Starting phenix.real_space_refine on Wed Jun 11 01:51:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9imz_60697/06_2025/9imz_60697_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9imz_60697/06_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_60697/06_2025/9imz_60697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9imz_60697/06_2025/9imz_60697.map" model { file = "/net/cci-nas-00/data/ceres_data/9imz_60697/06_2025/9imz_60697_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9imz_60697/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.07, per 1000 atoms: 0.66 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: 2.89 Conformation dependent library (CDL) restraints added in 1.4 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: 1.56 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: 3.42 Time building geometry restraints manager: 3.43 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 29.430 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.840 ------------------------------------------------------------------------------- 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 : 2.076 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: 0.2684 time to fit residues: 79.7121 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 : 1.264 ------------------------------------------------------------------------------- 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 = 0.115853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.084110 restraints weight = 34382.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.082179 restraints weight = 22033.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.082722 restraints weight = 24677.109| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 4.84225 ( 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 : 1.732 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: 0.8489 (p90) cc_final: 0.7791 (p90) REVERT: C 8 ASN cc_start: 0.7661 (t0) cc_final: 0.7442 (t0) REVERT: D 72 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6684 (p90) REVERT: D 88 ASP cc_start: 0.8100 (m-30) cc_final: 0.7219 (t0) REVERT: E 40 TRP cc_start: 0.8272 (m100) cc_final: 0.8028 (m100) REVERT: E 99 CYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7441 (p) REVERT: E 132 PHE cc_start: 0.7074 (m-80) cc_final: 0.6735 (m-80) REVERT: E 139 ILE cc_start: 0.9294 (mp) cc_final: 0.8817 (mm) outliers start: 49 outliers final: 22 residues processed: 151 average time/residue: 0.2396 time to fit residues: 56.4512 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 : 1.960 ------------------------------------------------------------------------------- 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: 0.9980 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 68 optimal weight: 0.2980 chunk 93 optimal weight: 0.5980 chunk 124 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.116723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.087494 restraints weight = 34447.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.086191 restraints weight = 30698.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.086821 restraints weight = 32216.552| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12453 Z= 0.114 Angle : 0.547 9.328 16893 Z= 0.273 Chirality : 0.041 0.171 1885 Planarity : 0.004 0.044 2192 Dihedral : 3.967 16.098 1637 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.68 % Allowed : 21.59 % Favored : 75.73 % 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: 1.22 (0.22), residues: 1476 helix: 1.94 (0.20), residues: 641 sheet: 0.98 (0.36), residues: 216 loop : -0.45 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 40 HIS 0.003 0.000 HIS D 70 PHE 0.019 0.001 PHE E 106 TYR 0.017 0.001 TYR B 801 ARG 0.006 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 541) hydrogen bonds : angle 4.34383 ( 1590) covalent geometry : bond 0.00261 (12453) covalent geometry : angle 0.54673 (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 143 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 TYR cc_start: 0.9204 (OUTLIER) cc_final: 0.8706 (m-10) REVERT: B 22 ILE cc_start: 0.8746 (mm) cc_final: 0.8484 (mt) REVERT: B 385 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8477 (p0) REVERT: B 801 TYR cc_start: 0.8241 (p90) cc_final: 0.7928 (p90) REVERT: D 69 ARG cc_start: 0.8489 (ptp90) cc_final: 0.7943 (ptm-80) REVERT: D 72 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6596 (p90) REVERT: D 88 ASP cc_start: 0.7980 (m-30) cc_final: 0.7095 (t0) REVERT: E 40 TRP cc_start: 0.8288 (m100) cc_final: 0.7904 (m100) REVERT: E 132 PHE cc_start: 0.7193 (m-80) cc_final: 0.6747 (m-80) REVERT: E 139 ILE cc_start: 0.9257 (mp) cc_final: 0.8842 (mm) REVERT: E 145 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7514 (tmt170) outliers start: 36 outliers final: 17 residues processed: 136 average time/residue: 0.2980 time to fit residues: 61.6954 Evaluate side-chains 116 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 1.675 ------------------------------------------------------------------------------- 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 460 TYR 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 706 VAL Chi-restraints excluded: chain B residue 738 CYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 13 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 74 optimal weight: 0.3980 chunk 70 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN E 5 GLN E 23 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.116633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.088029 restraints weight = 34060.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.088290 restraints weight = 32410.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.088284 restraints weight = 34765.464| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2818 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= 0.110 Angle : 0.531 11.477 16893 Z= 0.262 Chirality : 0.041 0.264 1885 Planarity : 0.004 0.047 2192 Dihedral : 3.803 14.791 1637 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.05 % Allowed : 21.89 % 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: 1.22 (0.22), residues: 1476 helix: 2.02 (0.20), residues: 643 sheet: 0.63 (0.35), residues: 234 loop : -0.43 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 40 HIS 0.002 0.000 HIS B 500 PHE 0.015 0.001 PHE B 505 TYR 0.011 0.001 TYR E 19 ARG 0.007 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 541) hydrogen bonds : angle 4.04714 ( 1590) covalent geometry : bond 0.00255 (12453) covalent geometry : angle 0.53063 (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 148 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 TYR cc_start: 0.9306 (OUTLIER) cc_final: 0.8733 (m-10) REVERT: B 1 MET cc_start: 0.3881 (mmm) cc_final: 0.3606 (mmm) REVERT: B 22 ILE cc_start: 0.8806 (mm) cc_final: 0.8525 (mt) REVERT: B 385 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8445 (p0) REVERT: B 553 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.6694 (tm-30) REVERT: B 801 TYR cc_start: 0.8298 (p90) cc_final: 0.7890 (p90) REVERT: D 69 ARG cc_start: 0.8490 (ptp90) cc_final: 0.8148 (ptm-80) REVERT: D 72 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.6475 (p90) REVERT: D 88 ASP cc_start: 0.7789 (m-30) cc_final: 0.6985 (t0) REVERT: E 112 TYR cc_start: 0.7110 (m-80) cc_final: 0.6879 (m-80) REVERT: E 132 PHE cc_start: 0.7290 (m-80) cc_final: 0.6749 (m-80) REVERT: E 145 ARG cc_start: 0.7790 (ttp80) cc_final: 0.7509 (tpt90) outliers start: 41 outliers final: 22 residues processed: 140 average time/residue: 0.2075 time to fit residues: 44.4221 Evaluate side-chains 125 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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 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 118 THR Chi-restraints excluded: chain D residue 72 PHE 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 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: 10.0000 chunk 95 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 111 optimal weight: 0.4980 chunk 38 optimal weight: 0.0980 overall best weight: 0.4382 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.117990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.080523 restraints weight = 34047.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.082104 restraints weight = 25233.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.082234 restraints weight = 18793.809| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3041 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= 0.093 Angle : 0.512 10.456 16893 Z= 0.251 Chirality : 0.040 0.176 1885 Planarity : 0.004 0.047 2192 Dihedral : 3.636 15.746 1637 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.79 % Allowed : 22.26 % Favored : 75.95 % 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: 1.35 (0.22), residues: 1476 helix: 2.14 (0.20), residues: 646 sheet: 0.66 (0.35), residues: 234 loop : -0.38 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 40 HIS 0.002 0.000 HIS D 70 PHE 0.018 0.001 PHE A 49 TYR 0.015 0.001 TYR B 801 ARG 0.003 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.03057 ( 541) hydrogen bonds : angle 3.86467 ( 1590) covalent geometry : bond 0.00203 (12453) covalent geometry : angle 0.51178 (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 126 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 823 PHE cc_start: 0.6077 (p90) cc_final: 0.5857 (p90) REVERT: B 22 ILE cc_start: 0.8628 (mm) cc_final: 0.8411 (mt) REVERT: B 385 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8378 (p0) REVERT: B 553 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6314 (tm-30) REVERT: B 709 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9106 (mm) REVERT: B 801 TYR cc_start: 0.8005 (p90) cc_final: 0.7466 (p90) REVERT: D 13 ASP cc_start: 0.7631 (t0) cc_final: 0.7430 (t0) REVERT: D 69 ARG cc_start: 0.8362 (ptp90) cc_final: 0.7909 (ptm-80) REVERT: D 88 ASP cc_start: 0.8111 (m-30) cc_final: 0.7081 (t0) REVERT: E 132 PHE cc_start: 0.7629 (m-80) cc_final: 0.6857 (m-80) REVERT: E 145 ARG cc_start: 0.7237 (ttp80) cc_final: 0.6926 (tpt90) outliers start: 24 outliers final: 14 residues processed: 121 average time/residue: 0.2547 time to fit residues: 47.9580 Evaluate side-chains 109 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain E residue 99 CYS 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: 0.8980 chunk 145 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.113701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.076887 restraints weight = 34590.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.077139 restraints weight = 25817.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076167 restraints weight = 23158.432| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12453 Z= 0.217 Angle : 0.627 10.276 16893 Z= 0.309 Chirality : 0.044 0.214 1885 Planarity : 0.004 0.050 2192 Dihedral : 3.922 15.809 1637 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.35 % Allowed : 21.30 % Favored : 75.35 % 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: 1.02 (0.22), residues: 1476 helix: 1.83 (0.20), residues: 644 sheet: 0.44 (0.35), residues: 234 loop : -0.46 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 40 HIS 0.007 0.001 HIS D 70 PHE 0.032 0.002 PHE B 505 TYR 0.016 0.002 TYR B 309 ARG 0.004 0.000 ARG D 137 Details of bonding type rmsd hydrogen bonds : bond 0.05294 ( 541) hydrogen bonds : angle 4.24877 ( 1590) covalent geometry : bond 0.00526 (12453) covalent geometry : angle 0.62734 (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 143 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 98 time to evaluate : 1.497 Fit side-chains revert: symmetry clash REVERT: A 460 TYR cc_start: 0.9261 (OUTLIER) cc_final: 0.8553 (m-10) REVERT: A 479 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8216 (tptt) REVERT: B 385 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8513 (p0) REVERT: B 553 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.6430 (tm-30) REVERT: B 709 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9136 (mm) REVERT: B 801 TYR cc_start: 0.8368 (p90) cc_final: 0.7868 (p90) REVERT: C 131 ASP cc_start: 0.8448 (t0) cc_final: 0.7856 (t0) REVERT: D 13 ASP cc_start: 0.7838 (t0) cc_final: 0.7588 (t0) REVERT: D 88 ASP cc_start: 0.8189 (m-30) cc_final: 0.7419 (t0) REVERT: E 40 TRP cc_start: 0.9083 (m100) cc_final: 0.8744 (m100) REVERT: E 96 LEU cc_start: 0.8879 (pp) cc_final: 0.8074 (tt) REVERT: E 111 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8714 (t80) REVERT: E 132 PHE cc_start: 0.7449 (m-80) cc_final: 0.6685 (m-80) REVERT: E 145 ARG cc_start: 0.7214 (ttp80) cc_final: 0.6909 (tpt90) outliers start: 45 outliers final: 25 residues processed: 137 average time/residue: 0.2079 time to fit residues: 43.9112 Evaluate side-chains 125 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 313 ILE 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 462 VAL 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 13 VAL Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 389 LEU 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 709 LEU 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 118 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 111 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 2 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 28 optimal weight: 0.0980 chunk 18 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 chunk 124 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 39 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.116557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.087555 restraints weight = 34188.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.086167 restraints weight = 31834.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.086781 restraints weight = 31352.128| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3410 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= 0.100 Angle : 0.541 10.094 16893 Z= 0.263 Chirality : 0.040 0.179 1885 Planarity : 0.004 0.047 2192 Dihedral : 3.731 15.260 1637 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.16 % Allowed : 22.49 % Favored : 75.35 % 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: 1.25 (0.22), residues: 1476 helix: 2.10 (0.21), residues: 646 sheet: 0.43 (0.35), residues: 234 loop : -0.40 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 40 HIS 0.002 0.000 HIS D 70 PHE 0.018 0.001 PHE E 72 TYR 0.008 0.001 TYR E 111 ARG 0.003 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 541) hydrogen bonds : angle 3.93864 ( 1590) covalent geometry : bond 0.00235 (12453) covalent geometry : angle 0.54080 (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 125 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 479 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8255 (tptt) REVERT: B 385 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8371 (p0) REVERT: B 553 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: B 709 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9116 (mm) REVERT: B 801 TYR cc_start: 0.8141 (p90) cc_final: 0.7684 (p90) REVERT: D 13 ASP cc_start: 0.7494 (t0) cc_final: 0.7288 (t0) REVERT: D 69 ARG cc_start: 0.8527 (ptp90) cc_final: 0.8116 (ptm-80) REVERT: D 88 ASP cc_start: 0.7820 (m-30) cc_final: 0.7004 (t0) REVERT: E 74 PHE cc_start: 0.7527 (t80) cc_final: 0.6973 (m-80) REVERT: E 96 LEU cc_start: 0.8617 (pp) cc_final: 0.7708 (tt) REVERT: E 111 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.8369 (t80) REVERT: E 132 PHE cc_start: 0.7313 (m-80) cc_final: 0.6793 (m-80) REVERT: E 145 ARG cc_start: 0.7693 (ttp80) cc_final: 0.7426 (tpt90) outliers start: 29 outliers final: 19 residues processed: 120 average time/residue: 0.1980 time to fit residues: 36.8759 Evaluate side-chains 116 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 133 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 41 optimal weight: 0.0980 chunk 84 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.115523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.083067 restraints weight = 34280.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.080936 restraints weight = 21981.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.081484 restraints weight = 24155.698| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12453 Z= 0.123 Angle : 0.549 9.825 16893 Z= 0.269 Chirality : 0.041 0.174 1885 Planarity : 0.004 0.047 2192 Dihedral : 3.702 14.441 1637 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.61 % Allowed : 22.19 % Favored : 75.20 % 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: 1.23 (0.22), residues: 1476 helix: 2.07 (0.21), residues: 647 sheet: 0.37 (0.35), residues: 234 loop : -0.36 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 40 HIS 0.004 0.001 HIS D 70 PHE 0.018 0.001 PHE B 505 TYR 0.017 0.001 TYR E 101 ARG 0.003 0.000 ARG A 667 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 541) hydrogen bonds : angle 3.95071 ( 1590) covalent geometry : bond 0.00299 (12453) covalent geometry : angle 0.54946 (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 132 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 460 TYR cc_start: 0.9268 (OUTLIER) cc_final: 0.8524 (m-10) REVERT: A 479 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8335 (tptt) REVERT: B 385 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8457 (p0) REVERT: B 553 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6341 (tm-30) REVERT: B 801 TYR cc_start: 0.8142 (p90) cc_final: 0.7683 (p90) REVERT: D 13 ASP cc_start: 0.7709 (t0) cc_final: 0.7481 (t0) REVERT: D 69 ARG cc_start: 0.8450 (ptp90) cc_final: 0.7990 (ptm-80) REVERT: D 88 ASP cc_start: 0.8006 (m-30) cc_final: 0.7117 (t0) REVERT: E 96 LEU cc_start: 0.8746 (pp) cc_final: 0.7875 (tt) REVERT: E 111 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.8570 (t80) REVERT: E 132 PHE cc_start: 0.7438 (m-80) cc_final: 0.6613 (m-80) REVERT: E 145 ARG cc_start: 0.7461 (ttp80) cc_final: 0.7130 (tpt90) outliers start: 35 outliers final: 22 residues processed: 127 average time/residue: 0.2027 time to fit residues: 39.8842 Evaluate side-chains 118 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 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 13 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 389 LEU 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 142 SER 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: 5.9990 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 782 HIS E 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.115965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.083432 restraints weight = 34071.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.081344 restraints weight = 21629.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.081936 restraints weight = 23963.669| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3646 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= 0.113 Angle : 0.551 10.473 16893 Z= 0.267 Chirality : 0.040 0.173 1885 Planarity : 0.004 0.046 2192 Dihedral : 3.680 14.778 1637 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.38 % Allowed : 22.11 % Favored : 75.50 % 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: 1.29 (0.23), residues: 1476 helix: 2.13 (0.20), residues: 647 sheet: 0.37 (0.36), residues: 234 loop : -0.35 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 40 HIS 0.004 0.001 HIS D 70 PHE 0.017 0.001 PHE E 72 TYR 0.008 0.001 TYR E 111 ARG 0.003 0.000 ARG B 825 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 541) hydrogen bonds : angle 3.88848 ( 1590) covalent geometry : bond 0.00272 (12453) covalent geometry : angle 0.55074 (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 127 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 460 TYR cc_start: 0.9246 (OUTLIER) cc_final: 0.8508 (m-10) REVERT: A 479 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8341 (tptt) REVERT: B 385 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8416 (p0) REVERT: B 553 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.6247 (tm-30) REVERT: B 801 TYR cc_start: 0.8041 (p90) cc_final: 0.7619 (p90) REVERT: D 13 ASP cc_start: 0.7625 (t0) cc_final: 0.7369 (t0) REVERT: D 27 THR cc_start: 0.9146 (p) cc_final: 0.8898 (t) REVERT: D 69 ARG cc_start: 0.8478 (ptp90) cc_final: 0.8003 (ptm-80) REVERT: D 88 ASP cc_start: 0.8019 (m-30) cc_final: 0.6963 (t0) REVERT: E 40 TRP cc_start: 0.9182 (m100) cc_final: 0.8748 (m100) REVERT: E 96 LEU cc_start: 0.8705 (pp) cc_final: 0.7953 (tt) REVERT: E 111 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.8616 (t80) REVERT: E 112 TYR cc_start: 0.7786 (m-80) cc_final: 0.7452 (m-80) REVERT: E 132 PHE cc_start: 0.7417 (m-80) cc_final: 0.6798 (m-80) REVERT: E 145 ARG cc_start: 0.7408 (ttp80) cc_final: 0.7097 (tpt90) outliers start: 32 outliers final: 24 residues processed: 120 average time/residue: 0.2143 time to fit residues: 39.4977 Evaluate side-chains 121 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 1.474 ------------------------------------------------------------------------------- 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 460 TYR Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 633 LEU 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 13 VAL Chi-restraints excluded: chain B residue 313 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 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 97 ILE 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: 4.9990 chunk 99 optimal weight: 0.0030 chunk 133 optimal weight: 0.9990 chunk 33 optimal weight: 0.0770 chunk 92 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 3 optimal weight: 0.0050 chunk 140 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 overall best weight: 0.3562 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.117402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.088876 restraints weight = 34099.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.089032 restraints weight = 32323.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.089629 restraints weight = 30130.357| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3785 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= 0.094 Angle : 0.542 10.641 16893 Z= 0.261 Chirality : 0.040 0.172 1885 Planarity : 0.004 0.045 2192 Dihedral : 3.537 14.791 1637 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.71 % Allowed : 22.86 % Favored : 75.43 % 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: 1.43 (0.23), residues: 1476 helix: 2.23 (0.20), residues: 643 sheet: 0.50 (0.36), residues: 234 loop : -0.26 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 40 HIS 0.004 0.000 HIS D 70 PHE 0.016 0.001 PHE D 72 TYR 0.018 0.001 TYR E 101 ARG 0.003 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.02904 ( 541) hydrogen bonds : angle 3.76217 ( 1590) covalent geometry : bond 0.00216 (12453) covalent geometry : angle 0.54172 (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 116 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 1.567 Fit side-chains revert: symmetry clash REVERT: A 460 TYR cc_start: 0.9241 (OUTLIER) cc_final: 0.8493 (m-10) REVERT: A 479 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8313 (tptt) REVERT: B 385 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8389 (p0) REVERT: B 553 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.6488 (tm-30) REVERT: B 801 TYR cc_start: 0.8127 (p90) cc_final: 0.7689 (p90) REVERT: D 13 ASP cc_start: 0.7541 (t0) cc_final: 0.7336 (t0) REVERT: D 27 THR cc_start: 0.8983 (p) cc_final: 0.8742 (t) REVERT: D 69 ARG cc_start: 0.8509 (ptp90) cc_final: 0.8112 (ptm-80) REVERT: D 88 ASP cc_start: 0.7737 (m-30) cc_final: 0.6777 (t0) REVERT: E 96 LEU cc_start: 0.8483 (pp) cc_final: 0.7721 (tt) REVERT: E 112 TYR cc_start: 0.7314 (m-80) cc_final: 0.7095 (m-80) REVERT: E 132 PHE cc_start: 0.7334 (m-80) cc_final: 0.6586 (m-80) REVERT: E 145 ARG cc_start: 0.7553 (ttp80) cc_final: 0.7153 (tpt90) outliers start: 23 outliers final: 17 residues processed: 110 average time/residue: 0.2184 time to fit residues: 37.3547 Evaluate side-chains 110 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 633 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 313 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 719 LEU Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 97 ILE 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 97 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 52 optimal weight: 0.0060 chunk 50 optimal weight: 0.2980 chunk 144 optimal weight: 30.0000 chunk 15 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 141 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.117309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.080369 restraints weight = 33887.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.080759 restraints weight = 26086.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.081769 restraints weight = 20095.228| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12453 Z= 0.094 Angle : 0.537 10.543 16893 Z= 0.259 Chirality : 0.039 0.169 1885 Planarity : 0.004 0.044 2192 Dihedral : 3.501 15.223 1637 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.64 % Allowed : 23.23 % 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: 1.49 (0.23), residues: 1476 helix: 2.30 (0.21), residues: 643 sheet: 0.48 (0.36), residues: 234 loop : -0.22 (0.26), residues: 599 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 0.020 0.001 PHE E 72 TYR 0.006 0.001 TYR B 309 ARG 0.007 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.03000 ( 541) hydrogen bonds : angle 3.72578 ( 1590) covalent geometry : bond 0.00221 (12453) covalent geometry : angle 0.53729 (16893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3650.58 seconds wall clock time: 65 minutes 50.82 seconds (3950.82 seconds total)