Starting phenix.real_space_refine on Sun Dec 29 21:56:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dtg_27697/12_2024/8dtg_27697.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dtg_27697/12_2024/8dtg_27697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dtg_27697/12_2024/8dtg_27697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dtg_27697/12_2024/8dtg_27697.map" model { file = "/net/cci-nas-00/data/ceres_data/8dtg_27697/12_2024/8dtg_27697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dtg_27697/12_2024/8dtg_27697.cif" } resolution = 3.9 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= 1.000 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 7290 2.51 5 N 1935 2.21 5 O 2146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11451 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 5985 Classifications: {'peptide': 802} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 766} Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 5466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5466 Classifications: {'peptide': 737} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 702} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 410 Unresolved non-hydrogen dihedrals: 273 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 5, 'ASP:plan': 4, 'GLU:plan': 13, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 179 Time building chain proxies: 8.15, per 1000 atoms: 0.71 Number of scatterers: 11451 At special positions: 0 Unit cell: (97.68, 99.44, 168.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2146 8.00 N 1935 7.00 C 7290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2904 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 4 sheets defined 71.2% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 58 through 73 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 92 through 107 Processing helix chain 'A' and resid 110 through 124 removed outlier: 3.587A pdb=" N LEU A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 141 Processing helix chain 'A' and resid 144 through 165 removed outlier: 3.676A pdb=" N ALA A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 185 through 199 removed outlier: 3.832A pdb=" N TYR A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 219 through 233 removed outlier: 3.528A pdb=" N TYR A 223 " --> pdb=" O TYR A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 253 through 275 Processing helix chain 'A' and resid 276 through 291 removed outlier: 3.599A pdb=" N TYR A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 309 Processing helix chain 'A' and resid 310 through 325 Processing helix chain 'A' and resid 328 through 342 removed outlier: 3.619A pdb=" N CYS A 332 " --> pdb=" O CYS A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 362 through 377 Processing helix chain 'A' and resid 378 through 393 Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 412 through 427 Processing helix chain 'A' and resid 430 through 442 Processing helix chain 'A' and resid 450 through 466 Processing helix chain 'A' and resid 497 through 507 removed outlier: 5.305A pdb=" N ALA A 503 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Proline residue: A 504 - end of helix Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.709A pdb=" N LYS A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 560 Processing helix chain 'A' and resid 576 through 582 removed outlier: 3.853A pdb=" N MET A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS A 582 " --> pdb=" O GLY A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 653 removed outlier: 3.964A pdb=" N SER A 651 " --> pdb=" O THR A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 667 through 681 removed outlier: 3.612A pdb=" N LEU A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN A 672 " --> pdb=" O PRO A 668 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 694 Processing helix chain 'A' and resid 695 through 709 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 724 through 731 Processing helix chain 'A' and resid 732 through 735 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 767 through 781 removed outlier: 5.105A pdb=" N GLY A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL A 774 " --> pdb=" O HIS A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 784 No H-bonds generated for 'chain 'A' and resid 782 through 784' Processing helix chain 'A' and resid 789 through 803 removed outlier: 3.734A pdb=" N ASP A 803 " --> pdb=" O ASP A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 820 removed outlier: 4.238A pdb=" N ARG A 815 " --> pdb=" O ARG A 811 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP A 816 " --> pdb=" O MET A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 824 Processing helix chain 'A' and resid 825 through 846 Processing helix chain 'B' and resid 111 through 124 Processing helix chain 'B' and resid 126 through 141 Processing helix chain 'B' and resid 144 through 166 Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 185 through 199 removed outlier: 3.605A pdb=" N TYR B 189 " --> pdb=" O TYR B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 219 through 233 removed outlier: 3.966A pdb=" N TYR B 223 " --> pdb=" O TYR B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 250 Processing helix chain 'B' and resid 253 through 274 Processing helix chain 'B' and resid 276 through 291 Processing helix chain 'B' and resid 294 through 308 Processing helix chain 'B' and resid 311 through 325 Processing helix chain 'B' and resid 328 through 342 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 362 through 377 Processing helix chain 'B' and resid 378 through 393 Processing helix chain 'B' and resid 396 through 410 removed outlier: 3.641A pdb=" N PHE B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 430 through 445 removed outlier: 3.818A pdb=" N TYR B 443 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 467 Processing helix chain 'B' and resid 497 through 507 removed outlier: 5.344A pdb=" N ALA B 503 " --> pdb=" O TYR B 499 " (cutoff:3.500A) Proline residue: B 504 - end of helix Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 549 through 561 Processing helix chain 'B' and resid 576 through 582 removed outlier: 3.609A pdb=" N CYS B 582 " --> pdb=" O GLY B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 642 removed outlier: 3.677A pdb=" N ALA B 641 " --> pdb=" O SER B 638 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY B 642 " --> pdb=" O PRO B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 638 through 642' Processing helix chain 'B' and resid 647 through 652 removed outlier: 4.051A pdb=" N SER B 651 " --> pdb=" O THR B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 681 Processing helix chain 'B' and resid 690 through 694 Processing helix chain 'B' and resid 695 through 709 removed outlier: 3.619A pdb=" N LEU B 709 " --> pdb=" O THR B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 716 Processing helix chain 'B' and resid 724 through 731 Processing helix chain 'B' and resid 732 through 735 Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 767 through 780 removed outlier: 5.243A pdb=" N GLY B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 774 " --> pdb=" O HIS B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 784 No H-bonds generated for 'chain 'B' and resid 782 through 784' Processing helix chain 'B' and resid 789 through 803 removed outlier: 3.701A pdb=" N ASP B 803 " --> pdb=" O ASP B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 821 removed outlier: 4.194A pdb=" N ARG B 815 " --> pdb=" O ARG B 811 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASP B 816 " --> pdb=" O MET B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 824 No H-bonds generated for 'chain 'B' and resid 822 through 824' Processing helix chain 'B' and resid 825 through 846 Processing sheet with id=AA1, first strand: chain 'A' and resid 541 through 544 removed outlier: 8.418A pdb=" N VAL A 541 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL A 515 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LYS A 543 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL A 517 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE A 483 " --> pdb=" O LYS A 514 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL A 516 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 485 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N TYR A 518 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TYR A 487 " --> pdb=" O TYR A 518 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLN A 588 " --> pdb=" O TYR A 605 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE A 607 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR A 590 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N ASP A 609 " --> pdb=" O THR A 590 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 716 through 719 removed outlier: 8.462A pdb=" N ASP A 717 " --> pdb=" O SER A 684 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 686 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU A 719 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 688 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A 655 " --> pdb=" O ARG A 685 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL A 687 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE A 657 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N LYS A 689 " --> pdb=" O PHE A 657 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER A 659 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER A 738 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N MET A 763 " --> pdb=" O SER A 738 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA A 787 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR A 762 " --> pdb=" O ALA A 787 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 543 through 544 removed outlier: 8.269A pdb=" N LYS B 543 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 517 " --> pdb=" O LYS B 543 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE B 483 " --> pdb=" O LYS B 514 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL B 516 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 485 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N TYR B 518 " --> pdb=" O ILE B 485 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR B 487 " --> pdb=" O TYR B 518 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR B 484 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL B 566 " --> pdb=" O THR B 484 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY B 486 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN B 588 " --> pdb=" O TYR B 605 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE B 607 " --> pdb=" O GLN B 588 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR B 590 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N ASP B 609 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ARG B 606 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU B 628 " --> pdb=" O ARG B 606 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR B 608 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 684 through 688 removed outlier: 3.959A pdb=" N SER B 659 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER B 738 " --> pdb=" O VAL B 761 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N MET B 763 " --> pdb=" O SER B 738 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA B 787 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR B 762 " --> pdb=" O ALA B 787 " (cutoff:3.500A) 762 hydrogen bonds defined for protein. 2247 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: 3.98 Time building geometry restraints manager: 3.69 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: 3763 1.34 - 1.46: 2496 1.46 - 1.58: 5329 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 11708 Sorted by residual: bond pdb=" CG LEU A 155 " pdb=" CD1 LEU A 155 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CA LEU A 288 " pdb=" C LEU A 288 " ideal model delta sigma weight residual 1.523 1.508 0.015 1.34e-02 5.57e+03 1.30e+00 bond pdb=" CG GLN A 435 " pdb=" CD GLN A 435 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.18e+00 bond pdb=" CB TRP A 459 " pdb=" CG TRP A 459 " ideal model delta sigma weight residual 1.498 1.465 0.033 3.10e-02 1.04e+03 1.15e+00 bond pdb=" CB GLU B 567 " pdb=" CG GLU B 567 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.10e+00 ... (remaining 11703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 15345 1.39 - 2.79: 516 2.79 - 4.18: 92 4.18 - 5.57: 21 5.57 - 6.97: 8 Bond angle restraints: 15982 Sorted by residual: angle pdb=" N HIS A 508 " pdb=" CA HIS A 508 " pdb=" CB HIS A 508 " ideal model delta sigma weight residual 110.77 115.71 -4.94 1.63e+00 3.76e-01 9.20e+00 angle pdb=" CA GLN A 435 " pdb=" CB GLN A 435 " pdb=" CG GLN A 435 " ideal model delta sigma weight residual 114.10 119.34 -5.24 2.00e+00 2.50e-01 6.86e+00 angle pdb=" C ILE A 592 " pdb=" CA ILE A 592 " pdb=" CB ILE A 592 " ideal model delta sigma weight residual 111.29 107.13 4.16 1.64e+00 3.72e-01 6.44e+00 angle pdb=" N LEU B 309 " pdb=" CA LEU B 309 " pdb=" C LEU B 309 " ideal model delta sigma weight residual 110.80 116.14 -5.34 2.13e+00 2.20e-01 6.28e+00 angle pdb=" N TRP B 591 " pdb=" CA TRP B 591 " pdb=" C TRP B 591 " ideal model delta sigma weight residual 110.80 116.06 -5.26 2.13e+00 2.20e-01 6.09e+00 ... (remaining 15977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 6376 16.41 - 32.82: 469 32.82 - 49.23: 101 49.23 - 65.63: 12 65.63 - 82.04: 8 Dihedral angle restraints: 6966 sinusoidal: 2441 harmonic: 4525 Sorted by residual: dihedral pdb=" CA PRO A 108 " pdb=" C PRO A 108 " pdb=" N HIS A 109 " pdb=" CA HIS A 109 " ideal model delta harmonic sigma weight residual -180.00 -162.73 -17.27 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CG ARG B 685 " pdb=" CD ARG B 685 " pdb=" NE ARG B 685 " pdb=" CZ ARG B 685 " ideal model delta sinusoidal sigma weight residual -90.00 -134.89 44.89 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA TRP B 591 " pdb=" C TRP B 591 " pdb=" N ILE B 592 " pdb=" CA ILE B 592 " ideal model delta harmonic sigma weight residual -180.00 -164.12 -15.88 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 6963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1450 0.046 - 0.092: 307 0.092 - 0.138: 67 0.138 - 0.184: 5 0.184 - 0.230: 2 Chirality restraints: 1831 Sorted by residual: chirality pdb=" CA LEU A 155 " pdb=" N LEU A 155 " pdb=" C LEU A 155 " pdb=" CB LEU A 155 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU A 151 " pdb=" CB LEU A 151 " pdb=" CD1 LEU A 151 " pdb=" CD2 LEU A 151 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CG LEU A 155 " pdb=" CB LEU A 155 " pdb=" CD1 LEU A 155 " pdb=" CD2 LEU A 155 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 1828 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 393 " 0.060 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO A 394 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 508 " 0.023 2.00e-02 2.50e+03 2.78e-02 1.16e+01 pdb=" CG HIS A 508 " -0.059 2.00e-02 2.50e+03 pdb=" ND1 HIS A 508 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 HIS A 508 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 HIS A 508 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS A 508 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 427 " 0.052 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO A 428 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 428 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 428 " 0.044 5.00e-02 4.00e+02 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 251 2.69 - 3.24: 12632 3.24 - 3.79: 19196 3.79 - 4.35: 24246 4.35 - 4.90: 38994 Nonbonded interactions: 95319 Sorted by model distance: nonbonded pdb=" OH TYR B 635 " pdb=" OE2 GLU B 752 " model vdw 2.136 3.040 nonbonded pdb=" OG1 THR B 569 " pdb=" OG1 THR B 572 " model vdw 2.203 3.040 nonbonded pdb=" OD1 ASN B 442 " pdb=" OH TYR B 594 " model vdw 2.255 3.040 nonbonded pdb=" O SER B 813 " pdb=" OD1 ASP B 816 " model vdw 2.280 3.040 nonbonded pdb=" O ILE A 417 " pdb=" OE1 GLU A 421 " model vdw 2.285 3.040 ... (remaining 95314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 110 through 117 and (name N or name CA or name C or name \ O or name CB )) or resid 118 through 119 or (resid 120 through 124 and (name N o \ r name CA or name C or name O or name CB )) or (resid 125 through 140 and (name \ N or name CA or name C or name O or name CB )) or resid 141 through 142 or (resi \ d 143 through 149 and (name N or name CA or name C or name O or name CB )) or re \ sid 150 or (resid 151 through 158 and (name N or name CA or name C or name O or \ name CB )) or resid 159 or (resid 160 through 165 and (name N or name CA or name \ C or name O or name CB )) or resid 166 or (resid 167 through 170 and (name N or \ name CA or name C or name O or name CB )) or resid 171 or (resid 172 through 18 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 182 through \ 183 or (resid 184 and (name N or name CA or name C or name O or name CB )) or re \ sid 185 through 188 or (resid 189 through 190 and (name N or name CA or name C o \ r name O or name CB )) or resid 191 or (resid 192 and (name N or name CA or name \ C or name O or name CB )) or resid 193 or (resid 194 through 196 and (name N or \ name CA or name C or name O or name CB )) or resid 197 or (resid 198 through 20 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 202 through \ 203 or (resid 204 through 208 and (name N or name CA or name C or name O or name \ CB )) or resid 209 or (resid 210 through 213 and (name N or name CA or name C o \ r name O or name CB )) or resid 214 or (resid 215 through 216 and (name N or nam \ e CA or name C or name O or name CB )) or resid 217 or (resid 218 through 220 an \ d (name N or name CA or name C or name O or name CB )) or resid 221 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 386 or (resid 387 and (name N or name CA or name C or name O or name \ CB )) or resid 388 through 444 or (resid 445 and (name N or name CA or name C o \ r name O or name CB )) or resid 446 through 501 or (resid 502 through 503 and (n \ ame N or name CA or name C or name O or name CB )) or resid 504 through 526 or ( \ resid 527 and (name N or name CA or name C or name O or name CB )) or resid 528 \ through 555 or (resid 556 and (name N or name CA or name C or name O or name CB \ )) or resid 557 through 563 or (resid 564 and (name N or name CA or name C or na \ me O or name CB )) or resid 565 through 651 or (resid 652 and (name N or name CA \ or name C or name O or name CB )) or resid 653 through 695 or (resid 696 and (n \ ame N or name CA or name C or name O or name CB )) or resid 697 through 713 or ( \ resid 714 and (name N or name CA or name C or name O or name CB )) or resid 715 \ through 729 or (resid 730 through 731 and (name N or name CA or name C or name O \ or name CB )) or resid 732 through 765 or (resid 766 and (name N or name CA or \ name C or name O or name CB )) or resid 767 through 794 or (resid 795 and (name \ N or name CA or name C or name O or name CB )) or resid 796 through 841 or (resi \ d 842 and (name N or name CA or name C or name O or name CB )) or resid 843 thro \ ugh 846)) selection = (chain 'B' and (resid 110 through 125 or (resid 126 through 140 and (name N or n \ ame CA or name C or name O or name CB )) or resid 141 through 290 or (resid 291 \ and (name N or name CA or name C or name O or name CB )) or resid 292 through 37 \ 7 or (resid 378 and (name N or name CA or name C or name O or name CB )) or resi \ d 379 through 473 or (resid 474 and (name N or name CA or name C or name O or na \ me CB )) or resid 475 or (resid 476 through 478 and (name N or name CA or name C \ or name O or name CB )) or resid 479 or (resid 480 through 481 and (name N or n \ ame CA or name C or name O or name CB )) or resid 482 through 536 or (resid 537 \ and (name N or name CA or name C or name O or name CB )) or resid 538 through 54 \ 8 or (resid 549 through 550 and (name N or name CA or name C or name O or name C \ B )) or resid 551 or (resid 552 and (name N or name CA or name C or name O or na \ me CB )) or resid 553 through 554 or (resid 555 through 556 and (name N or name \ CA or name C or name O or name CB )) or resid 557 through 560 or (resid 561 and \ (name N or name CA or name C or name O or name CB )) or resid 562 through 575 or \ (resid 576 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 7 through 617 or (resid 618 and (name N or name CA or name C or name O or name C \ B )) or resid 619 through 629 or (resid 630 through 631 and (name N or name CA o \ r name C or name O or name CB )) or resid 632 through 644 or (resid 645 and (nam \ e N or name CA or name C or name O or name CB )) or resid 646 through 671 or (re \ sid 672 and (name N or name CA or name C or name O or name CB )) or resid 673 th \ rough 683 or (resid 684 and (name N or name CA or name C or name O or name CB )) \ or resid 685 through 689 or (resid 690 and (name N or name CA or name C or name \ O or name CB )) or resid 691 through 706 or (resid 707 and (name N or name CA o \ r name C or name O or name CB )) or resid 708 through 721 or (resid 722 through \ 724 and (name N or name CA or name C or name O or name CB )) or resid 725 throug \ h 727 or (resid 728 and (name N or name CA or name C or name O or name CB )) or \ resid 729 through 734 or (resid 735 and (name N or name CA or name C or name O o \ r name CB )) or resid 736 through 751 or (resid 752 and (name N or name CA or na \ me C or name O or name CB )) or resid 753 through 845 or (resid 846 and (name N \ or name CA or name C or name O or name CB )))) } 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 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: 4.300 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.230 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 0.048 11708 Z= 0.242 Angle : 0.632 6.968 15982 Z= 0.341 Chirality : 0.040 0.230 1831 Planarity : 0.006 0.091 2070 Dihedral : 12.356 82.042 4062 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.05 (0.21), residues: 1535 helix: 0.97 (0.16), residues: 1039 sheet: -0.69 (0.56), residues: 105 loop : -2.28 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 591 HIS 0.033 0.002 HIS A 508 PHE 0.033 0.002 PHE A 463 TYR 0.053 0.002 TYR A 837 ARG 0.009 0.001 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.282 Fit side-chains REVERT: A 491 ASP cc_start: 0.8120 (m-30) cc_final: 0.7752 (m-30) REVERT: A 566 VAL cc_start: 0.8467 (t) cc_final: 0.7994 (t) REVERT: A 580 MET cc_start: 0.8624 (mtt) cc_final: 0.8381 (mtt) REVERT: A 818 MET cc_start: 0.8215 (ppp) cc_final: 0.7831 (ptt) REVERT: B 209 TYR cc_start: 0.8219 (m-80) cc_final: 0.7870 (m-80) REVERT: B 473 TRP cc_start: 0.7923 (m-90) cc_final: 0.7711 (m-90) REVERT: B 494 THR cc_start: 0.8122 (p) cc_final: 0.7835 (t) REVERT: B 793 TYR cc_start: 0.8215 (t80) cc_final: 0.7797 (t80) REVERT: B 837 TYR cc_start: 0.8642 (m-10) cc_final: 0.8417 (m-10) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1841 time to fit residues: 55.0931 Evaluate side-chains 162 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.0870 chunk 115 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 0.3980 chunk 89 optimal weight: 20.0000 chunk 138 optimal weight: 2.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 167 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11708 Z= 0.226 Angle : 0.595 8.691 15982 Z= 0.305 Chirality : 0.041 0.161 1831 Planarity : 0.005 0.058 2070 Dihedral : 3.874 17.388 1670 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.98 % Allowed : 7.56 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.55 (0.22), residues: 1535 helix: 2.00 (0.16), residues: 1035 sheet: -0.51 (0.49), residues: 125 loop : -1.21 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 591 HIS 0.018 0.002 HIS A 508 PHE 0.017 0.002 PHE A 463 TYR 0.028 0.002 TYR A 837 ARG 0.004 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 ASP cc_start: 0.8181 (m-30) cc_final: 0.7707 (m-30) REVERT: A 818 MET cc_start: 0.8124 (ppp) cc_final: 0.7905 (ptt) REVERT: B 209 TYR cc_start: 0.8178 (m-80) cc_final: 0.7946 (m-80) REVERT: B 231 LYS cc_start: 0.8824 (tttm) cc_final: 0.8501 (ttmt) REVERT: B 244 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8158 (mm-30) REVERT: B 473 TRP cc_start: 0.7939 (m-90) cc_final: 0.7560 (m-90) REVERT: B 494 THR cc_start: 0.8058 (p) cc_final: 0.7768 (t) REVERT: B 840 MET cc_start: 0.8527 (ptt) cc_final: 0.8303 (ptt) outliers start: 11 outliers final: 7 residues processed: 195 average time/residue: 0.1993 time to fit residues: 59.1175 Evaluate side-chains 165 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 30.0000 chunk 115 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11708 Z= 0.274 Angle : 0.606 12.187 15982 Z= 0.305 Chirality : 0.040 0.135 1831 Planarity : 0.005 0.060 2070 Dihedral : 3.910 21.196 1670 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.25 % Allowed : 10.94 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.73 (0.22), residues: 1535 helix: 2.11 (0.16), residues: 1039 sheet: -0.31 (0.51), residues: 119 loop : -1.13 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 591 HIS 0.013 0.001 HIS A 508 PHE 0.019 0.002 PHE A 253 TYR 0.023 0.002 TYR A 837 ARG 0.007 0.001 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 ASP cc_start: 0.8248 (m-30) cc_final: 0.7872 (m-30) REVERT: A 632 PHE cc_start: 0.8169 (p90) cc_final: 0.7936 (p90) REVERT: A 812 MET cc_start: 0.8739 (mmp) cc_final: 0.8538 (mmp) REVERT: B 209 TYR cc_start: 0.8275 (m-80) cc_final: 0.8074 (m-80) REVERT: B 494 THR cc_start: 0.8119 (p) cc_final: 0.7844 (t) REVERT: B 633 LEU cc_start: 0.9088 (mt) cc_final: 0.8763 (mt) REVERT: B 760 CYS cc_start: 0.8449 (p) cc_final: 0.8174 (p) REVERT: B 840 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8300 (ptt) outliers start: 14 outliers final: 9 residues processed: 181 average time/residue: 0.1976 time to fit residues: 54.9051 Evaluate side-chains 171 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 840 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 147 optimal weight: 0.1980 chunk 132 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11708 Z= 0.197 Angle : 0.561 11.339 15982 Z= 0.280 Chirality : 0.039 0.126 1831 Planarity : 0.004 0.062 2070 Dihedral : 3.839 22.951 1670 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.25 % Allowed : 12.54 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.93 (0.22), residues: 1535 helix: 2.24 (0.16), residues: 1039 sheet: -0.18 (0.51), residues: 121 loop : -1.02 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 591 HIS 0.011 0.001 HIS A 508 PHE 0.012 0.001 PHE A 253 TYR 0.019 0.001 TYR A 837 ARG 0.004 0.001 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.8601 (tpp) cc_final: 0.8391 (tpp) REVERT: A 491 ASP cc_start: 0.8323 (m-30) cc_final: 0.7970 (m-30) REVERT: A 729 MET cc_start: 0.7786 (mmp) cc_final: 0.7396 (mmm) REVERT: A 812 MET cc_start: 0.8694 (mmp) cc_final: 0.8456 (mmp) REVERT: B 244 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8076 (mm-30) REVERT: B 494 THR cc_start: 0.8139 (p) cc_final: 0.7832 (t) REVERT: B 709 LEU cc_start: 0.8618 (mm) cc_final: 0.8348 (mm) REVERT: B 760 CYS cc_start: 0.8374 (p) cc_final: 0.8138 (p) REVERT: B 840 MET cc_start: 0.8594 (ptt) cc_final: 0.8354 (ptt) outliers start: 14 outliers final: 8 residues processed: 189 average time/residue: 0.1839 time to fit residues: 54.1000 Evaluate side-chains 165 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 451 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 11708 Z= 0.341 Angle : 0.639 10.298 15982 Z= 0.324 Chirality : 0.041 0.180 1831 Planarity : 0.005 0.061 2070 Dihedral : 4.086 22.218 1670 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.78 % Allowed : 13.61 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 (0.22), residues: 1535 helix: 2.07 (0.16), residues: 1031 sheet: -0.53 (0.50), residues: 127 loop : -0.92 (0.35), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 591 HIS 0.010 0.001 HIS A 508 PHE 0.019 0.002 PHE A 253 TYR 0.017 0.002 TYR A 755 ARG 0.004 0.001 ARG B 685 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8559 (t80) REVERT: A 556 MET cc_start: 0.8678 (ppp) cc_final: 0.8249 (ppp) REVERT: A 632 PHE cc_start: 0.8223 (p90) cc_final: 0.7918 (p90) REVERT: A 729 MET cc_start: 0.8051 (mmp) cc_final: 0.7688 (mmp) REVERT: A 812 MET cc_start: 0.8714 (mmp) cc_final: 0.8464 (mmp) REVERT: A 818 MET cc_start: 0.7724 (ppp) cc_final: 0.6968 (ptm) REVERT: B 244 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8230 (mm-30) REVERT: B 494 THR cc_start: 0.8172 (p) cc_final: 0.7846 (t) REVERT: B 709 LEU cc_start: 0.8583 (mm) cc_final: 0.8304 (mm) REVERT: B 729 MET cc_start: 0.8576 (mmm) cc_final: 0.8240 (mmm) REVERT: B 760 CYS cc_start: 0.8465 (p) cc_final: 0.8207 (p) REVERT: B 840 MET cc_start: 0.8595 (ptt) cc_final: 0.8384 (ptt) outliers start: 20 outliers final: 15 residues processed: 182 average time/residue: 0.1883 time to fit residues: 53.5209 Evaluate side-chains 181 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 716 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11708 Z= 0.185 Angle : 0.581 12.064 15982 Z= 0.283 Chirality : 0.039 0.160 1831 Planarity : 0.004 0.062 2070 Dihedral : 3.925 22.973 1670 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.42 % Allowed : 15.21 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.98 (0.22), residues: 1535 helix: 2.30 (0.16), residues: 1031 sheet: -0.44 (0.49), residues: 127 loop : -0.85 (0.35), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 591 HIS 0.009 0.001 HIS A 768 PHE 0.014 0.001 PHE B 531 TYR 0.014 0.001 TYR A 837 ARG 0.004 0.000 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8524 (t80) REVERT: A 632 PHE cc_start: 0.8125 (p90) cc_final: 0.7912 (p90) REVERT: A 729 MET cc_start: 0.8023 (mmp) cc_final: 0.7672 (mmp) REVERT: A 818 MET cc_start: 0.7587 (ppp) cc_final: 0.6970 (ptm) REVERT: B 494 THR cc_start: 0.8193 (p) cc_final: 0.7889 (t) REVERT: B 709 LEU cc_start: 0.8565 (mm) cc_final: 0.8304 (mm) REVERT: B 711 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6958 (tt) REVERT: B 760 CYS cc_start: 0.8363 (p) cc_final: 0.8104 (p) REVERT: B 840 MET cc_start: 0.8578 (ptt) cc_final: 0.8353 (ptt) outliers start: 16 outliers final: 12 residues processed: 185 average time/residue: 0.1885 time to fit residues: 54.5816 Evaluate side-chains 181 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 726 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 11708 Z= 0.465 Angle : 0.731 11.715 15982 Z= 0.370 Chirality : 0.044 0.182 1831 Planarity : 0.005 0.064 2070 Dihedral : 4.289 21.349 1670 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.22 % Allowed : 15.93 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.28 (0.22), residues: 1535 helix: 1.74 (0.16), residues: 1042 sheet: -0.60 (0.51), residues: 116 loop : -1.14 (0.35), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 591 HIS 0.009 0.002 HIS A 768 PHE 0.018 0.002 PHE A 253 TYR 0.020 0.002 TYR A 755 ARG 0.004 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8468 (t80) REVERT: A 632 PHE cc_start: 0.8241 (p90) cc_final: 0.8027 (p90) REVERT: A 674 TRP cc_start: 0.8589 (m-10) cc_final: 0.8244 (m-10) REVERT: A 729 MET cc_start: 0.8285 (mmp) cc_final: 0.7860 (mmp) REVERT: A 818 MET cc_start: 0.7835 (ppp) cc_final: 0.7315 (ptm) REVERT: B 244 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8246 (mm-30) REVERT: B 709 LEU cc_start: 0.8622 (mm) cc_final: 0.8331 (mm) REVERT: B 735 MET cc_start: 0.6722 (tpp) cc_final: 0.6475 (tpt) REVERT: B 760 CYS cc_start: 0.8662 (p) cc_final: 0.8337 (p) REVERT: B 840 MET cc_start: 0.8641 (ptt) cc_final: 0.8434 (ptt) outliers start: 25 outliers final: 17 residues processed: 184 average time/residue: 0.1889 time to fit residues: 54.4980 Evaluate side-chains 176 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 817 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 0.0070 chunk 88 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11708 Z= 0.181 Angle : 0.619 13.736 15982 Z= 0.297 Chirality : 0.040 0.175 1831 Planarity : 0.004 0.063 2070 Dihedral : 4.020 22.147 1670 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.25 % Allowed : 17.53 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.83 (0.22), residues: 1535 helix: 2.18 (0.16), residues: 1037 sheet: -0.64 (0.51), residues: 116 loop : -0.90 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 591 HIS 0.009 0.001 HIS A 768 PHE 0.012 0.001 PHE B 531 TYR 0.020 0.001 TYR B 510 ARG 0.004 0.000 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8442 (t80) REVERT: A 729 MET cc_start: 0.8105 (mmp) cc_final: 0.7716 (mmp) REVERT: A 812 MET cc_start: 0.8719 (mmm) cc_final: 0.8490 (mmp) REVERT: A 818 MET cc_start: 0.7632 (ppp) cc_final: 0.7198 (ptm) REVERT: B 244 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8198 (mm-30) REVERT: B 709 LEU cc_start: 0.8603 (mm) cc_final: 0.8311 (mm) REVERT: B 735 MET cc_start: 0.6493 (tpp) cc_final: 0.6245 (tpt) REVERT: B 760 CYS cc_start: 0.8554 (p) cc_final: 0.8299 (p) REVERT: B 840 MET cc_start: 0.8576 (ptt) cc_final: 0.8347 (ptt) outliers start: 14 outliers final: 10 residues processed: 186 average time/residue: 0.1956 time to fit residues: 57.3762 Evaluate side-chains 179 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 726 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 0.3980 chunk 137 optimal weight: 2.9990 chunk 141 optimal weight: 0.4980 chunk 82 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 129 optimal weight: 0.2980 chunk 136 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11708 Z= 0.182 Angle : 0.623 14.049 15982 Z= 0.298 Chirality : 0.039 0.168 1831 Planarity : 0.004 0.064 2070 Dihedral : 3.926 21.934 1670 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.07 % Allowed : 17.88 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.92 (0.22), residues: 1535 helix: 2.23 (0.16), residues: 1037 sheet: -0.60 (0.51), residues: 116 loop : -0.82 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 591 HIS 0.008 0.001 HIS A 768 PHE 0.029 0.001 PHE A 632 TYR 0.025 0.001 TYR B 510 ARG 0.003 0.000 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.7803 (m-80) cc_final: 0.7510 (m-10) REVERT: A 463 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8463 (t80) REVERT: A 632 PHE cc_start: 0.7850 (p90) cc_final: 0.7362 (p90) REVERT: A 729 MET cc_start: 0.8117 (mmp) cc_final: 0.7731 (mmp) REVERT: A 812 MET cc_start: 0.8789 (mmm) cc_final: 0.8535 (mmp) REVERT: A 818 MET cc_start: 0.7594 (ppp) cc_final: 0.7154 (ptm) REVERT: A 841 TRP cc_start: 0.7873 (t-100) cc_final: 0.7178 (t-100) REVERT: B 244 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8160 (mm-30) REVERT: B 709 LEU cc_start: 0.8580 (mm) cc_final: 0.8278 (mm) REVERT: B 760 CYS cc_start: 0.8487 (p) cc_final: 0.8251 (p) REVERT: B 840 MET cc_start: 0.8552 (ptt) cc_final: 0.8337 (ptt) outliers start: 12 outliers final: 11 residues processed: 181 average time/residue: 0.1900 time to fit residues: 54.1431 Evaluate side-chains 178 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 716 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 0.0070 chunk 101 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11708 Z= 0.180 Angle : 0.626 13.760 15982 Z= 0.296 Chirality : 0.039 0.167 1831 Planarity : 0.004 0.065 2070 Dihedral : 3.904 22.547 1670 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.16 % Allowed : 19.13 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.99 (0.22), residues: 1535 helix: 2.30 (0.16), residues: 1032 sheet: -0.55 (0.50), residues: 121 loop : -0.81 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 591 HIS 0.007 0.001 HIS A 508 PHE 0.027 0.001 PHE A 632 TYR 0.021 0.001 TYR B 510 ARG 0.003 0.000 ARG A 532 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.7725 (m-80) cc_final: 0.7508 (m-10) REVERT: A 189 TYR cc_start: 0.7866 (m-80) cc_final: 0.7578 (m-10) REVERT: A 463 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8480 (t80) REVERT: A 632 PHE cc_start: 0.7823 (p90) cc_final: 0.7366 (p90) REVERT: A 674 TRP cc_start: 0.8575 (m-10) cc_final: 0.8315 (m-10) REVERT: A 729 MET cc_start: 0.8105 (mmp) cc_final: 0.7670 (mmp) REVERT: A 812 MET cc_start: 0.8787 (mmm) cc_final: 0.8511 (mmp) REVERT: A 818 MET cc_start: 0.7596 (ppp) cc_final: 0.7135 (ptm) REVERT: B 709 LEU cc_start: 0.8573 (mm) cc_final: 0.8269 (mm) REVERT: B 735 MET cc_start: 0.6080 (tpt) cc_final: 0.5502 (tpp) REVERT: B 760 CYS cc_start: 0.8366 (p) cc_final: 0.8129 (p) outliers start: 13 outliers final: 11 residues processed: 177 average time/residue: 0.2029 time to fit residues: 57.4163 Evaluate side-chains 181 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 716 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.114181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.078694 restraints weight = 31350.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.081220 restraints weight = 16147.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.082830 restraints weight = 10551.218| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11708 Z= 0.208 Angle : 0.626 13.765 15982 Z= 0.300 Chirality : 0.039 0.161 1831 Planarity : 0.004 0.065 2070 Dihedral : 3.920 22.873 1670 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.42 % Allowed : 18.42 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.99 (0.22), residues: 1535 helix: 2.28 (0.16), residues: 1033 sheet: -0.51 (0.50), residues: 121 loop : -0.78 (0.35), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 591 HIS 0.009 0.001 HIS A 768 PHE 0.025 0.001 PHE A 632 TYR 0.019 0.001 TYR B 510 ARG 0.003 0.000 ARG A 532 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2495.31 seconds wall clock time: 46 minutes 44.56 seconds (2804.56 seconds total)