Starting phenix.real_space_refine on Wed May 14 21:19:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9imz_60697/05_2025/9imz_60697_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9imz_60697/05_2025/9imz_60697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9imz_60697/05_2025/9imz_60697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9imz_60697/05_2025/9imz_60697.map" model { file = "/net/cci-nas-00/data/ceres_data/9imz_60697/05_2025/9imz_60697_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9imz_60697/05_2025/9imz_60697_neut.cif" } resolution = 3.75 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= -0.000 sd= 0.075 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 53 5.16 5 C 7835 2.51 5 N 2083 2.21 5 O 2196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12167 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4325 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 505} Chain breaks: 9 Chain: "B" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4122 Classifications: {'peptide': 516} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 484} Chain breaks: 7 Chain: "C" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1240 Classifications: {'peptide': 154} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 141} Chain: "D" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1240 Classifications: {'peptide': 154} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 141} Chain: "E" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1240 Classifications: {'peptide': 154} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 141} Time building chain proxies: 7.37, per 1000 atoms: 0.61 Number of scatterers: 12167 At special positions: 0 Unit cell: (85.8, 122.1, 149.6, 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 53 16.00 O 2196 8.00 N 2083 7.00 C 7835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.6 seconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2882 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 52.6% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 removed outlier: 4.478A pdb=" N LEU A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 23 Processing helix chain 'A' and resid 34 through 41 Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 292 through 296 removed outlier: 4.071A pdb=" N ARG A 295 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 296 " --> pdb=" O PRO A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 296' Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 320 through 332 removed outlier: 3.875A pdb=" N GLU A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.667A pdb=" N CYS A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 385 through 394 removed outlier: 3.684A pdb=" N LEU A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'A' and resid 402 through 416 removed outlier: 3.527A pdb=" N GLN A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 467 removed outlier: 3.864A pdb=" N LYS A 454 " --> pdb=" O HIS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 482 removed outlier: 3.668A pdb=" N GLY A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'A' and resid 497 through 515 removed outlier: 3.883A pdb=" N PHE A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A 515 " --> pdb=" O GLN A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 547 removed outlier: 3.842A pdb=" N ARG A 544 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 547 " --> pdb=" O TRP A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 568 through 579 removed outlier: 3.803A pdb=" N ARG A 572 " --> pdb=" O GLN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 600 removed outlier: 3.876A pdb=" N ASN A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 585 " --> pdb=" O PHE A 581 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY A 600 " --> pdb=" O GLN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 645 removed outlier: 3.791A pdb=" N VAL A 628 " --> pdb=" O LYS A 624 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 645 " --> pdb=" O GLY A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 649 removed outlier: 3.586A pdb=" N ARG A 649 " --> pdb=" O LEU A 646 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 646 through 649' Processing helix chain 'A' and resid 659 through 669 removed outlier: 3.922A pdb=" N ILE A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 686 removed outlier: 3.589A pdb=" N ALA A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 700 removed outlier: 3.739A pdb=" N THR A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 701 through 703 No H-bonds generated for 'chain 'A' and resid 701 through 703' Processing helix chain 'A' and resid 706 through 710 Processing helix chain 'A' and resid 711 through 727 removed outlier: 4.463A pdb=" N ASP A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE A 716 " --> pdb=" O TYR A 712 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 726 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 727 " --> pdb=" O LEU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 753 removed outlier: 3.601A pdb=" N LEU A 752 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 766 removed outlier: 3.549A pdb=" N GLU A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 799 Processing helix chain 'A' and resid 800 through 802 No H-bonds generated for 'chain 'A' and resid 800 through 802' Processing helix chain 'A' and resid 803 through 815 removed outlier: 3.604A pdb=" N LYS A 807 " --> pdb=" O GLY A 803 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 Processing helix chain 'B' and resid 14 through 24 Processing helix chain 'B' and resid 34 through 41 Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 48 through 61 Processing helix chain 'B' and resid 292 through 296 removed outlier: 4.123A pdb=" N VAL B 296 " --> pdb=" O PRO B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 315 Processing helix chain 'B' and resid 320 through 333 removed outlier: 3.639A pdb=" N THR B 333 " --> pdb=" O PHE B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 375 removed outlier: 3.510A pdb=" N CYS B 366 " --> pdb=" O SER B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.578A pdb=" N LEU B 381 " --> pdb=" O HIS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 395 removed outlier: 3.583A pdb=" N GLU B 394 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 402 removed outlier: 4.163A pdb=" N LEU B 399 " --> pdb=" O ASN B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 413 Processing helix chain 'B' and resid 450 through 470 removed outlier: 3.751A pdb=" N LYS B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 482 Processing helix chain 'B' and resid 483 through 496 Processing helix chain 'B' and resid 497 through 515 removed outlier: 3.806A pdb=" N PHE B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLN B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER B 515 " --> pdb=" O GLN B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 547 removed outlier: 3.991A pdb=" N TRP B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG B 544 " --> pdb=" O GLY B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 551 Processing helix chain 'B' and resid 565 through 567 No H-bonds generated for 'chain 'B' and resid 565 through 567' Processing helix chain 'B' and resid 568 through 579 removed outlier: 4.149A pdb=" N ARG B 572 " --> pdb=" O GLN B 568 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP B 573 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER B 579 " --> pdb=" O ILE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 599 Processing helix chain 'B' and resid 624 through 645 removed outlier: 3.881A pdb=" N VAL B 628 " --> pdb=" O LYS B 624 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 645 " --> pdb=" O GLY B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 668 removed outlier: 4.330A pdb=" N ASP B 661 " --> pdb=" O GLY B 657 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER B 662 " --> pdb=" O GLU B 658 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 686 removed outlier: 3.924A pdb=" N LEU B 679 " --> pdb=" O ASP B 675 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 701 removed outlier: 3.510A pdb=" N THR B 692 " --> pdb=" O ARG B 688 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 705 through 710 removed outlier: 4.359A pdb=" N LEU B 709 " --> pdb=" O HIS B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 725 removed outlier: 4.148A pdb=" N ASP B 715 " --> pdb=" O GLU B 711 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE B 716 " --> pdb=" O TYR B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 736 removed outlier: 3.603A pdb=" N LYS B 736 " --> pdb=" O GLU B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 753 removed outlier: 3.792A pdb=" N PHE B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 764 removed outlier: 3.558A pdb=" N LEU B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE B 763 " --> pdb=" O GLU B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 799 Processing helix chain 'B' and resid 800 through 802 No H-bonds generated for 'chain 'B' and resid 800 through 802' Processing helix chain 'B' and resid 803 through 815 removed outlier: 3.560A pdb=" N LYS B 807 " --> pdb=" O GLY B 803 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP B 812 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL B 813 " --> pdb=" O LEU B 809 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY B 815 " --> pdb=" O SER B 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 52 No H-bonds generated for 'chain 'C' and resid 50 through 52' Processing helix chain 'C' and resid 119 through 125 Processing helix chain 'D' and resid 50 through 54 removed outlier: 4.176A pdb=" N TYR D 53 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP D 54 " --> pdb=" O GLU D 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 50 through 54' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.762A pdb=" N LEU D 83 " --> pdb=" O ASN D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 125 Processing helix chain 'E' and resid 85 through 90 removed outlier: 3.766A pdb=" N VAL E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 125 removed outlier: 3.774A pdb=" N ASN E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 197 removed outlier: 3.736A pdb=" N ARG A 195 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE E 42 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER E 59 " --> pdb=" O TRP E 40 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP E 40 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU E 61 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU E 38 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE E 107 " --> pdb=" O CYS E 99 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR E 101 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N GLU E 105 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 13.648A pdb=" N GLN E 104 " --> pdb=" O ARG E 148 " (cutoff:3.500A) removed outlier: 12.128A pdb=" N ARG E 148 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 11.957A pdb=" N PHE E 106 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N VAL E 146 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 11.094A pdb=" N ARG E 108 " --> pdb=" O PRO E 144 " (cutoff:3.500A) removed outlier: 11.305A pdb=" N GLY E 110 " --> pdb=" O SER E 142 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N SER E 142 " --> pdb=" O GLY E 110 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR E 112 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER E 16 " --> pdb=" O ARG E 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 826 through 827 removed outlier: 7.307A pdb=" N ILE C 42 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER C 59 " --> pdb=" O TRP C 40 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TRP C 40 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU C 61 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU C 38 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL C 94 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLY C 91 " --> pdb=" O ASN C 114 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN C 114 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR C 93 " --> pdb=" O TYR C 112 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR C 112 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 95 " --> pdb=" O GLY C 110 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY C 110 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE C 97 " --> pdb=" O ARG C 108 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ARG C 108 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N CYS C 99 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 826 through 827 removed outlier: 7.307A pdb=" N ILE C 42 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER C 59 " --> pdb=" O TRP C 40 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TRP C 40 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU C 61 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU C 38 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL C 94 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLY C 91 " --> pdb=" O ASN C 114 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN C 114 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR C 93 " --> pdb=" O TYR C 112 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR C 112 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 95 " --> pdb=" O GLY C 110 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY C 110 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE C 97 " --> pdb=" O ARG C 108 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ARG C 108 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N CYS C 99 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 830 through 832 removed outlier: 3.693A pdb=" N THR A 832 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ARG C 69 " --> pdb=" O THR A 832 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLN C 23 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL C 11 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU C 25 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL C 9 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR C 27 " --> pdb=" O ASN C 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 11 removed outlier: 6.677A pdb=" N THR D 27 " --> pdb=" O ASN D 7 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL D 9 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU D 25 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL D 11 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLN D 23 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 76 " --> pdb=" O PHE D 22 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE D 24 " --> pdb=" O PHE D 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 16 through 17 removed outlier: 3.647A pdb=" N ASN D 114 " --> pdb=" O ASN D 138 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR D 101 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE D 107 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY D 91 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 42 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP D 58 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TYR D 44 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL D 56 " --> pdb=" O TYR D 44 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 16 through 17 removed outlier: 3.647A pdb=" N ASN D 114 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 4 through 12 removed outlier: 5.605A pdb=" N VAL E 6 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU E 29 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLN E 23 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE E 26 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE E 72 " --> pdb=" O ILE E 26 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1590 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: 3.51 Time building geometry restraints manager: 3.19 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: 3853 1.34 - 1.46: 1927 1.46 - 1.58: 6595 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 12453 Sorted by residual: bond pdb=" CZ ARG A 410 " pdb=" NH2 ARG A 410 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.46e+00 bond pdb=" CZ ARG A 336 " pdb=" NH2 ARG A 336 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.93e+00 bond pdb=" CZ ARG A 63 " pdb=" NH2 ARG A 63 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.91e+00 bond pdb=" CZ ARG B 725 " pdb=" NH2 ARG B 725 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.62e+00 bond pdb=" CZ ARG A 819 " pdb=" NH2 ARG A 819 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.52e+00 ... (remaining 12448 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 16187 1.86 - 3.72: 595 3.72 - 5.58: 98 5.58 - 7.44: 11 7.44 - 9.30: 2 Bond angle restraints: 16893 Sorted by residual: angle pdb=" OE1 GLN B 754 " pdb=" CD GLN B 754 " pdb=" NE2 GLN B 754 " ideal model delta sigma weight residual 122.60 118.34 4.26 1.00e+00 1.00e+00 1.82e+01 angle pdb=" C ASN D 14 " pdb=" N PRO D 15 " pdb=" CD PRO D 15 " ideal model delta sigma weight residual 120.60 129.90 -9.30 2.20e+00 2.07e-01 1.79e+01 angle pdb=" OE1 GLN A 330 " pdb=" CD GLN A 330 " pdb=" NE2 GLN A 330 " ideal model delta sigma weight residual 122.60 118.65 3.95 1.00e+00 1.00e+00 1.56e+01 angle pdb=" OE1 GLN A 67 " pdb=" CD GLN A 67 " pdb=" NE2 GLN A 67 " ideal model delta sigma weight residual 122.60 118.65 3.95 1.00e+00 1.00e+00 1.56e+01 angle pdb=" CA ASP C 86 " pdb=" CB ASP C 86 " pdb=" CG ASP C 86 " ideal model delta sigma weight residual 112.60 116.49 -3.89 1.00e+00 1.00e+00 1.51e+01 ... (remaining 16888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 6468 17.55 - 35.10: 784 35.10 - 52.65: 194 52.65 - 70.19: 34 70.19 - 87.74: 25 Dihedral angle restraints: 7505 sinusoidal: 3089 harmonic: 4416 Sorted by residual: dihedral pdb=" CA PRO A 293 " pdb=" C PRO A 293 " pdb=" N ALA A 294 " pdb=" CA ALA A 294 " ideal model delta harmonic sigma weight residual -180.00 -159.81 -20.19 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA PRO C 130 " pdb=" C PRO C 130 " pdb=" N ASP C 131 " pdb=" CA ASP C 131 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ALA A 334 " pdb=" C ALA A 334 " pdb=" N ARG A 335 " pdb=" CA ARG A 335 " ideal model delta harmonic sigma weight residual 180.00 -162.65 -17.35 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 7502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1543 0.053 - 0.106: 260 0.106 - 0.160: 71 0.160 - 0.213: 8 0.213 - 0.266: 3 Chirality restraints: 1885 Sorted by residual: chirality pdb=" CA PHE A 360 " pdb=" N PHE A 360 " pdb=" C PHE A 360 " pdb=" CB PHE A 360 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ASN B 316 " pdb=" N ASN B 316 " pdb=" C ASN B 316 " pdb=" CB ASN B 316 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA PRO A 293 " pdb=" N PRO A 293 " pdb=" C PRO A 293 " pdb=" CB PRO A 293 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1882 not shown) Planarity restraints: 2192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 812 " 0.067 2.00e-02 2.50e+03 4.34e-02 4.71e+01 pdb=" CG TRP A 812 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP A 812 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 812 " -0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP A 812 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP A 812 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 812 " -0.076 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 812 " 0.030 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 812 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP A 812 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 117 " -0.049 2.00e-02 2.50e+03 2.67e-02 1.43e+01 pdb=" CG TYR C 117 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR C 117 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR C 117 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR C 117 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR C 117 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR C 117 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 117 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 801 " -0.035 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" CG TYR B 801 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR B 801 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 801 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR B 801 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR B 801 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR B 801 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 801 " -0.046 2.00e-02 2.50e+03 ... (remaining 2189 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 89 2.60 - 3.17: 9851 3.17 - 3.75: 17529 3.75 - 4.32: 21574 4.32 - 4.90: 36564 Nonbonded interactions: 85607 Sorted by model distance: nonbonded pdb=" NE ARG A 687 " pdb=" O GLU A 781 " model vdw 2.021 3.120 nonbonded pdb=" OH TYR A 309 " pdb=" OE1 GLU A 324 " model vdw 2.201 3.040 nonbonded pdb=" O GLU B 698 " pdb=" OG SER B 701 " model vdw 2.216 3.040 nonbonded pdb=" O ALA B 3 " pdb=" OG SER B 7 " model vdw 2.219 3.040 nonbonded pdb=" NE2 GLN A 669 " pdb=" OG SER B 592 " model vdw 2.242 3.120 ... (remaining 85602 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 1 through 67 or resid 287 through 515 or resid 538 through \ 832)) selection = (chain 'B' and (resid 1 through 23 or resid 33 through 606 or resid 621 through \ 767 or resid 780 through 832)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.200 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.190 Find NCS groups from input model: 0.440 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 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 : 0.005 0.083 12453 Z= 0.277 Angle : 0.765 9.300 16893 Z= 0.457 Chirality : 0.046 0.266 1885 Planarity : 0.005 0.064 2192 Dihedral : 16.758 87.743 4623 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 23.23 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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: 1.07 (0.22), residues: 1476 helix: 1.61 (0.21), residues: 629 sheet: 1.23 (0.36), residues: 207 loop : -0.34 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP A 812 HIS 0.003 0.000 HIS B 469 PHE 0.030 0.002 PHE B 326 TYR 0.049 0.003 TYR C 117 ARG 0.009 0.000 ARG B 295 Details of bonding type rmsd hydrogen bonds : bond 0.21357 ( 541) hydrogen bonds : angle 6.20791 ( 1590) covalent geometry : bond 0.00509 (12453) covalent geometry : angle 0.76543 (16893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 MET cc_start: 0.8352 (ttp) cc_final: 0.8138 (tmm) REVERT: A 791 ASP cc_start: 0.8250 (t0) cc_final: 0.8037 (t0) REVERT: B 1 MET cc_start: 0.3669 (mpp) cc_final: 0.2019 (tpt) REVERT: B 22 ILE cc_start: 0.8173 (mm) cc_final: 0.7925 (mt) REVERT: B 45 LEU cc_start: 0.8561 (mt) cc_final: 0.8348 (pp) REVERT: B 371 VAL cc_start: 0.9464 (t) cc_final: 0.9232 (m) REVERT: B 488 MET cc_start: 0.8636 (ttp) cc_final: 0.8419 (ttt) REVERT: B 512 MET cc_start: 0.8311 (ttt) cc_final: 0.8037 (ttm) REVERT: B 801 TYR cc_start: 0.8538 (p90) cc_final: 0.8154 (p90) REVERT: C 143 ASN cc_start: 0.8644 (m110) cc_final: 0.8325 (p0) REVERT: D 30 CYS cc_start: 0.8427 (m) cc_final: 0.7684 (t) REVERT: D 33 ASP cc_start: 0.7255 (m-30) cc_final: 0.7020 (t0) REVERT: D 88 ASP cc_start: 0.7898 (m-30) cc_final: 0.7058 (t0) REVERT: D 107 ILE cc_start: 0.9071 (tt) cc_final: 0.8835 (mt) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2335 time to fit residues: 68.3649 Evaluate side-chains 113 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 508 GLN A 705 HIS B 55 ASN B 67 GLN B 508 GLN C 20 ASN E 5 GLN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.115852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.084102 restraints weight = 34382.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.082163 restraints weight = 22041.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.082706 restraints weight = 24712.429| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12453 Z= 0.174 Angle : 0.641 11.067 16893 Z= 0.323 Chirality : 0.043 0.191 1885 Planarity : 0.005 0.050 2192 Dihedral : 4.168 18.995 1637 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.65 % Allowed : 22.41 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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: 1.08 (0.22), residues: 1476 helix: 1.67 (0.20), residues: 648 sheet: 1.03 (0.36), residues: 216 loop : -0.41 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 40 HIS 0.005 0.001 HIS B 500 PHE 0.023 0.002 PHE B 505 TYR 0.014 0.002 TYR B 309 ARG 0.007 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.05459 ( 541) hydrogen bonds : angle 4.84226 ( 1590) covalent geometry : bond 0.00415 (12453) covalent geometry : angle 0.64123 (16893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 115 time to evaluate : 1.309 Fit side-chains revert: symmetry clash REVERT: B 22 ILE cc_start: 0.8739 (mm) cc_final: 0.8483 (mt) REVERT: B 385 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8460 (p0) REVERT: B 719 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8759 (tt) REVERT: B 801 TYR cc_start: 0.8488 (p90) cc_final: 0.7790 (p90) REVERT: C 8 ASN cc_start: 0.7661 (t0) cc_final: 0.7443 (t0) REVERT: D 72 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6686 (p90) REVERT: D 88 ASP cc_start: 0.8101 (m-30) cc_final: 0.7219 (t0) REVERT: E 40 TRP cc_start: 0.8273 (m100) cc_final: 0.8028 (m100) REVERT: E 99 CYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7443 (p) REVERT: E 132 PHE cc_start: 0.7077 (m-80) cc_final: 0.6737 (m-80) REVERT: E 139 ILE cc_start: 0.9295 (mp) cc_final: 0.8818 (mm) outliers start: 49 outliers final: 22 residues processed: 151 average time/residue: 0.1930 time to fit residues: 45.1478 Evaluate side-chains 123 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 782 HIS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 104 GLN Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 99 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 110 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 124 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN E 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.117044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.087951 restraints weight = 34453.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.086623 restraints weight = 30687.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.087139 restraints weight = 32751.487| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12453 Z= 0.107 Angle : 0.543 9.500 16893 Z= 0.271 Chirality : 0.041 0.172 1885 Planarity : 0.004 0.043 2192 Dihedral : 3.960 16.069 1637 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.53 % Allowed : 21.67 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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: 1.24 (0.22), residues: 1476 helix: 1.94 (0.20), residues: 643 sheet: 0.99 (0.36), residues: 216 loop : -0.42 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 40 HIS 0.002 0.000 HIS D 70 PHE 0.019 0.001 PHE E 106 TYR 0.018 0.001 TYR B 801 ARG 0.007 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 541) hydrogen bonds : angle 4.34691 ( 1590) covalent geometry : bond 0.00240 (12453) covalent geometry : angle 0.54338 (16893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 ILE cc_start: 0.8738 (mm) cc_final: 0.8471 (mt) REVERT: B 385 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8469 (p0) REVERT: B 801 TYR cc_start: 0.8278 (p90) cc_final: 0.8014 (p90) REVERT: D 69 ARG cc_start: 0.8479 (ptp90) cc_final: 0.7929 (ptm-80) REVERT: D 72 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6593 (p90) REVERT: D 88 ASP cc_start: 0.7968 (m-30) cc_final: 0.7101 (t0) REVERT: E 99 CYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7482 (p) REVERT: E 132 PHE cc_start: 0.7216 (m-80) cc_final: 0.6796 (m-80) REVERT: E 139 ILE cc_start: 0.9249 (mp) cc_final: 0.8834 (mm) REVERT: E 145 ARG cc_start: 0.7778 (ttp80) cc_final: 0.7518 (tmt170) outliers start: 34 outliers final: 17 residues processed: 133 average time/residue: 0.2164 time to fit residues: 43.1285 Evaluate side-chains 118 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 470 HIS Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 104 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 99 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 13 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 117 optimal weight: 0.0270 chunk 61 optimal weight: 8.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN E 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.117348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.088728 restraints weight = 34088.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.087283 restraints weight = 32441.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.088148 restraints weight = 32148.370| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12453 Z= 0.098 Angle : 0.518 11.418 16893 Z= 0.255 Chirality : 0.040 0.167 1885 Planarity : 0.004 0.046 2192 Dihedral : 3.777 15.165 1637 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.53 % Allowed : 21.82 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.22), residues: 1476 helix: 2.02 (0.20), residues: 646 sheet: 0.64 (0.35), residues: 234 loop : -0.35 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 40 HIS 0.002 0.000 HIS B 500 PHE 0.013 0.001 PHE B 505 TYR 0.010 0.001 TYR E 19 ARG 0.006 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 541) hydrogen bonds : angle 4.05638 ( 1590) covalent geometry : bond 0.00222 (12453) covalent geometry : angle 0.51784 (16893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 TYR cc_start: 0.9296 (OUTLIER) cc_final: 0.8713 (m-10) REVERT: B 1 MET cc_start: 0.3755 (mmm) cc_final: 0.3431 (mmm) REVERT: B 22 ILE cc_start: 0.8781 (mm) cc_final: 0.8504 (mt) REVERT: B 385 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8393 (p0) REVERT: B 553 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.6674 (tm-30) REVERT: B 709 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9144 (mm) REVERT: B 801 TYR cc_start: 0.8254 (p90) cc_final: 0.7874 (p90) REVERT: D 69 ARG cc_start: 0.8489 (ptp90) cc_final: 0.8118 (ptm-80) REVERT: D 72 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6570 (p90) REVERT: D 88 ASP cc_start: 0.7855 (m-30) cc_final: 0.6998 (t0) REVERT: E 112 TYR cc_start: 0.7239 (m-80) cc_final: 0.7029 (m-80) REVERT: E 132 PHE cc_start: 0.7363 (m-80) cc_final: 0.6789 (m-80) REVERT: E 139 ILE cc_start: 0.9235 (mp) cc_final: 0.8830 (mm) REVERT: E 145 ARG cc_start: 0.7713 (ttp80) cc_final: 0.7367 (tpt90) outliers start: 34 outliers final: 19 residues processed: 134 average time/residue: 0.2014 time to fit residues: 41.2970 Evaluate side-chains 121 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 470 HIS Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 104 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 148 ARG Chi-restraints excluded: chain E residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 10 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 132 optimal weight: 0.0980 chunk 94 optimal weight: 0.0970 chunk 48 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN E 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.118234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.082632 restraints weight = 34055.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.082766 restraints weight = 23707.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.083108 restraints weight = 18935.847| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 12453 Z= 0.093 Angle : 0.506 9.704 16893 Z= 0.251 Chirality : 0.040 0.214 1885 Planarity : 0.003 0.047 2192 Dihedral : 3.618 16.035 1637 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.79 % Allowed : 22.56 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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: 1.34 (0.22), residues: 1476 helix: 2.13 (0.20), residues: 648 sheet: 0.59 (0.35), residues: 234 loop : -0.34 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 40 HIS 0.002 0.000 HIS D 70 PHE 0.018 0.001 PHE A 49 TYR 0.017 0.001 TYR E 101 ARG 0.003 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 541) hydrogen bonds : angle 3.86434 ( 1590) covalent geometry : bond 0.00208 (12453) covalent geometry : angle 0.50592 (16893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3848 (mmm) cc_final: 0.3645 (mmm) REVERT: B 22 ILE cc_start: 0.8610 (mm) cc_final: 0.8400 (mt) REVERT: B 385 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8386 (p0) REVERT: B 553 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6280 (tm-30) REVERT: B 709 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9123 (mm) REVERT: B 801 TYR cc_start: 0.8001 (p90) cc_final: 0.7452 (p90) REVERT: D 13 ASP cc_start: 0.7577 (t0) cc_final: 0.7371 (t0) REVERT: D 69 ARG cc_start: 0.8361 (ptp90) cc_final: 0.7924 (ptm-80) REVERT: D 88 ASP cc_start: 0.8207 (m-30) cc_final: 0.6979 (t0) REVERT: E 132 PHE cc_start: 0.7650 (m-80) cc_final: 0.6876 (m-80) REVERT: E 139 ILE cc_start: 0.9206 (mp) cc_final: 0.8709 (mm) REVERT: E 145 ARG cc_start: 0.7120 (ttp80) cc_final: 0.6709 (tpt90) outliers start: 24 outliers final: 12 residues processed: 127 average time/residue: 0.2081 time to fit residues: 40.5725 Evaluate side-chains 110 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 470 HIS Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 104 GLN Chi-restraints excluded: chain D residue 148 ARG Chi-restraints excluded: chain E residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 103 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 145 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN B 782 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.115783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.083623 restraints weight = 34589.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.081547 restraints weight = 22440.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.082100 restraints weight = 24487.949| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12453 Z= 0.140 Angle : 0.558 10.584 16893 Z= 0.270 Chirality : 0.041 0.204 1885 Planarity : 0.004 0.048 2192 Dihedral : 3.652 14.034 1637 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.76 % Allowed : 22.11 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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: 1.31 (0.22), residues: 1476 helix: 2.13 (0.20), residues: 644 sheet: 0.58 (0.35), residues: 234 loop : -0.39 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 40 HIS 0.006 0.001 HIS D 70 PHE 0.022 0.002 PHE B 505 TYR 0.019 0.001 TYR E 101 ARG 0.004 0.000 ARG D 137 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 541) hydrogen bonds : angle 4.00448 ( 1590) covalent geometry : bond 0.00341 (12453) covalent geometry : angle 0.55751 (16893) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: A 460 TYR cc_start: 0.9312 (OUTLIER) cc_final: 0.8683 (m-10) REVERT: A 479 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8208 (tptt) REVERT: B 22 ILE cc_start: 0.8760 (mm) cc_final: 0.8494 (mt) REVERT: B 385 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8444 (p0) REVERT: B 553 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6486 (tm-30) REVERT: B 801 TYR cc_start: 0.8133 (p90) cc_final: 0.7506 (p90) REVERT: C 131 ASP cc_start: 0.8027 (t0) cc_final: 0.7342 (t0) REVERT: D 13 ASP cc_start: 0.7587 (t0) cc_final: 0.7360 (t0) REVERT: D 69 ARG cc_start: 0.8501 (ptp90) cc_final: 0.8046 (ptm-80) REVERT: D 88 ASP cc_start: 0.7973 (m-30) cc_final: 0.7006 (t0) REVERT: E 96 LEU cc_start: 0.8624 (pp) cc_final: 0.7745 (tt) REVERT: E 112 TYR cc_start: 0.7641 (m-80) cc_final: 0.7412 (m-80) REVERT: E 132 PHE cc_start: 0.7468 (m-80) cc_final: 0.6750 (m-80) REVERT: E 139 ILE cc_start: 0.9281 (mp) cc_final: 0.8579 (mm) REVERT: E 145 ARG cc_start: 0.7504 (ttp80) cc_final: 0.7179 (tpt90) outliers start: 37 outliers final: 26 residues processed: 128 average time/residue: 0.2170 time to fit residues: 42.0385 Evaluate side-chains 121 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 470 HIS Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 104 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 99 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 2 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 64 optimal weight: 0.4980 chunk 124 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 39 optimal weight: 0.0060 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN B 782 HIS E 23 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.117264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.087964 restraints weight = 34269.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.086699 restraints weight = 30332.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.087227 restraints weight = 32840.695| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12453 Z= 0.097 Angle : 0.534 10.292 16893 Z= 0.258 Chirality : 0.040 0.177 1885 Planarity : 0.004 0.046 2192 Dihedral : 3.602 15.146 1637 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.31 % Allowed : 22.78 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.23), residues: 1476 helix: 2.17 (0.20), residues: 652 sheet: 0.53 (0.35), residues: 234 loop : -0.35 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 40 HIS 0.004 0.000 HIS D 70 PHE 0.018 0.001 PHE E 72 TYR 0.006 0.001 TYR B 801 ARG 0.002 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.03270 ( 541) hydrogen bonds : angle 3.86916 ( 1590) covalent geometry : bond 0.00225 (12453) covalent geometry : angle 0.53366 (16893) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8245 (tptt) REVERT: B 22 ILE cc_start: 0.8788 (mm) cc_final: 0.8553 (mt) REVERT: B 385 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8391 (p0) REVERT: B 553 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.6466 (tm-30) REVERT: B 801 TYR cc_start: 0.8196 (p90) cc_final: 0.7722 (p90) REVERT: D 27 THR cc_start: 0.9079 (p) cc_final: 0.8864 (t) REVERT: D 69 ARG cc_start: 0.8492 (ptp90) cc_final: 0.8053 (ptm-80) REVERT: D 88 ASP cc_start: 0.7944 (m-30) cc_final: 0.6849 (t0) REVERT: E 96 LEU cc_start: 0.8574 (pp) cc_final: 0.7705 (tt) REVERT: E 112 TYR cc_start: 0.7581 (m-80) cc_final: 0.7256 (m-80) REVERT: E 132 PHE cc_start: 0.7369 (m-80) cc_final: 0.6799 (m-80) REVERT: E 139 ILE cc_start: 0.9229 (mp) cc_final: 0.8971 (mm) REVERT: E 145 ARG cc_start: 0.7549 (ttp80) cc_final: 0.7174 (tpt90) outliers start: 31 outliers final: 19 residues processed: 120 average time/residue: 0.2154 time to fit residues: 39.2150 Evaluate side-chains 113 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 470 HIS Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 104 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 148 ARG Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 99 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 133 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 741 ASN B 782 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.117094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.087960 restraints weight = 34339.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.087425 restraints weight = 31867.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.088033 restraints weight = 31387.489| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12453 Z= 0.099 Angle : 0.532 10.437 16893 Z= 0.257 Chirality : 0.040 0.175 1885 Planarity : 0.004 0.047 2192 Dihedral : 3.562 14.827 1637 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.53 % Allowed : 22.41 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.23), residues: 1476 helix: 2.15 (0.20), residues: 654 sheet: 0.52 (0.35), residues: 234 loop : -0.32 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP E 40 HIS 0.004 0.000 HIS D 70 PHE 0.014 0.001 PHE E 106 TYR 0.018 0.001 TYR E 101 ARG 0.003 0.000 ARG D 137 Details of bonding type rmsd hydrogen bonds : bond 0.03294 ( 541) hydrogen bonds : angle 3.82753 ( 1590) covalent geometry : bond 0.00233 (12453) covalent geometry : angle 0.53232 (16893) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.4967 (mpp) cc_final: 0.4562 (mpp) REVERT: A 460 TYR cc_start: 0.9295 (OUTLIER) cc_final: 0.8666 (m-10) REVERT: A 479 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8217 (tptt) REVERT: B 385 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8424 (p0) REVERT: B 553 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6494 (tm-30) REVERT: B 709 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9089 (mm) REVERT: B 801 TYR cc_start: 0.8039 (p90) cc_final: 0.7552 (p90) REVERT: D 27 THR cc_start: 0.9029 (p) cc_final: 0.8794 (t) REVERT: D 69 ARG cc_start: 0.8527 (ptp90) cc_final: 0.8098 (ptm-80) REVERT: D 88 ASP cc_start: 0.7876 (m-30) cc_final: 0.6774 (t0) REVERT: E 40 TRP cc_start: 0.8639 (m100) cc_final: 0.8240 (m100) REVERT: E 96 LEU cc_start: 0.8443 (pp) cc_final: 0.7596 (tt) REVERT: E 111 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7960 (t80) REVERT: E 132 PHE cc_start: 0.7268 (m-80) cc_final: 0.6693 (m-80) REVERT: E 139 ILE cc_start: 0.9264 (mp) cc_final: 0.8793 (mm) REVERT: E 145 ARG cc_start: 0.7533 (ttp80) cc_final: 0.7125 (tpt90) outliers start: 34 outliers final: 21 residues processed: 123 average time/residue: 0.1963 time to fit residues: 37.5070 Evaluate side-chains 119 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 470 HIS Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 104 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 148 ARG Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 111 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 10 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 80 optimal weight: 0.0060 chunk 15 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 782 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.116378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.083598 restraints weight = 34124.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.081984 restraints weight = 22101.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.082525 restraints weight = 23340.076| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12453 Z= 0.114 Angle : 0.556 10.467 16893 Z= 0.267 Chirality : 0.040 0.170 1885 Planarity : 0.004 0.047 2192 Dihedral : 3.617 15.927 1637 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.16 % Allowed : 22.93 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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: 1.40 (0.23), residues: 1476 helix: 2.19 (0.20), residues: 650 sheet: 0.48 (0.35), residues: 234 loop : -0.28 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 40 HIS 0.004 0.001 HIS D 70 PHE 0.017 0.001 PHE E 72 TYR 0.016 0.001 TYR E 111 ARG 0.003 0.000 ARG B 825 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 541) hydrogen bonds : angle 3.81575 ( 1590) covalent geometry : bond 0.00274 (12453) covalent geometry : angle 0.55623 (16893) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.5034 (mpp) cc_final: 0.4623 (mpp) REVERT: A 460 TYR cc_start: 0.9258 (OUTLIER) cc_final: 0.8520 (m-10) REVERT: A 479 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8266 (tptt) REVERT: B 385 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8450 (p0) REVERT: B 553 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6279 (tm-30) REVERT: B 782 HIS cc_start: 0.6383 (t-170) cc_final: 0.6112 (t70) REVERT: B 801 TYR cc_start: 0.8130 (p90) cc_final: 0.7625 (p90) REVERT: C 1 MET cc_start: 0.7113 (tpp) cc_final: 0.6854 (ptm) REVERT: D 27 THR cc_start: 0.9100 (p) cc_final: 0.8852 (t) REVERT: D 69 ARG cc_start: 0.8479 (ptp90) cc_final: 0.8014 (ptm-80) REVERT: D 88 ASP cc_start: 0.8055 (m-30) cc_final: 0.6997 (t0) REVERT: E 40 TRP cc_start: 0.8931 (m100) cc_final: 0.8432 (m100) REVERT: E 96 LEU cc_start: 0.8680 (pp) cc_final: 0.7910 (tt) REVERT: E 111 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8199 (t80) REVERT: E 112 TYR cc_start: 0.7684 (m-80) cc_final: 0.7379 (m-80) REVERT: E 132 PHE cc_start: 0.7376 (m-80) cc_final: 0.6742 (m-80) REVERT: E 139 ILE cc_start: 0.9297 (mp) cc_final: 0.8760 (mm) REVERT: E 145 ARG cc_start: 0.7366 (ttp80) cc_final: 0.6911 (tpt90) outliers start: 29 outliers final: 21 residues processed: 120 average time/residue: 0.2242 time to fit residues: 41.7350 Evaluate side-chains 119 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 470 HIS Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 104 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 148 ARG Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 111 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 44 optimal weight: 0.0070 chunk 99 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 33 optimal weight: 0.0470 chunk 92 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.117600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.080767 restraints weight = 34250.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.081024 restraints weight = 26389.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082093 restraints weight = 19919.781| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12453 Z= 0.097 Angle : 0.555 12.889 16893 Z= 0.265 Chirality : 0.040 0.172 1885 Planarity : 0.004 0.045 2192 Dihedral : 3.556 15.240 1637 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.71 % Allowed : 23.53 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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: 1.48 (0.23), residues: 1476 helix: 2.27 (0.20), residues: 644 sheet: 0.49 (0.36), residues: 234 loop : -0.21 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 40 HIS 0.004 0.000 HIS D 70 PHE 0.015 0.001 PHE B 52 TYR 0.015 0.001 TYR E 111 ARG 0.003 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.03064 ( 541) hydrogen bonds : angle 3.75478 ( 1590) covalent geometry : bond 0.00226 (12453) covalent geometry : angle 0.55527 (16893) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.5061 (mpp) cc_final: 0.4669 (mpp) REVERT: A 460 TYR cc_start: 0.9218 (OUTLIER) cc_final: 0.8470 (m-10) REVERT: B 22 ILE cc_start: 0.8627 (mm) cc_final: 0.8411 (mt) REVERT: B 385 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8378 (p0) REVERT: B 553 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6123 (tm-30) REVERT: B 709 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8972 (mm) REVERT: B 801 TYR cc_start: 0.8252 (p90) cc_final: 0.7746 (p90) REVERT: D 27 THR cc_start: 0.9037 (p) cc_final: 0.8817 (t) REVERT: D 69 ARG cc_start: 0.8390 (ptp90) cc_final: 0.7915 (ptm-80) REVERT: D 88 ASP cc_start: 0.8136 (m-30) cc_final: 0.7033 (t0) REVERT: E 72 PHE cc_start: 0.8506 (p90) cc_final: 0.8288 (p90) REVERT: E 74 PHE cc_start: 0.7907 (t80) cc_final: 0.7367 (m-80) REVERT: E 96 LEU cc_start: 0.8809 (pp) cc_final: 0.8103 (tt) REVERT: E 111 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8445 (t80) REVERT: E 112 TYR cc_start: 0.7935 (m-80) cc_final: 0.7576 (m-80) REVERT: E 132 PHE cc_start: 0.7566 (m-80) cc_final: 0.6914 (m-80) REVERT: E 139 ILE cc_start: 0.9224 (mp) cc_final: 0.8609 (mm) REVERT: E 145 ARG cc_start: 0.7016 (ttp80) cc_final: 0.6560 (tpt90) outliers start: 23 outliers final: 17 residues processed: 116 average time/residue: 0.2045 time to fit residues: 36.6175 Evaluate side-chains 112 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 470 HIS Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 104 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 148 ARG Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 111 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 52 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 782 HIS ** E 136 GLN ** 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 = 0.3966 r_free = 0.3966 target = 0.116004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.077310 restraints weight = 34130.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.079450 restraints weight = 24152.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.079471 restraints weight = 16276.877| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12453 Z= 0.132 Angle : 0.578 12.152 16893 Z= 0.278 Chirality : 0.040 0.167 1885 Planarity : 0.004 0.047 2192 Dihedral : 3.639 14.839 1637 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.79 % Allowed : 23.45 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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: 1.39 (0.23), residues: 1476 helix: 2.22 (0.21), residues: 648 sheet: 0.36 (0.35), residues: 234 loop : -0.25 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 40 HIS 0.004 0.001 HIS D 70 PHE 0.019 0.001 PHE B 505 TYR 0.015 0.001 TYR E 111 ARG 0.003 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 541) hydrogen bonds : angle 3.84995 ( 1590) covalent geometry : bond 0.00322 (12453) covalent geometry : angle 0.57752 (16893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3319.43 seconds wall clock time: 58 minutes 58.11 seconds (3538.11 seconds total)