Starting phenix.real_space_refine on Sat Dec 28 15:29:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t54_25694/12_2024/7t54_25694.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t54_25694/12_2024/7t54_25694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t54_25694/12_2024/7t54_25694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t54_25694/12_2024/7t54_25694.map" model { file = "/net/cci-nas-00/data/ceres_data/7t54_25694/12_2024/7t54_25694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t54_25694/12_2024/7t54_25694.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 20 5.16 5 C 5310 2.51 5 N 1570 2.21 5 O 1646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8552 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 4245 Classifications: {'peptide': 708} Incomplete info: {'truncation_to_alanine': 386} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 694} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1336 Unresolved non-hydrogen angles: 1697 Unresolved non-hydrogen dihedrals: 1098 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 5, 'TYR:plan': 15, 'ASN:plan1': 22, 'TRP:plan': 2, 'ASP:plan': 33, 'PHE:plan': 22, 'GLU:plan': 19, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 629 Chain: "B" Number of atoms: 4245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 4245 Classifications: {'peptide': 708} Incomplete info: {'truncation_to_alanine': 386} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 694} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1336 Unresolved non-hydrogen angles: 1697 Unresolved non-hydrogen dihedrals: 1098 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 5, 'TYR:plan': 15, 'ASN:plan1': 22, 'TRP:plan': 2, 'ASP:plan': 33, 'PHE:plan': 22, 'GLU:plan': 19, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 629 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.19, per 1000 atoms: 0.72 Number of scatterers: 8552 At special positions: 0 Unit cell: (128.75, 87.55, 135.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 6 15.00 O 1646 8.00 N 1570 7.00 C 5310 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: 2.62 Conformation dependent library (CDL) restraints added in 1.4 seconds 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2628 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 11 sheets defined 62.7% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 21 through 33 Processing helix chain 'A' and resid 38 through 47 removed outlier: 4.059A pdb=" N ILE A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.592A pdb=" N LEU A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 124 through 132 removed outlier: 3.784A pdb=" N CYS A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N SER A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TRP A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 165 through 197 Processing helix chain 'A' and resid 202 through 250 removed outlier: 3.509A pdb=" N SER A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.636A pdb=" N PHE A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 removed outlier: 4.337A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 305 removed outlier: 3.934A pdb=" N ILE A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 326 removed outlier: 3.864A pdb=" N PHE A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 354 removed outlier: 3.912A pdb=" N ILE A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 removed outlier: 3.604A pdb=" N PHE A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 418 removed outlier: 3.845A pdb=" N THR A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 446 Proline residue: A 438 - end of helix Processing helix chain 'A' and resid 448 through 463 removed outlier: 3.762A pdb=" N VAL A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 533 removed outlier: 3.811A pdb=" N LEU A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 553 Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 576 through 582 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.584A pdb=" N ILE A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 608 removed outlier: 4.251A pdb=" N LYS A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 639 removed outlier: 3.673A pdb=" N LYS A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 669 removed outlier: 3.812A pdb=" N HIS A 660 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ALA A 664 " --> pdb=" O HIS A 660 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 669 " --> pdb=" O ILE A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 711 removed outlier: 3.579A pdb=" N LYS A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 722 Processing helix chain 'B' and resid 20 through 34 removed outlier: 4.050A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 removed outlier: 3.611A pdb=" N ILE B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 66 removed outlier: 3.648A pdb=" N LEU B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 124 through 132 removed outlier: 3.926A pdb=" N TRP B 132 " --> pdb=" O PHE B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 165 through 197 Processing helix chain 'B' and resid 202 through 252 removed outlier: 3.574A pdb=" N LEU B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.866A pdb=" N PHE B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 removed outlier: 4.271A pdb=" N ARG B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 305 removed outlier: 3.712A pdb=" N ILE B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 354 removed outlier: 4.679A pdb=" N LYS B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix removed outlier: 3.728A pdb=" N ASN B 332 " --> pdb=" O LYS B 328 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 363 through 418 removed outlier: 3.508A pdb=" N SER B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 446 Proline residue: B 438 - end of helix Processing helix chain 'B' and resid 448 through 460 removed outlier: 3.691A pdb=" N VAL B 454 " --> pdb=" O GLN B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 removed outlier: 4.186A pdb=" N GLU B 470 " --> pdb=" O ALA B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 533 removed outlier: 3.825A pdb=" N LEU B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 553 Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 576 through 582 Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.546A pdb=" N ILE B 592 " --> pdb=" O ASP B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 607 removed outlier: 4.320A pdb=" N LYS B 607 " --> pdb=" O ASP B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 639 removed outlier: 3.592A pdb=" N LYS B 639 " --> pdb=" O ARG B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 658 through 669 removed outlier: 4.985A pdb=" N ALA B 664 " --> pdb=" O HIS B 660 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 669 " --> pdb=" O ILE B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 711 removed outlier: 3.565A pdb=" N LYS B 711 " --> pdb=" O LEU B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 722 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 removed outlier: 3.951A pdb=" N ILE A 88 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 502 through 505 removed outlier: 4.066A pdb=" N ASN A 504 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 491 " --> pdb=" O ASN A 504 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A 491 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS A 540 " --> pdb=" O VAL A 491 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 643 through 646 removed outlier: 6.609A pdb=" N LEU A 644 " --> pdb=" O ILE A 675 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE A 677 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 646 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N TYR A 691 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA A 516 " --> pdb=" O TYR A 691 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N LEU A 693 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL A 518 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 690 " --> pdb=" O SER A 701 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER A 701 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU A 692 " --> pdb=" O VAL A 699 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 574 through 575 removed outlier: 3.688A pdb=" N GLY A 574 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 71 through 72 removed outlier: 3.899A pdb=" N ILE B 88 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 113 removed outlier: 4.072A pdb=" N ILE B 111 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR B 123 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL B 113 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 502 through 505 removed outlier: 4.063A pdb=" N ASN B 504 " --> pdb=" O VAL B 491 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 491 " --> pdb=" O ASN B 504 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL B 491 " --> pdb=" O LYS B 540 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS B 540 " --> pdb=" O VAL B 491 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 643 through 646 removed outlier: 8.724A pdb=" N TYR B 691 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ALA B 516 " --> pdb=" O TYR B 691 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N LEU B 693 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL B 518 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 690 " --> pdb=" O SER B 701 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER B 701 " --> pdb=" O ILE B 690 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 692 " --> pdb=" O VAL B 699 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 574 through 575 655 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3042 1.34 - 1.46: 748 1.46 - 1.58: 4780 1.58 - 1.69: 12 1.69 - 1.81: 36 Bond restraints: 8618 Sorted by residual: bond pdb=" N ILE B 656 " pdb=" CA ILE B 656 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.85e+00 bond pdb=" N ILE A 656 " pdb=" CA ILE A 656 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.48e+00 bond pdb=" N VAL A 250 " pdb=" CA VAL A 250 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.12e+00 bond pdb=" N LEU A 653 " pdb=" CA LEU A 653 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.22e-02 6.72e+03 6.53e+00 bond pdb=" N SER A 655 " pdb=" CA SER A 655 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.41e+00 ... (remaining 8613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 11545 2.01 - 4.03: 245 4.03 - 6.04: 20 6.04 - 8.06: 8 8.06 - 10.07: 2 Bond angle restraints: 11820 Sorted by residual: angle pdb=" N PHE B 478 " pdb=" CA PHE B 478 " pdb=" C PHE B 478 " ideal model delta sigma weight residual 111.36 121.43 -10.07 1.09e+00 8.42e-01 8.53e+01 angle pdb=" N ASP B 477 " pdb=" CA ASP B 477 " pdb=" C ASP B 477 " ideal model delta sigma weight residual 109.07 118.60 -9.53 1.61e+00 3.86e-01 3.51e+01 angle pdb=" C ASP B 654 " pdb=" CA ASP B 654 " pdb=" CB ASP B 654 " ideal model delta sigma weight residual 117.23 111.55 5.68 1.36e+00 5.41e-01 1.74e+01 angle pdb=" C GLU B 648 " pdb=" CA GLU B 648 " pdb=" CB GLU B 648 " ideal model delta sigma weight residual 116.54 112.00 4.54 1.15e+00 7.56e-01 1.56e+01 angle pdb=" C GLU A 44 " pdb=" N MET A 45 " pdb=" CA MET A 45 " ideal model delta sigma weight residual 122.38 115.67 6.71 1.81e+00 3.05e-01 1.37e+01 ... (remaining 11815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 4793 16.13 - 32.26: 231 32.26 - 48.40: 58 48.40 - 64.53: 24 64.53 - 80.66: 2 Dihedral angle restraints: 5108 sinusoidal: 1048 harmonic: 4060 Sorted by residual: dihedral pdb=" N SER B 481 " pdb=" C SER B 481 " pdb=" CA SER B 481 " pdb=" CB SER B 481 " ideal model delta harmonic sigma weight residual 122.80 133.61 -10.81 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" C SER B 481 " pdb=" N SER B 481 " pdb=" CA SER B 481 " pdb=" CB SER B 481 " ideal model delta harmonic sigma weight residual -122.60 -132.85 10.25 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" CA GLU B 339 " pdb=" C GLU B 339 " pdb=" N ASP B 340 " pdb=" CA ASP B 340 " ideal model delta harmonic sigma weight residual 180.00 163.06 16.94 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 5105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1381 0.081 - 0.162: 123 0.162 - 0.242: 4 0.242 - 0.323: 1 0.323 - 0.404: 1 Chirality restraints: 1510 Sorted by residual: chirality pdb=" CA SER B 481 " pdb=" N SER B 481 " pdb=" C SER B 481 " pdb=" CB SER B 481 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CA PHE B 478 " pdb=" N PHE B 478 " pdb=" C PHE B 478 " pdb=" CB PHE B 478 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA ASP B 477 " pdb=" N ASP B 477 " pdb=" C ASP B 477 " pdb=" CB ASP B 477 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1507 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 475 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C SER B 475 " -0.060 2.00e-02 2.50e+03 pdb=" O SER B 475 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP B 476 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 247 " 0.009 2.00e-02 2.50e+03 9.27e-03 1.72e+00 pdb=" CG TYR B 247 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR B 247 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 247 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 247 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 247 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 247 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 247 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 480 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C ILE B 480 " 0.020 2.00e-02 2.50e+03 pdb=" O ILE B 480 " -0.008 2.00e-02 2.50e+03 pdb=" N SER B 481 " -0.007 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 49 2.64 - 3.21: 8175 3.21 - 3.77: 12763 3.77 - 4.34: 14680 4.34 - 4.90: 24423 Nonbonded interactions: 60090 Sorted by model distance: nonbonded pdb=" O ASN A 622 " pdb=" ND2 ASN A 622 " model vdw 2.078 3.120 nonbonded pdb=" OH TYR B 246 " pdb=" OE2 GLU B 461 " model vdw 2.215 3.040 nonbonded pdb=" N SER B 68 " pdb=" O GLU B 140 " model vdw 2.360 3.120 nonbonded pdb=" NH1 ARG B 269 " pdb=" OD1 ASN B 457 " model vdw 2.418 3.120 nonbonded pdb=" OE2 GLU B 339 " pdb=" ND2 ASN B 457 " model vdw 2.426 3.120 ... (remaining 60085 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.770 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8618 Z= 0.253 Angle : 0.696 10.069 11820 Z= 0.464 Chirality : 0.045 0.404 1510 Planarity : 0.003 0.038 1578 Dihedral : 12.143 80.661 2480 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.40 % Favored : 95.53 % Rotamer: Outliers : 0.68 % Allowed : 0.68 % Favored : 98.63 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 7.69 % 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: 0.70 (0.23), residues: 1408 helix: 2.25 (0.19), residues: 786 sheet: -1.46 (0.43), residues: 146 loop : -2.09 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 718 HIS 0.003 0.001 HIS B 249 PHE 0.009 0.001 PHE B 270 TYR 0.022 0.001 TYR B 247 ARG 0.008 0.001 ARG A 498 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 57 average time/residue: 0.2140 time to fit residues: 15.0522 Evaluate side-chains 29 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.4980 chunk 106 optimal weight: 9.9990 chunk 58 optimal weight: 0.0170 chunk 36 optimal weight: 10.0000 chunk 71 optimal weight: 40.0000 chunk 56 optimal weight: 0.0370 chunk 109 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 127 optimal weight: 0.0670 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 ASN B 679 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8618 Z= 0.172 Angle : 0.598 8.640 11820 Z= 0.354 Chirality : 0.042 0.154 1510 Planarity : 0.003 0.053 1578 Dihedral : 7.059 56.397 1518 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.84 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: 0.99 (0.23), residues: 1408 helix: 2.43 (0.18), residues: 822 sheet: -1.09 (0.44), residues: 152 loop : -2.34 (0.25), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 718 HIS 0.003 0.001 HIS B 249 PHE 0.008 0.001 PHE A 361 TYR 0.010 0.001 TYR B 536 ARG 0.005 0.001 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1732 time to fit residues: 7.6866 Evaluate side-chains 26 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 50.0000 chunk 39 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 126 optimal weight: 0.0060 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 GLN B 679 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8618 Z= 0.141 Angle : 0.505 6.434 11820 Z= 0.305 Chirality : 0.040 0.141 1510 Planarity : 0.003 0.036 1578 Dihedral : 6.629 56.096 1518 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.83 % Favored : 95.03 % Rotamer: Outliers : 0.46 % Allowed : 4.11 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.23), residues: 1408 helix: 2.20 (0.18), residues: 832 sheet: -0.35 (0.50), residues: 126 loop : -2.37 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 718 HIS 0.010 0.002 HIS A 679 PHE 0.009 0.001 PHE B 535 TYR 0.007 0.001 TYR B 247 ARG 0.003 0.001 ARG B 458 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 31 average time/residue: 0.2004 time to fit residues: 8.1397 Evaluate side-chains 24 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 40.0000 chunk 60 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 135 optimal weight: 0.0060 chunk 121 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 112 optimal weight: 0.1980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8618 Z= 0.125 Angle : 0.472 6.423 11820 Z= 0.279 Chirality : 0.040 0.131 1510 Planarity : 0.002 0.034 1578 Dihedral : 5.871 54.765 1518 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.97 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.23), residues: 1408 helix: 2.04 (0.18), residues: 836 sheet: 0.10 (0.54), residues: 106 loop : -2.17 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 718 HIS 0.002 0.001 HIS B 679 PHE 0.010 0.001 PHE A 257 TYR 0.006 0.001 TYR B 247 ARG 0.004 0.001 ARG B 489 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1643 time to fit residues: 6.3974 Evaluate side-chains 23 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 30.0000 chunk 1 optimal weight: 30.0000 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 115 optimal weight: 0.4980 chunk 93 optimal weight: 0.7980 chunk 0 optimal weight: 50.0000 chunk 69 optimal weight: 30.0000 chunk 121 optimal weight: 0.0980 chunk 34 optimal weight: 8.9990 chunk 45 optimal weight: 0.4980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 602 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8618 Z= 0.129 Angle : 0.454 4.971 11820 Z= 0.270 Chirality : 0.039 0.124 1510 Planarity : 0.002 0.026 1578 Dihedral : 5.898 51.505 1518 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.99 (0.23), residues: 1408 helix: 2.10 (0.18), residues: 850 sheet: -0.07 (0.53), residues: 106 loop : -2.12 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 718 HIS 0.005 0.001 HIS B 602 PHE 0.010 0.001 PHE A 257 TYR 0.005 0.001 TYR A 247 ARG 0.005 0.001 ARG B 489 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.458 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1462 time to fit residues: 5.6831 Evaluate side-chains 22 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 79 optimal weight: 40.0000 chunk 33 optimal weight: 9.9990 chunk 135 optimal weight: 0.0770 chunk 112 optimal weight: 0.0020 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 0.0010 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 30.0000 chunk 130 optimal weight: 2.9990 overall best weight: 1.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8618 Z= 0.117 Angle : 0.449 5.763 11820 Z= 0.263 Chirality : 0.039 0.122 1510 Planarity : 0.002 0.018 1578 Dihedral : 5.858 59.265 1518 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.23), residues: 1408 helix: 2.21 (0.18), residues: 838 sheet: -0.15 (0.53), residues: 106 loop : -2.06 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 718 HIS 0.001 0.000 HIS B 679 PHE 0.010 0.001 PHE B 257 TYR 0.005 0.001 TYR A 247 ARG 0.005 0.001 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.528 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1447 time to fit residues: 5.4235 Evaluate side-chains 22 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 chunk 114 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 134 optimal weight: 30.0000 chunk 84 optimal weight: 30.0000 chunk 82 optimal weight: 40.0000 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.7360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8618 Z= 0.400 Angle : 0.726 8.039 11820 Z= 0.425 Chirality : 0.042 0.140 1510 Planarity : 0.005 0.055 1578 Dihedral : 7.698 57.772 1518 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.36 (0.22), residues: 1408 helix: 1.11 (0.17), residues: 826 sheet: -1.44 (0.51), residues: 92 loop : -2.41 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 718 HIS 0.006 0.002 HIS A 548 PHE 0.050 0.004 PHE B 361 TYR 0.021 0.002 TYR B 612 ARG 0.006 0.001 ARG A 489 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.458 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1155 time to fit residues: 4.0014 Evaluate side-chains 19 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 91 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 50.0000 chunk 106 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.7600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8618 Z= 0.223 Angle : 0.537 6.095 11820 Z= 0.320 Chirality : 0.040 0.131 1510 Planarity : 0.003 0.026 1578 Dihedral : 6.719 59.542 1518 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.19 (0.23), residues: 1408 helix: 1.59 (0.18), residues: 840 sheet: -1.51 (0.47), residues: 104 loop : -2.30 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 718 HIS 0.003 0.001 HIS B 679 PHE 0.028 0.002 PHE A 361 TYR 0.012 0.001 TYR A 612 ARG 0.005 0.001 ARG B 489 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0879 time to fit residues: 3.6393 Evaluate side-chains 19 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.3980 chunk 125 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 118 optimal weight: 0.4980 chunk 82 optimal weight: 40.0000 chunk 132 optimal weight: 0.0060 overall best weight: 2.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.7755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8618 Z= 0.142 Angle : 0.490 6.155 11820 Z= 0.285 Chirality : 0.040 0.125 1510 Planarity : 0.002 0.019 1578 Dihedral : 6.293 59.426 1518 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.64 (0.23), residues: 1408 helix: 2.02 (0.18), residues: 848 sheet: -1.37 (0.49), residues: 106 loop : -2.36 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 718 HIS 0.001 0.001 HIS B 249 PHE 0.014 0.001 PHE A 361 TYR 0.012 0.001 TYR A 612 ARG 0.005 0.001 ARG B 489 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0904 time to fit residues: 3.4394 Evaluate side-chains 21 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 0.0470 chunk 139 optimal weight: 30.0000 chunk 128 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 68 optimal weight: 0.0060 chunk 88 optimal weight: 40.0000 chunk 118 optimal weight: 9.9990 overall best weight: 4.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.8355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8618 Z= 0.218 Angle : 0.551 7.072 11820 Z= 0.322 Chirality : 0.040 0.133 1510 Planarity : 0.003 0.036 1578 Dihedral : 6.766 57.506 1518 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.27 (0.23), residues: 1408 helix: 1.72 (0.18), residues: 848 sheet: -1.68 (0.48), residues: 108 loop : -2.45 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 718 HIS 0.003 0.001 HIS A 602 PHE 0.024 0.002 PHE B 361 TYR 0.017 0.001 TYR B 612 ARG 0.005 0.001 ARG B 489 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.469 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0932 time to fit residues: 3.5958 Evaluate side-chains 19 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 16 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 46 optimal weight: 40.0000 chunk 114 optimal weight: 4.9990 chunk 14 optimal weight: 40.0000 chunk 20 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 579 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.033058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.026954 restraints weight = 71074.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.027240 restraints weight = 59404.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.027462 restraints weight = 52093.842| |-----------------------------------------------------------------------------| r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.9170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8618 Z= 0.326 Angle : 0.678 14.119 11820 Z= 0.390 Chirality : 0.041 0.139 1510 Planarity : 0.004 0.051 1578 Dihedral : 7.546 53.656 1518 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.85 (0.22), residues: 1408 helix: 0.94 (0.17), residues: 848 sheet: -2.52 (0.43), residues: 110 loop : -3.04 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 718 HIS 0.004 0.002 HIS B 602 PHE 0.026 0.003 PHE B 361 TYR 0.021 0.002 TYR B 612 ARG 0.006 0.001 ARG A 489 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1366.61 seconds wall clock time: 25 minutes 48.13 seconds (1548.13 seconds total)