalent geometry : bond 0.00392 ( 8830) covalent geometry : angle 0.53906 (11980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3866.64 seconds wall clock time: 67 minutes 47.75 seconds (4067.75 seconds total)