Starting phenix.real_space_refine on Wed May 14 06:39:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dtg_27697/05_2025/8dtg_27697.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dtg_27697/05_2025/8dtg_27697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dtg_27697/05_2025/8dtg_27697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dtg_27697/05_2025/8dtg_27697.map" model { file = "/net/cci-nas-00/data/ceres_data/8dtg_27697/05_2025/8dtg_27697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dtg_27697/05_2025/8dtg_27697.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 7290 2.51 5 N 1935 2.21 5 O 2146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11451 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 5985 Classifications: {'peptide': 802} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 766} Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 5466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5466 Classifications: {'peptide': 737} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 702} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 410 Unresolved non-hydrogen dihedrals: 273 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 5, 'ASP:plan': 4, 'GLU:plan': 13, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 179 Time building chain proxies: 8.41, per 1000 atoms: 0.73 Number of scatterers: 11451 At special positions: 0 Unit cell: (97.68, 99.44, 168.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2146 8.00 N 1935 7.00 C 7290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.6 seconds 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2904 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 4 sheets defined 71.2% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 58 through 73 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 92 through 107 Processing helix chain 'A' and resid 110 through 124 removed outlier: 3.587A pdb=" N LEU A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 141 Processing helix chain 'A' and resid 144 through 165 removed outlier: 3.676A pdb=" N ALA A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 185 through 199 removed outlier: 3.832A pdb=" N TYR A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 219 through 233 removed outlier: 3.528A pdb=" N TYR A 223 " --> pdb=" O TYR A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 253 through 275 Processing helix chain 'A' and resid 276 through 291 removed outlier: 3.599A pdb=" N TYR A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 309 Processing helix chain 'A' and resid 310 through 325 Processing helix chain 'A' and resid 328 through 342 removed outlier: 3.619A pdb=" N CYS A 332 " --> pdb=" O CYS A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 362 through 377 Processing helix chain 'A' and resid 378 through 393 Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 412 through 427 Processing helix chain 'A' and resid 430 through 442 Processing helix chain 'A' and resid 450 through 466 Processing helix chain 'A' and resid 497 through 507 removed outlier: 5.305A pdb=" N ALA A 503 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Proline residue: A 504 - end of helix Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.709A pdb=" N LYS A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 560 Processing helix chain 'A' and resid 576 through 582 removed outlier: 3.853A pdb=" N MET A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS A 582 " --> pdb=" O GLY A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 653 removed outlier: 3.964A pdb=" N SER A 651 " --> pdb=" O THR A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 667 through 681 removed outlier: 3.612A pdb=" N LEU A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN A 672 " --> pdb=" O PRO A 668 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 694 Processing helix chain 'A' and resid 695 through 709 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 724 through 731 Processing helix chain 'A' and resid 732 through 735 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 767 through 781 removed outlier: 5.105A pdb=" N GLY A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL A 774 " --> pdb=" O HIS A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 784 No H-bonds generated for 'chain 'A' and resid 782 through 784' Processing helix chain 'A' and resid 789 through 803 removed outlier: 3.734A pdb=" N ASP A 803 " --> pdb=" O ASP A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 820 removed outlier: 4.238A pdb=" N ARG A 815 " --> pdb=" O ARG A 811 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP A 816 " --> pdb=" O MET A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 824 Processing helix chain 'A' and resid 825 through 846 Processing helix chain 'B' and resid 111 through 124 Processing helix chain 'B' and resid 126 through 141 Processing helix chain 'B' and resid 144 through 166 Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 185 through 199 removed outlier: 3.605A pdb=" N TYR B 189 " --> pdb=" O TYR B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 219 through 233 removed outlier: 3.966A pdb=" N TYR B 223 " --> pdb=" O TYR B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 250 Processing helix chain 'B' and resid 253 through 274 Processing helix chain 'B' and resid 276 through 291 Processing helix chain 'B' and resid 294 through 308 Processing helix chain 'B' and resid 311 through 325 Processing helix chain 'B' and resid 328 through 342 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 362 through 377 Processing helix chain 'B' and resid 378 through 393 Processing helix chain 'B' and resid 396 through 410 removed outlier: 3.641A pdb=" N PHE B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 430 through 445 removed outlier: 3.818A pdb=" N TYR B 443 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 467 Processing helix chain 'B' and resid 497 through 507 removed outlier: 5.344A pdb=" N ALA B 503 " --> pdb=" O TYR B 499 " (cutoff:3.500A) Proline residue: B 504 - end of helix Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 549 through 561 Processing helix chain 'B' and resid 576 through 582 removed outlier: 3.609A pdb=" N CYS B 582 " --> pdb=" O GLY B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 642 removed outlier: 3.677A pdb=" N ALA B 641 " --> pdb=" O SER B 638 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY B 642 " --> pdb=" O PRO B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 638 through 642' Processing helix chain 'B' and resid 647 through 652 removed outlier: 4.051A pdb=" N SER B 651 " --> pdb=" O THR B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 681 Processing helix chain 'B' and resid 690 through 694 Processing helix chain 'B' and resid 695 through 709 removed outlier: 3.619A pdb=" N LEU B 709 " --> pdb=" O THR B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 716 Processing helix chain 'B' and resid 724 through 731 Processing helix chain 'B' and resid 732 through 735 Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 767 through 780 removed outlier: 5.243A pdb=" N GLY B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 774 " --> pdb=" O HIS B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 784 No H-bonds generated for 'chain 'B' and resid 782 through 784' Processing helix chain 'B' and resid 789 through 803 removed outlier: 3.701A pdb=" N ASP B 803 " --> pdb=" O ASP B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 821 removed outlier: 4.194A pdb=" N ARG B 815 " --> pdb=" O ARG B 811 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASP B 816 " --> pdb=" O MET B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 824 No H-bonds generated for 'chain 'B' and resid 822 through 824' Processing helix chain 'B' and resid 825 through 846 Processing sheet with id=AA1, first strand: chain 'A' and resid 541 through 544 removed outlier: 8.418A pdb=" N VAL A 541 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL A 515 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LYS A 543 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL A 517 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE A 483 " --> pdb=" O LYS A 514 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL A 516 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 485 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N TYR A 518 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TYR A 487 " --> pdb=" O TYR A 518 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLN A 588 " --> pdb=" O TYR A 605 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE A 607 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR A 590 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N ASP A 609 " --> pdb=" O THR A 590 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 716 through 719 removed outlier: 8.462A pdb=" N ASP A 717 " --> pdb=" O SER A 684 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 686 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU A 719 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 688 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A 655 " --> pdb=" O ARG A 685 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL A 687 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE A 657 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N LYS A 689 " --> pdb=" O PHE A 657 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER A 659 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER A 738 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N MET A 763 " --> pdb=" O SER A 738 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA A 787 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR A 762 " --> pdb=" O ALA A 787 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 543 through 544 removed outlier: 8.269A pdb=" N LYS B 543 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 517 " --> pdb=" O LYS B 543 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE B 483 " --> pdb=" O LYS B 514 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL B 516 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 485 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N TYR B 518 " --> pdb=" O ILE B 485 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR B 487 " --> pdb=" O TYR B 518 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR B 484 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL B 566 " --> pdb=" O THR B 484 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY B 486 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN B 588 " --> pdb=" O TYR B 605 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE B 607 " --> pdb=" O GLN B 588 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR B 590 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N ASP B 609 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ARG B 606 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU B 628 " --> pdb=" O ARG B 606 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR B 608 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 684 through 688 removed outlier: 3.959A pdb=" N SER B 659 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER B 738 " --> pdb=" O VAL B 761 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N MET B 763 " --> pdb=" O SER B 738 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA B 787 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR B 762 " --> pdb=" O ALA B 787 " (cutoff:3.500A) 762 hydrogen bonds defined for protein. 2247 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 3.72 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.890 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.060 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1535 helix: 0.97 (0.16), residues: 1039 sheet: -0.69 (0.56), residues: 105 loop : -2.28 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 591 HIS 0.033 0.002 HIS A 508 PHE 0.033 0.002 PHE A 463 TYR 0.053 0.002 TYR A 837 ARG 0.009 0.001 ARG B 701 Details of bonding type rmsd hydrogen bonds : bond 0.12265 ( 762) hydrogen bonds : angle 5.37708 ( 2247) covalent geometry : bond 0.00375 (11708) covalent geometry : angle 0.63210 (15982) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.250 Fit side-chains REVERT: A 491 ASP cc_start: 0.8120 (m-30) cc_final: 0.7752 (m-30) REVERT: A 566 VAL cc_start: 0.8467 (t) cc_final: 0.7994 (t) REVERT: A 580 MET cc_start: 0.8624 (mtt) cc_final: 0.8381 (mtt) REVERT: A 818 MET cc_start: 0.8215 (ppp) cc_final: 0.7831 (ptt) REVERT: B 209 TYR cc_start: 0.8219 (m-80) cc_final: 0.7870 (m-80) REVERT: B 473 TRP cc_start: 0.7923 (m-90) cc_final: 0.7711 (m-90) REVERT: B 494 THR cc_start: 0.8122 (p) cc_final: 0.7835 (t) REVERT: B 793 TYR cc_start: 0.8215 (t80) cc_final: 0.7797 (t80) REVERT: B 837 TYR cc_start: 0.8642 (m-10) cc_final: 0.8417 (m-10) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1666 time to fit residues: 49.5926 Evaluate side-chains 162 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.0870 chunk 115 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 0.3980 chunk 89 optimal weight: 20.0000 chunk 138 optimal weight: 2.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 167 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.115247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.084299 restraints weight = 31151.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.084339 restraints weight = 17347.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.083947 restraints weight = 14480.025| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11708 Z= 0.155 Angle : 0.595 8.691 15982 Z= 0.305 Chirality : 0.041 0.161 1831 Planarity : 0.005 0.058 2070 Dihedral : 3.874 17.388 1670 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.98 % Allowed : 7.56 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.22), residues: 1535 helix: 2.00 (0.16), residues: 1035 sheet: -0.51 (0.49), residues: 125 loop : -1.21 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 591 HIS 0.018 0.002 HIS A 508 PHE 0.017 0.002 PHE A 463 TYR 0.028 0.002 TYR A 837 ARG 0.004 0.001 ARG A 532 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 762) hydrogen bonds : angle 4.04411 ( 2247) covalent geometry : bond 0.00348 (11708) covalent geometry : angle 0.59499 (15982) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 ASP cc_start: 0.8371 (m-30) cc_final: 0.7866 (m-30) REVERT: A 816 ASP cc_start: 0.9050 (m-30) cc_final: 0.8846 (p0) REVERT: A 818 MET cc_start: 0.8538 (ppp) cc_final: 0.8222 (ptt) REVERT: B 209 TYR cc_start: 0.8244 (m-80) cc_final: 0.7999 (m-80) REVERT: B 231 LYS cc_start: 0.8859 (tttm) cc_final: 0.8531 (ttmt) REVERT: B 244 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8248 (mm-30) REVERT: B 473 TRP cc_start: 0.8016 (m-90) cc_final: 0.7478 (m-90) REVERT: B 494 THR cc_start: 0.8230 (p) cc_final: 0.7974 (t) REVERT: B 531 PHE cc_start: 0.8894 (m-80) cc_final: 0.8663 (m-80) REVERT: B 567 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8569 (tm-30) outliers start: 11 outliers final: 7 residues processed: 195 average time/residue: 0.2137 time to fit residues: 63.6226 Evaluate side-chains 166 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 96 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 30.0000 chunk 106 optimal weight: 0.8980 chunk 63 optimal weight: 0.0070 chunk 40 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 445 ASN ** B 442 ASN ** 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 = 0.116826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.081254 restraints weight = 31557.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.083875 restraints weight = 16273.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.085500 restraints weight = 10543.056| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1874 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= 0.119 Angle : 0.566 11.840 15982 Z= 0.280 Chirality : 0.039 0.140 1831 Planarity : 0.004 0.059 2070 Dihedral : 3.775 18.190 1670 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.98 % Allowed : 10.94 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.22), residues: 1535 helix: 2.27 (0.16), residues: 1038 sheet: -0.18 (0.51), residues: 119 loop : -1.08 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 591 HIS 0.013 0.001 HIS A 508 PHE 0.013 0.001 PHE A 253 TYR 0.024 0.001 TYR A 837 ARG 0.007 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 762) hydrogen bonds : angle 3.70553 ( 2247) covalent geometry : bond 0.00265 (11708) covalent geometry : angle 0.56613 (15982) *********************** 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 191 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.8248 (mmm) cc_final: 0.7954 (ptp) REVERT: A 202 TYR cc_start: 0.8572 (m-10) cc_final: 0.8372 (m-10) REVERT: A 491 ASP cc_start: 0.8400 (m-30) cc_final: 0.7964 (m-30) REVERT: A 632 PHE cc_start: 0.8344 (p90) cc_final: 0.8006 (p90) REVERT: A 812 MET cc_start: 0.8844 (mmp) cc_final: 0.8643 (mmp) REVERT: A 818 MET cc_start: 0.8315 (ppp) cc_final: 0.8045 (ptt) REVERT: B 244 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8573 (mm-30) REVERT: B 494 THR cc_start: 0.8226 (p) cc_final: 0.7990 (t) REVERT: B 760 CYS cc_start: 0.8552 (p) cc_final: 0.8342 (p) outliers start: 11 outliers final: 9 residues processed: 187 average time/residue: 0.1922 time to fit residues: 55.0551 Evaluate side-chains 167 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 767 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.5682 > 50: distance: 50 - 56: 15.533 distance: 56 - 57: 21.310 distance: 56 - 62: 20.063 distance: 57 - 58: 3.965 distance: 57 - 60: 24.780 distance: 58 - 59: 30.677 distance: 58 - 63: 16.295 distance: 60 - 61: 24.343 distance: 61 - 62: 39.900 distance: 63 - 64: 19.307 distance: 64 - 65: 7.050 distance: 64 - 67: 11.965 distance: 65 - 66: 34.082 distance: 65 - 71: 27.096 distance: 67 - 68: 18.806 distance: 68 - 69: 15.746 distance: 68 - 70: 21.239 distance: 72 - 75: 13.514 distance: 73 - 74: 4.607 distance: 73 - 77: 44.798 distance: 75 - 76: 48.806 distance: 77 - 78: 7.184 distance: 78 - 79: 42.368 distance: 78 - 81: 12.308 distance: 79 - 80: 43.347 distance: 79 - 88: 4.425 distance: 81 - 82: 8.564 distance: 82 - 83: 7.102 distance: 82 - 84: 19.524 distance: 83 - 85: 22.842 distance: 84 - 86: 21.462 distance: 85 - 87: 28.061 distance: 86 - 87: 14.211 distance: 88 - 89: 39.187 distance: 89 - 90: 26.714 distance: 89 - 92: 29.319 distance: 90 - 91: 25.517 distance: 90 - 96: 24.441 distance: 92 - 93: 21.309 distance: 93 - 94: 30.301 distance: 93 - 95: 43.743 distance: 97 - 98: 35.036 distance: 98 - 99: 7.277 distance: 98 - 102: 27.672 distance: 102 - 103: 14.182 distance: 103 - 104: 7.704 distance: 103 - 106: 8.082 distance: 104 - 105: 21.818 distance: 104 - 114: 22.502 distance: 107 - 108: 29.290 distance: 107 - 109: 9.315 distance: 108 - 110: 15.823 distance: 110 - 112: 29.084 distance: 111 - 112: 11.973 distance: 112 - 113: 23.762 distance: 114 - 115: 21.581 distance: 115 - 116: 8.810 distance: 115 - 118: 26.144 distance: 116 - 121: 16.862 distance: 118 - 119: 15.677 distance: 118 - 120: 48.106 distance: 121 - 122: 23.334 distance: 121 - 127: 51.644 distance: 122 - 125: 37.430 distance: 123 - 128: 16.764 distance: 125 - 126: 4.809 distance: 126 - 127: 43.619 distance: 128 - 129: 32.818 distance: 129 - 130: 35.746 distance: 129 - 132: 26.581 distance: 130 - 131: 18.718 distance: 130 - 134: 19.244 distance: 132 - 133: 16.941