Starting phenix.real_space_refine on Wed Mar 4 06:22:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dtg_27697/03_2026/8dtg_27697.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dtg_27697/03_2026/8dtg_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dtg_27697/03_2026/8dtg_27697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dtg_27697/03_2026/8dtg_27697.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dtg_27697/03_2026/8dtg_27697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dtg_27697/03_2026/8dtg_27697.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ASP:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 4, 'ARG:plan': 5, 'GLU:plan': 11, 'HIS:plan': 2, 'GLN:plan1': 3, 'PHE:plan': 3} 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: {'ASN:plan1': 5, 'HIS:plan': 3, 'GLU:plan': 13, 'TYR:plan': 8, 'GLN:plan1': 6, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 179 Time building chain proxies: 2.74, per 1000 atoms: 0.24 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: 1.17 Conformation dependent library (CDL) restraints added in 722.1 milliseconds 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: 0.45 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: 1.73 Time building geometry restraints manager: 1.55 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: 5.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.290 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.630 ------------------------------------------------------------------------------- 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= 0.172 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (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 ARG 0.009 0.001 ARG B 701 TYR 0.053 0.002 TYR A 837 PHE 0.033 0.002 PHE A 463 TRP 0.045 0.002 TRP A 591 HIS 0.033 0.002 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00375 (11708) covalent geometry : angle 0.63210 (15982) hydrogen bonds : bond 0.12265 ( 762) hydrogen bonds : angle 5.37708 ( 2247) *********************** 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 : 0.435 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: 0.7832 (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: 0.0724 time to fit residues: 22.0544 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 : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0060 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 167 ASN A 445 ASN ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.115818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.080148 restraints weight = 31115.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.082691 restraints weight = 16127.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.084306 restraints weight = 10475.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.085339 restraints weight = 7946.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.085966 restraints weight = 6687.175| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1401 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= 0.139 Angle : 0.580 8.730 15982 Z= 0.297 Chirality : 0.040 0.155 1831 Planarity : 0.005 0.057 2070 Dihedral : 3.820 17.119 1670 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.98 % Allowed : 7.30 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.22), residues: 1535 helix: 2.00 (0.16), residues: 1040 sheet: -0.34 (0.50), residues: 119 loop : -1.29 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 532 TYR 0.028 0.002 TYR A 837 PHE 0.017 0.002 PHE A 463 TRP 0.033 0.002 TRP A 591 HIS 0.018 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00314 (11708) covalent geometry : angle 0.58022 (15982) hydrogen bonds : bond 0.03798 ( 762) hydrogen bonds : angle 3.99911 ( 2247) *********************** 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 200 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 ASP cc_start: 0.8317 (m-30) cc_final: 0.7797 (m-30) REVERT: A 818 MET cc_start: 0.8319 (ppp) cc_final: 0.8048 (ptt) REVERT: B 209 TYR cc_start: 0.8213 (m-80) cc_final: 0.7987 (m-80) REVERT: B 231 LYS cc_start: 0.8853 (tttm) cc_final: 0.8516 (ttmt) REVERT: B 244 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8185 (mm-30) REVERT: B 473 TRP cc_start: 0.7944 (m-90) cc_final: 0.7564 (m-90) REVERT: B 494 THR cc_start: 0.8188 (p) cc_final: 0.7912 (t) REVERT: B 567 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8530 (tm-30) REVERT: B 840 MET cc_start: 0.8587 (ptt) cc_final: 0.8374 (ptt) outliers start: 11 outliers final: 8 residues processed: 198 average time/residue: 0.0850 time to fit residues: 26.0460 Evaluate side-chains 166 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 346 ASP 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 5 optimal weight: 10.0000 chunk 106 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 151 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN B 293 HIS ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.116731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.081254 restraints weight = 31620.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.083850 restraints weight = 16438.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.085460 restraints weight = 10650.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.086516 restraints weight = 8058.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.087049 restraints weight = 6796.614| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11708 Z= 0.127 Angle : 0.564 12.287 15982 Z= 0.282 Chirality : 0.039 0.136 1831 Planarity : 0.004 0.059 2070 Dihedral : 3.789 17.972 1670 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.16 % Allowed : 10.50 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.22), residues: 1535 helix: 2.21 (0.16), residues: 1039 sheet: -0.24 (0.51), residues: 119 loop : -1.09 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 342 TYR 0.024 0.001 TYR A 837 PHE 0.014 0.001 PHE A 253 TRP 0.019 0.002 TRP A 591 HIS 0.013 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00286 (11708) covalent geometry : angle 0.56423 (15982) hydrogen bonds : bond 0.03392 ( 762) hydrogen bonds : angle 3.77925 ( 2247) *********************** 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 192 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 ASP cc_start: 0.8378 (m-30) cc_final: 0.7927 (m-30) REVERT: A 632 PHE cc_start: 0.8294 (p90) cc_final: 0.8024 (p90) REVERT: A 812 MET cc_start: 0.8909 (mmp) cc_final: 0.8573 (mmp) REVERT: A 818 MET cc_start: 0.8247 (ppp) cc_final: 0.7974 (ptt) REVERT: B 209 TYR cc_start: 0.8259 (m-80) cc_final: 0.8022 (m-80) REVERT: B 231 LYS cc_start: 0.8836 (tttm) cc_final: 0.8543 (ttmm) REVERT: B 473 TRP cc_start: 0.7948 (m-90) cc_final: 0.7469 (m-90) REVERT: B 494 THR cc_start: 0.8230 (p) cc_final: 0.7958 (t) REVERT: B 729 MET cc_start: 0.8675 (mmm) cc_final: 0.8336 (mmm) REVERT: B 760 CYS cc_start: 0.8531 (p) cc_final: 0.8301 (p) REVERT: B 840 MET cc_start: 0.8585 (ptt) cc_final: 0.8373 (ptt) outliers start: 13 outliers final: 9 residues processed: 185 average time/residue: 0.0809 time to fit residues: 23.3602 Evaluate side-chains 169 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 706 LEU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 451 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 123 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.116379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.080943 restraints weight = 31509.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.083555 restraints weight = 16391.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.085085 restraints weight = 10652.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.086224 restraints weight = 8183.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.086889 restraints weight = 6841.720| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11708 Z= 0.118 Angle : 0.543 10.534 15982 Z= 0.272 Chirality : 0.039 0.136 1831 Planarity : 0.004 0.061 2070 Dihedral : 3.751 24.709 1670 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.42 % Allowed : 11.65 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.22), residues: 1535 helix: 2.33 (0.16), residues: 1033 sheet: -0.30 (0.49), residues: 127 loop : -1.01 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 342 TYR 0.020 0.001 TYR A 837 PHE 0.011 0.001 PHE B 657 TRP 0.015 0.001 TRP B 591 HIS 0.011 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00266 (11708) covalent geometry : angle 0.54292 (15982) hydrogen bonds : bond 0.03101 ( 762) hydrogen bonds : angle 3.63068 ( 2247) *********************** 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 189 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 ASP cc_start: 0.8420 (m-30) cc_final: 0.8036 (m-30) REVERT: A 729 MET cc_start: 0.7915 (mmp) cc_final: 0.7495 (mmm) REVERT: A 763 MET cc_start: 0.7518 (ptm) cc_final: 0.7011 (ppp) REVERT: A 812 MET cc_start: 0.8805 (mmp) cc_final: 0.8509 (mmp) REVERT: A 818 MET cc_start: 0.8218 (ppp) cc_final: 0.7947 (ptt) REVERT: B 494 THR cc_start: 0.8240 (p) cc_final: 0.7936 (t) REVERT: B 709 LEU cc_start: 0.8701 (mm) cc_final: 0.8440 (mm) REVERT: B 840 MET cc_start: 0.8584 (ptt) cc_final: 0.8379 (ptt) outliers start: 16 outliers final: 10 residues processed: 183 average time/residue: 0.0786 time to fit residues: 22.6494 Evaluate side-chains 167 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 700 GLN Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 763 MET Chi-restraints excluded: chain B residue 767 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 35 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** 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 = 0.3856 r_free = 0.3856 target = 0.116584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.081118 restraints weight = 31459.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.083822 restraints weight = 16024.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.085557 restraints weight = 10292.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.086588 restraints weight = 7741.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.087292 restraints weight = 6494.608| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11708 Z= 0.116 Angle : 0.541 11.272 15982 Z= 0.268 Chirality : 0.039 0.161 1831 Planarity : 0.004 0.062 2070 Dihedral : 3.701 22.342 1670 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.25 % Allowed : 13.17 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.22), residues: 1535 helix: 2.41 (0.16), residues: 1034 sheet: -0.28 (0.49), residues: 127 loop : -0.92 (0.35), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 342 TYR 0.017 0.001 TYR A 837 PHE 0.021 0.001 PHE B 531 TRP 0.018 0.001 TRP B 591 HIS 0.010 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00265 (11708) covalent geometry : angle 0.54114 (15982) hydrogen bonds : bond 0.02987 ( 762) hydrogen bonds : angle 3.56840 ( 2247) *********************** 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 187 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.8135 (mmm) cc_final: 0.7889 (ptp) REVERT: A 463 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8585 (t80) REVERT: A 632 PHE cc_start: 0.8201 (p90) cc_final: 0.7918 (p90) REVERT: A 729 MET cc_start: 0.7882 (mmp) cc_final: 0.7584 (mmm) REVERT: A 812 MET cc_start: 0.8814 (mmp) cc_final: 0.8533 (mmp) REVERT: B 494 THR cc_start: 0.8232 (p) cc_final: 0.7942 (t) REVERT: B 594 TYR cc_start: 0.7430 (t80) cc_final: 0.7174 (t80) REVERT: B 709 LEU cc_start: 0.8662 (mm) cc_final: 0.8391 (mm) REVERT: B 840 MET cc_start: 0.8609 (ptt) cc_final: 0.8396 (ptt) outliers start: 14 outliers final: 9 residues processed: 181 average time/residue: 0.0773 time to fit residues: 22.1891 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 : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU 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 791 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 451 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 44 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.115694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.080248 restraints weight = 31604.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.082752 restraints weight = 16799.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.084335 restraints weight = 11077.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.085397 restraints weight = 8479.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.086025 restraints weight = 7106.826| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2521 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= 0.131 Angle : 0.556 11.972 15982 Z= 0.274 Chirality : 0.039 0.160 1831 Planarity : 0.004 0.061 2070 Dihedral : 3.739 20.912 1670 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.51 % Allowed : 13.35 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.22), residues: 1535 helix: 2.41 (0.16), residues: 1039 sheet: -0.15 (0.51), residues: 121 loop : -0.90 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 532 TYR 0.016 0.001 TYR A 837 PHE 0.009 0.001 PHE A 253 TRP 0.018 0.001 TRP B 591 HIS 0.009 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00302 (11708) covalent geometry : angle 0.55643 (15982) hydrogen bonds : bond 0.03075 ( 762) hydrogen bonds : angle 3.57500 ( 2247) *********************** 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 184 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.8215 (mmm) cc_final: 0.8006 (ptp) REVERT: A 463 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8589 (t80) REVERT: A 559 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8653 (pt0) REVERT: A 632 PHE cc_start: 0.8198 (p90) cc_final: 0.7980 (p90) REVERT: A 729 MET cc_start: 0.7993 (mmp) cc_final: 0.7736 (mmp) REVERT: A 812 MET cc_start: 0.8842 (mmp) cc_final: 0.8633 (mmp) REVERT: A 818 MET cc_start: 0.7741 (ppp) cc_final: 0.7254 (ppp) REVERT: B 494 THR cc_start: 0.8236 (p) cc_final: 0.7950 (t) REVERT: B 594 TYR cc_start: 0.7571 (t80) cc_final: 0.7288 (t80) REVERT: B 709 LEU cc_start: 0.8552 (mm) cc_final: 0.8274 (mm) outliers start: 17 outliers final: 12 residues processed: 178 average time/residue: 0.0785 time to fit residues: 22.2158 Evaluate side-chains 177 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 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 791 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 451 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 chunk 106 optimal weight: 0.0980 chunk 112 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 HIS ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.114656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.078947 restraints weight = 31358.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.081340 restraints weight = 16768.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.082920 restraints weight = 11108.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.083963 restraints weight = 8481.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.084487 restraints weight = 7152.850| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11708 Z= 0.142 Angle : 0.578 13.100 15982 Z= 0.284 Chirality : 0.039 0.203 1831 Planarity : 0.004 0.062 2070 Dihedral : 3.753 20.210 1670 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.78 % Allowed : 14.15 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.22), residues: 1535 helix: 2.42 (0.16), residues: 1038 sheet: -0.17 (0.52), residues: 121 loop : -0.87 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 532 TYR 0.014 0.001 TYR A 837 PHE 0.012 0.001 PHE B 632 TRP 0.018 0.001 TRP B 591 HIS 0.008 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00330 (11708) covalent geometry : angle 0.57752 (15982) hydrogen bonds : bond 0.03074 ( 762) hydrogen bonds : angle 3.60424 ( 2247) *********************** 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 192 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.8231 (mmm) cc_final: 0.8026 (ptp) REVERT: A 415 MET cc_start: 0.8021 (ttm) cc_final: 0.7817 (ttm) REVERT: A 463 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8579 (t80) REVERT: A 559 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8664 (pt0) REVERT: A 632 PHE cc_start: 0.8288 (p90) cc_final: 0.8056 (p90) REVERT: A 729 MET cc_start: 0.8090 (mmp) cc_final: 0.7817 (mmp) REVERT: A 812 MET cc_start: 0.8906 (mmp) cc_final: 0.8688 (mmp) REVERT: A 818 MET cc_start: 0.7818 (ppp) cc_final: 0.7450 (ppp) REVERT: A 841 TRP cc_start: 0.7967 (t-100) cc_final: 0.7303 (t-100) REVERT: B 244 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8256 (mm-30) REVERT: B 494 THR cc_start: 0.8229 (p) cc_final: 0.7944 (t) REVERT: B 594 TYR cc_start: 0.7662 (t80) cc_final: 0.7391 (t80) REVERT: B 709 LEU cc_start: 0.8597 (mm) cc_final: 0.8330 (mm) outliers start: 20 outliers final: 16 residues processed: 182 average time/residue: 0.0800 time to fit residues: 22.7403 Evaluate side-chains 181 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 135 GLN 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 405 VAL Chi-restraints excluded: chain B residue 451 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 9 optimal weight: 5.9990 chunk 140 optimal weight: 0.0020 chunk 31 optimal weight: 0.3980 chunk 59 optimal weight: 0.9990 chunk 138 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 8 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 GLN ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 728 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.116448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.084597 restraints weight = 31554.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.085641 restraints weight = 17785.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.086004 restraints weight = 11695.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.086553 restraints weight = 12158.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.086328 restraints weight = 10431.310| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11708 Z= 0.108 Angle : 0.577 13.124 15982 Z= 0.277 Chirality : 0.039 0.214 1831 Planarity : 0.004 0.063 2070 Dihedral : 3.719 20.494 1670 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.78 % Allowed : 15.66 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.23), residues: 1535 helix: 2.48 (0.16), residues: 1039 sheet: -0.21 (0.51), residues: 121 loop : -0.83 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 532 TYR 0.012 0.001 TYR A 837 PHE 0.010 0.001 PHE B 632 TRP 0.019 0.001 TRP B 591 HIS 0.007 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00245 (11708) covalent geometry : angle 0.57718 (15982) hydrogen bonds : bond 0.02810 ( 762) hydrogen bonds : angle 3.52295 ( 2247) *********************** 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 194 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 463 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8763 (t80) REVERT: A 556 MET cc_start: 0.8542 (ppp) cc_final: 0.8180 (ppp) REVERT: A 559 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8722 (pt0) REVERT: A 729 MET cc_start: 0.8185 (mmp) cc_final: 0.7836 (mmp) REVERT: A 812 MET cc_start: 0.9037 (mmp) cc_final: 0.8723 (mmp) REVERT: A 818 MET cc_start: 0.7876 (ppp) cc_final: 0.7576 (ppp) REVERT: A 841 TRP cc_start: 0.8077 (t-100) cc_final: 0.7402 (t-100) REVERT: B 244 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8477 (mm-30) REVERT: B 494 THR cc_start: 0.8274 (p) cc_final: 0.8008 (t) REVERT: B 709 LEU cc_start: 0.8715 (mm) cc_final: 0.8428 (mm) REVERT: B 735 MET cc_start: 0.6477 (tpt) cc_final: 0.5727 (tpp) outliers start: 20 outliers final: 13 residues processed: 188 average time/residue: 0.0756 time to fit residues: 22.7146 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 : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 135 GLN 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 B residue 396 TYR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 726 HIS Chi-restraints excluded: chain B residue 734 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 78 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 80 optimal weight: 40.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.115206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.079506 restraints weight = 31849.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.082137 restraints weight = 16458.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.083831 restraints weight = 10699.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.084854 restraints weight = 8130.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.085544 restraints weight = 6831.658| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11708 Z= 0.140 Angle : 0.608 13.296 15982 Z= 0.295 Chirality : 0.040 0.283 1831 Planarity : 0.004 0.064 2070 Dihedral : 3.753 19.857 1670 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.69 % Allowed : 15.84 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.23), residues: 1535 helix: 2.45 (0.16), residues: 1040 sheet: -0.25 (0.50), residues: 121 loop : -0.84 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 532 TYR 0.013 0.001 TYR A 837 PHE 0.029 0.001 PHE A 632 TRP 0.021 0.002 TRP B 591 HIS 0.008 0.001 HIS A 768 Details of bonding type rmsd covalent geometry : bond 0.00324 (11708) covalent geometry : angle 0.60812 (15982) hydrogen bonds : bond 0.03028 ( 762) hydrogen bonds : angle 3.62881 ( 2247) *********************** 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: 19 poor density : 168 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 TYR cc_start: 0.8133 (m-80) cc_final: 0.7879 (m-10) REVERT: A 463 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8576 (t80) REVERT: A 559 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8684 (pt0) REVERT: A 729 MET cc_start: 0.8125 (mmp) cc_final: 0.7837 (mmp) REVERT: A 812 MET cc_start: 0.8840 (mmp) cc_final: 0.8635 (mmp) REVERT: A 818 MET cc_start: 0.7723 (ppp) cc_final: 0.7491 (ppp) REVERT: A 841 TRP cc_start: 0.7978 (t-100) cc_final: 0.7299 (t-100) REVERT: B 244 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8413 (mm-30) REVERT: B 494 THR cc_start: 0.8204 (p) cc_final: 0.7900 (t) REVERT: B 709 LEU cc_start: 0.8557 (mm) cc_final: 0.8279 (mm) outliers start: 19 outliers final: 14 residues processed: 179 average time/residue: 0.0783 time to fit residues: 22.4277 Evaluate side-chains 180 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 135 GLN 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 741 THR Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 405 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 114 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 148 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 GLN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.115558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.080194 restraints weight = 31705.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.082773 restraints weight = 16362.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.084457 restraints weight = 10629.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.085449 restraints weight = 8043.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.086098 restraints weight = 6783.086| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3013 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= 0.122 Angle : 0.612 13.758 15982 Z= 0.294 Chirality : 0.040 0.287 1831 Planarity : 0.004 0.064 2070 Dihedral : 3.772 20.061 1670 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.33 % Allowed : 16.37 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.23), residues: 1535 helix: 2.47 (0.16), residues: 1038 sheet: -0.22 (0.50), residues: 121 loop : -0.84 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 532 TYR 0.013 0.001 TYR A 837 PHE 0.014 0.001 PHE B 531 TRP 0.021 0.002 TRP B 674 HIS 0.007 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00285 (11708) covalent geometry : angle 0.61242 (15982) hydrogen bonds : bond 0.02939 ( 762) hydrogen bonds : angle 3.64541 ( 2247) ********************** 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 186 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 TYR cc_start: 0.8098 (m-80) cc_final: 0.7849 (m-10) REVERT: A 463 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8571 (t80) REVERT: A 559 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8671 (pt0) REVERT: A 729 MET cc_start: 0.8132 (mmp) cc_final: 0.7826 (mmp) REVERT: A 812 MET cc_start: 0.8838 (mmp) cc_final: 0.8619 (mmp) REVERT: A 841 TRP cc_start: 0.7962 (t-100) cc_final: 0.7287 (t-100) REVERT: B 244 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8381 (mm-30) REVERT: B 494 THR cc_start: 0.8237 (p) cc_final: 0.7929 (t) REVERT: B 709 LEU cc_start: 0.8580 (mm) cc_final: 0.8301 (mm) outliers start: 15 outliers final: 14 residues processed: 181 average time/residue: 0.0729 time to fit residues: 21.0289 Evaluate side-chains 181 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 135 GLN 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 791 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 405 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 Chi-restraints excluded: chain B residue 726 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 131 optimal weight: 0.1980 chunk 142 optimal weight: 0.2980 chunk 139 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** 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 = 0.3848 r_free = 0.3848 target = 0.116159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.080913 restraints weight = 31720.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.083527 restraints weight = 16370.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.085237 restraints weight = 10614.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.086285 restraints weight = 8007.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.086931 restraints weight = 6729.123| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11708 Z= 0.111 Angle : 0.613 14.175 15982 Z= 0.293 Chirality : 0.040 0.282 1831 Planarity : 0.004 0.064 2070 Dihedral : 3.746 19.814 1670 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.33 % Allowed : 17.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.23), residues: 1535 helix: 2.47 (0.16), residues: 1038 sheet: -0.21 (0.50), residues: 121 loop : -0.83 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 532 TYR 0.013 0.001 TYR A 837 PHE 0.019 0.001 PHE A 632 TRP 0.027 0.002 TRP B 674 HIS 0.008 0.001 HIS A 768 Details of bonding type rmsd covalent geometry : bond 0.00257 (11708) covalent geometry : angle 0.61327 (15982) hydrogen bonds : bond 0.02867 ( 762) hydrogen bonds : angle 3.61396 ( 2247) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2265.08 seconds wall clock time: 39 minutes 46.63 seconds (2386.63 seconds total)