Starting phenix.real_space_refine on Sun Sep 29 04:38:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9arg_43781/09_2024/9arg_43781.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9arg_43781/09_2024/9arg_43781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9arg_43781/09_2024/9arg_43781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9arg_43781/09_2024/9arg_43781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9arg_43781/09_2024/9arg_43781.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9arg_43781/09_2024/9arg_43781.cif" } resolution = 4.05 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 266 atoms to isotropic. 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 84 5.16 5 C 13626 2.51 5 N 3442 2.21 5 O 3856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21008 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 5321 Classifications: {'peptide': 798} Incomplete info: {'truncation_to_alanine': 239} Link IDs: {'PTRANS': 35, 'TRANS': 762} Chain breaks: 2 Unresolved non-hydrogen bonds: 1016 Unresolved non-hydrogen angles: 1231 Unresolved non-hydrogen dihedrals: 856 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 26, 'TYR:plan': 4, 'ASN:plan1': 14, 'TRP:plan': 1, 'HIS:plan': 10, 'PHE:plan': 8, 'GLU:plan': 46, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 724 Chain: "B" Number of atoms: 5183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5183 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 245} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 1055 Unresolved non-hydrogen angles: 1285 Unresolved non-hydrogen dihedrals: 913 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 21, 'ASP:plan': 33, 'TYR:plan': 14, 'ASN:plan1': 13, 'TRP:plan': 2, 'HIS:plan': 7, 'PHE:plan': 9, 'GLU:plan': 50, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 742 Restraints were copied for chains: C, D Time building chain proxies: 20.62, per 1000 atoms: 0.98 Number of scatterers: 21008 At special positions: 0 Unit cell: (151.512, 118.984, 181.472, 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 84 16.00 O 3856 8.00 N 3442 7.00 C 13626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.04 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 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: 5.31 Conformation dependent library (CDL) restraints added in 3.1 seconds 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5916 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 34 sheets defined 44.9% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'A' and resid 35 through 52 Processing helix chain 'A' and resid 71 through 86 Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.945A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 removed outlier: 3.882A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.757A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 261 removed outlier: 3.974A pdb=" N ALA A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 4.024A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.927A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.571A pdb=" N VAL A 575 " --> pdb=" O HIS A 571 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 616 removed outlier: 3.767A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 657 Processing helix chain 'A' and resid 669 through 674 removed outlier: 3.505A pdb=" N ASN A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.521A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 708 removed outlier: 4.277A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.677A pdb=" N GLN A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 723 " --> pdb=" O GLN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 742 removed outlier: 3.664A pdb=" N LEU A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 783 removed outlier: 4.049A pdb=" N GLN A 770 " --> pdb=" O SER A 766 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 810 through 812 No H-bonds generated for 'chain 'A' and resid 810 through 812' Processing helix chain 'A' and resid 813 through 841 removed outlier: 4.300A pdb=" N PHE A 817 " --> pdb=" O MET A 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.061A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 4.019A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 119 removed outlier: 3.960A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.612A pdb=" N MET B 132 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 165 removed outlier: 3.658A pdb=" N MET B 161 " --> pdb=" O MET B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 3.553A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 291 through 311 Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.732A pdb=" N ARG B 328 " --> pdb=" O HIS B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 340 Processing helix chain 'B' and resid 460 through 472 Processing helix chain 'B' and resid 489 through 493 removed outlier: 3.741A pdb=" N GLY B 492 " --> pdb=" O LYS B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 removed outlier: 3.848A pdb=" N MET B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 523 Processing helix chain 'B' and resid 548 through 552 removed outlier: 4.010A pdb=" N LEU B 551 " --> pdb=" O SER B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 578 removed outlier: 4.113A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 612 Processing helix chain 'B' and resid 626 through 654 Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 714 through 723 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 771 through 787 removed outlier: 4.163A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 Processing helix chain 'B' and resid 800 through 804 Processing helix chain 'B' and resid 814 through 817 Processing helix chain 'B' and resid 818 through 845 removed outlier: 3.925A pdb=" N GLN B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 55 removed outlier: 4.061A pdb=" N GLU D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 removed outlier: 4.019A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 119 removed outlier: 3.960A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 removed outlier: 3.613A pdb=" N MET D 132 " --> pdb=" O GLY D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 165 removed outlier: 3.659A pdb=" N MET D 161 " --> pdb=" O MET D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 192 removed outlier: 3.552A pdb=" N ASN D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 291 through 311 Processing helix chain 'D' and resid 324 through 328 removed outlier: 3.733A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 340 Processing helix chain 'D' and resid 460 through 472 Processing helix chain 'D' and resid 489 through 493 removed outlier: 3.741A pdb=" N GLY D 492 " --> pdb=" O LYS D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 503 removed outlier: 3.848A pdb=" N MET D 503 " --> pdb=" O GLY D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 523 Processing helix chain 'D' and resid 548 through 552 removed outlier: 4.009A pdb=" N LEU D 551 " --> pdb=" O SER D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 578 removed outlier: 4.112A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 612 Processing helix chain 'D' and resid 626 through 654 Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 708 through 710 No H-bonds generated for 'chain 'D' and resid 708 through 710' Processing helix chain 'D' and resid 714 through 723 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 771 through 787 removed outlier: 4.163A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 Processing helix chain 'D' and resid 800 through 804 Processing helix chain 'D' and resid 814 through 817 Processing helix chain 'D' and resid 818 through 845 removed outlier: 3.925A pdb=" N GLN D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.945A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 158 removed outlier: 3.882A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 224 through 238 removed outlier: 3.757A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.973A pdb=" N ALA C 258 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 296 removed outlier: 4.023A pdb=" N HIS C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 500 through 508 Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.927A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.570A pdb=" N VAL C 575 " --> pdb=" O HIS C 571 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 616 removed outlier: 3.766A pdb=" N LEU C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 657 Processing helix chain 'C' and resid 669 through 674 removed outlier: 3.504A pdb=" N ASN C 674 " --> pdb=" O PRO C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.521A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 708 removed outlier: 4.277A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.676A pdb=" N GLN C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP C 723 " --> pdb=" O GLN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 742 removed outlier: 3.664A pdb=" N LEU C 736 " --> pdb=" O ASP C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 783 removed outlier: 4.049A pdb=" N GLN C 770 " --> pdb=" O SER C 766 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 777 " --> pdb=" O SER C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 810 through 812 No H-bonds generated for 'chain 'C' and resid 810 through 812' Processing helix chain 'C' and resid 813 through 841 removed outlier: 4.300A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 removed outlier: 3.522A pdb=" N VAL A 65 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.816A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 222 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER A 168 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 268 removed outlier: 6.721A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 373 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A 371 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 340 removed outlier: 3.867A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 402 removed outlier: 3.675A pdb=" N ILE A 400 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR A 402 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 412 removed outlier: 3.649A pdb=" N LYS A 412 " --> pdb=" O CYS A 454 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS A 454 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 486 through 488 removed outlier: 3.661A pdb=" N THR A 486 " --> pdb=" O ASN A 499 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU A 497 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 513 through 517 removed outlier: 5.737A pdb=" N ALA A 515 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLY A 759 " --> pdb=" O ALA A 515 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 729 through 731 removed outlier: 6.413A pdb=" N GLN A 536 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ARG A 755 " --> pdb=" O GLN A 536 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 753 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE A 540 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N GLU A 751 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL A 542 " --> pdb=" O THR A 749 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR A 749 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 67 through 72 removed outlier: 5.700A pdb=" N GLY B 36 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL B 98 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA B 100 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE B 40 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 144 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 199 removed outlier: 3.894A pdb=" N PHE B 169 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE B 227 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.948A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 277 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 281 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 343 through 344 removed outlier: 3.596A pdb=" N PHE B 344 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 405 through 410 removed outlier: 4.045A pdb=" N ASP B 477 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 408 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 410 " --> pdb=" O TYR B 479 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 417 through 420 removed outlier: 3.690A pdb=" N CYS B 456 " --> pdb=" O GLU B 420 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 508 through 509 removed outlier: 3.657A pdb=" N ILE B 766 " --> pdb=" O ASP B 524 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP B 524 " --> pdb=" O ILE B 766 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 531 through 532 removed outlier: 3.508A pdb=" N THR B 760 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 729 through 732 removed outlier: 3.643A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 538 " --> pdb=" O VAL B 749 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 749 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 67 through 72 removed outlier: 5.700A pdb=" N GLY D 36 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL D 98 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA D 100 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE D 40 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE D 144 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 198 through 199 removed outlier: 3.894A pdb=" N PHE D 169 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE D 227 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 277 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 281 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 343 through 344 removed outlier: 3.596A pdb=" N PHE D 344 " --> pdb=" O ARG D 347 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 405 through 410 removed outlier: 4.045A pdb=" N ASP D 477 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 408 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR D 410 " --> pdb=" O TYR D 479 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 417 through 420 removed outlier: 3.691A pdb=" N CYS D 456 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 508 through 509 removed outlier: 3.657A pdb=" N ILE D 766 " --> pdb=" O ASP D 524 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP D 524 " --> pdb=" O ILE D 766 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 531 through 532 removed outlier: 3.507A pdb=" N THR D 760 " --> pdb=" O THR D 532 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 729 through 732 removed outlier: 3.642A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 538 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 749 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 59 through 65 removed outlier: 3.522A pdb=" N VAL C 65 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 193 through 197 removed outlier: 6.817A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER C 222 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER C 168 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 267 through 268 removed outlier: 6.721A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C 373 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS C 371 " --> pdb=" O ASN C 368 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 339 through 340 removed outlier: 3.867A pdb=" N GLU C 339 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 397 through 402 removed outlier: 3.675A pdb=" N ILE C 400 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR C 402 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 409 through 412 removed outlier: 3.649A pdb=" N LYS C 412 " --> pdb=" O CYS C 454 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS C 454 " --> pdb=" O LYS C 412 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 486 through 488 removed outlier: 3.661A pdb=" N THR C 486 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU C 497 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 513 through 517 removed outlier: 5.738A pdb=" N ALA C 515 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLY C 759 " --> pdb=" O ALA C 515 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 729 through 731 removed outlier: 6.414A pdb=" N GLN C 536 " --> pdb=" O ARG C 755 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ARG C 755 " --> pdb=" O GLN C 536 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE C 753 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE C 540 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N GLU C 751 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL C 542 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR C 749 " --> pdb=" O VAL C 542 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 3138 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: 7.96 Time building geometry restraints manager: 6.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6714 1.34 - 1.46: 5127 1.46 - 1.58: 9477 1.58 - 1.71: 0 1.71 - 1.83: 130 Bond restraints: 21448 Sorted by residual: bond pdb=" CA ASN D 615 " pdb=" CB ASN D 615 " ideal model delta sigma weight residual 1.539 1.514 0.025 1.20e-02 6.94e+03 4.36e+00 bond pdb=" CA ASN B 615 " pdb=" CB ASN B 615 " ideal model delta sigma weight residual 1.539 1.514 0.024 1.20e-02 6.94e+03 4.07e+00 bond pdb=" C PHE D 614 " pdb=" N ASN D 615 " ideal model delta sigma weight residual 1.332 1.308 0.024 1.36e-02 5.41e+03 3.20e+00 bond pdb=" C PHE B 614 " pdb=" N ASN B 615 " ideal model delta sigma weight residual 1.332 1.309 0.023 1.36e-02 5.41e+03 2.85e+00 bond pdb=" CA PRO A 447 " pdb=" C PRO A 447 " ideal model delta sigma weight residual 1.526 1.516 0.010 8.50e-03 1.38e+04 1.50e+00 ... (remaining 21443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 28718 1.42 - 2.84: 777 2.84 - 4.25: 103 4.25 - 5.67: 25 5.67 - 7.09: 5 Bond angle restraints: 29628 Sorted by residual: angle pdb=" C ASN B 615 " pdb=" CA ASN B 615 " pdb=" CB ASN B 615 " ideal model delta sigma weight residual 109.83 116.92 -7.09 9.90e-01 1.02e+00 5.13e+01 angle pdb=" C ASN D 615 " pdb=" CA ASN D 615 " pdb=" CB ASN D 615 " ideal model delta sigma weight residual 109.83 116.29 -6.46 9.90e-01 1.02e+00 4.26e+01 angle pdb=" N ASN B 615 " pdb=" CA ASN B 615 " pdb=" CB ASN B 615 " ideal model delta sigma weight residual 114.10 108.25 5.85 1.00e+00 1.00e+00 3.42e+01 angle pdb=" N ASN D 615 " pdb=" CA ASN D 615 " pdb=" CB ASN D 615 " ideal model delta sigma weight residual 114.10 108.98 5.12 1.00e+00 1.00e+00 2.62e+01 angle pdb=" CA ASN D 615 " pdb=" CB ASN D 615 " pdb=" CG ASN D 615 " ideal model delta sigma weight residual 112.60 109.07 3.53 1.00e+00 1.00e+00 1.24e+01 ... (remaining 29623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.21: 11555 11.21 - 22.42: 484 22.42 - 33.63: 182 33.63 - 44.84: 67 44.84 - 56.05: 34 Dihedral angle restraints: 12322 sinusoidal: 3176 harmonic: 9146 Sorted by residual: dihedral pdb=" CA GLN A 491 " pdb=" C GLN A 491 " pdb=" N ASN A 492 " pdb=" CA ASN A 492 " ideal model delta harmonic sigma weight residual 180.00 152.04 27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLN C 491 " pdb=" C GLN C 491 " pdb=" N ASN C 492 " pdb=" CA ASN C 492 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA MET D 503 " pdb=" C MET D 503 " pdb=" N LYS D 504 " pdb=" CA LYS D 504 " ideal model delta harmonic sigma weight residual -180.00 -158.21 -21.79 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 12319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3470 0.069 - 0.137: 362 0.137 - 0.206: 0 0.206 - 0.274: 0 0.274 - 0.343: 2 Chirality restraints: 3834 Sorted by residual: chirality pdb=" CA ASN D 615 " pdb=" N ASN D 615 " pdb=" C ASN D 615 " pdb=" CB ASN D 615 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ASN B 615 " pdb=" N ASN B 615 " pdb=" C ASN B 615 " pdb=" CB ASN B 615 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA ILE B 766 " pdb=" N ILE B 766 " pdb=" C ILE B 766 " pdb=" CB ILE B 766 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 3831 not shown) Planarity restraints: 3730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 615 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C ASN B 615 " 0.060 2.00e-02 2.50e+03 pdb=" O ASN B 615 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN B 616 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 615 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C ASN D 615 " -0.058 2.00e-02 2.50e+03 pdb=" O ASN D 615 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN D 616 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 318 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO C 319 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 319 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 319 " -0.026 5.00e-02 4.00e+02 ... (remaining 3727 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 92 2.60 - 3.18: 18166 3.18 - 3.75: 31038 3.75 - 4.33: 37294 4.33 - 4.90: 63319 Nonbonded interactions: 149909 Sorted by model distance: nonbonded pdb=" SG CYS D 86 " pdb=" SG CYS D 321 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS D 436 " pdb=" SG CYS D 457 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS C 744 " pdb=" SG CYS C 798 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS D 429 " pdb=" SG CYS D 456 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS D 746 " pdb=" SG CYS D 801 " model vdw 2.032 3.760 ... (remaining 149904 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.820 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 56.690 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.060 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 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 : 0.002 0.050 21448 Z= 0.146 Angle : 0.568 7.091 29628 Z= 0.353 Chirality : 0.039 0.343 3834 Planarity : 0.004 0.047 3730 Dihedral : 9.079 56.051 6382 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 4.82 % Allowed : 8.46 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.99 (0.13), residues: 3142 helix: -0.41 (0.13), residues: 1278 sheet: -2.65 (0.23), residues: 378 loop : -3.32 (0.13), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 636 HIS 0.001 0.000 HIS A 162 PHE 0.007 0.001 PHE D 550 TYR 0.008 0.001 TYR B 356 ARG 0.001 0.000 ARG C 663 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 482 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 TRP cc_start: 0.8668 (m-10) cc_final: 0.8104 (m-90) REVERT: A 184 LEU cc_start: 0.8794 (mt) cc_final: 0.8486 (tp) REVERT: A 830 LEU cc_start: 0.8937 (mm) cc_final: 0.8717 (mm) REVERT: B 230 LEU cc_start: 0.7097 (tp) cc_final: 0.6845 (tp) REVERT: B 626 THR cc_start: 0.4909 (OUTLIER) cc_final: 0.4389 (m) REVERT: B 721 LEU cc_start: 0.7052 (tp) cc_final: 0.6531 (pp) REVERT: D 230 LEU cc_start: 0.7106 (tp) cc_final: 0.6847 (tp) REVERT: D 626 THR cc_start: 0.4472 (OUTLIER) cc_final: 0.3842 (m) REVERT: D 653 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.7211 (t80) REVERT: D 721 LEU cc_start: 0.6916 (tp) cc_final: 0.6439 (pp) REVERT: C 184 LEU cc_start: 0.8727 (mt) cc_final: 0.8426 (tp) REVERT: C 219 ILE cc_start: 0.8000 (mt) cc_final: 0.7544 (mt) REVERT: C 296 LEU cc_start: 0.0938 (OUTLIER) cc_final: 0.0645 (tt) REVERT: C 541 LEU cc_start: 0.7698 (tp) cc_final: 0.7458 (tt) REVERT: C 571 HIS cc_start: 0.7661 (OUTLIER) cc_final: 0.7148 (m-70) REVERT: C 736 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8795 (mt) outliers start: 86 outliers final: 20 residues processed: 556 average time/residue: 0.2383 time to fit residues: 223.9792 Evaluate side-chains 310 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 284 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 9.9990 chunk 237 optimal weight: 30.0000 chunk 132 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 160 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 246 optimal weight: 8.9990 chunk 95 optimal weight: 20.0000 chunk 149 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 285 optimal weight: 4.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN B 118 GLN B 616 ASN B 688 ASN B 817 ASN D 616 ASN D 688 ASN D 817 ASN ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 21448 Z= 0.465 Angle : 0.747 8.314 29628 Z= 0.395 Chirality : 0.046 0.228 3834 Planarity : 0.005 0.055 3730 Dihedral : 4.434 30.493 3246 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.56 % Allowed : 5.77 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.09 (0.14), residues: 3142 helix: 0.21 (0.14), residues: 1328 sheet: -1.97 (0.25), residues: 380 loop : -2.85 (0.14), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 256 HIS 0.006 0.002 HIS C 780 PHE 0.033 0.003 PHE D 653 TYR 0.015 0.002 TYR A 410 ARG 0.006 0.001 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 284 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8502 (mt) cc_final: 0.7913 (mt) REVERT: A 247 TRP cc_start: 0.8129 (m100) cc_final: 0.7840 (m100) REVERT: B 249 LEU cc_start: 0.6853 (pt) cc_final: 0.6106 (mp) REVERT: B 554 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7735 (m-10) REVERT: D 171 ILE cc_start: 0.7627 (mp) cc_final: 0.7393 (mp) REVERT: D 249 LEU cc_start: 0.6787 (pt) cc_final: 0.5957 (mp) REVERT: D 554 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7408 (m-10) REVERT: C 184 LEU cc_start: 0.8877 (mt) cc_final: 0.8453 (tp) REVERT: C 219 ILE cc_start: 0.8556 (mt) cc_final: 0.8335 (mt) REVERT: C 247 TRP cc_start: 0.8189 (m100) cc_final: 0.7940 (m100) outliers start: 10 outliers final: 3 residues processed: 294 average time/residue: 0.2385 time to fit residues: 120.2406 Evaluate side-chains 225 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 220 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 40.0000 chunk 88 optimal weight: 20.0000 chunk 237 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 285 optimal weight: 0.8980 chunk 308 optimal weight: 3.9990 chunk 254 optimal weight: 8.9990 chunk 283 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 229 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 118 GLN B 153 GLN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 ASN C 134 HIS C 363 GLN C 650 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21448 Z= 0.306 Angle : 0.616 7.043 29628 Z= 0.325 Chirality : 0.043 0.193 3834 Planarity : 0.004 0.050 3730 Dihedral : 4.375 31.308 3246 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.06 % Allowed : 4.93 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 3142 helix: 0.56 (0.14), residues: 1342 sheet: -1.76 (0.25), residues: 402 loop : -2.70 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 373 HIS 0.005 0.001 HIS C 780 PHE 0.045 0.002 PHE D 114 TYR 0.055 0.001 TYR C 109 ARG 0.002 0.000 ARG A 763 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 157 MET cc_start: 0.8214 (ppp) cc_final: 0.7978 (ppp) REVERT: B 249 LEU cc_start: 0.6693 (pt) cc_final: 0.5928 (mp) REVERT: D 142 MET cc_start: 0.1226 (tpp) cc_final: 0.0847 (ttp) REVERT: D 249 LEU cc_start: 0.6719 (pt) cc_final: 0.5850 (mp) REVERT: C 184 LEU cc_start: 0.8863 (mt) cc_final: 0.8432 (tp) REVERT: C 219 ILE cc_start: 0.8706 (mt) cc_final: 0.8155 (mt) REVERT: C 247 TRP cc_start: 0.8217 (m100) cc_final: 0.7914 (m100) outliers start: 1 outliers final: 1 residues processed: 265 average time/residue: 0.2623 time to fit residues: 120.3223 Evaluate side-chains 227 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 0.8980 chunk 214 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 136 optimal weight: 0.7980 chunk 191 optimal weight: 20.0000 chunk 286 optimal weight: 4.9990 chunk 303 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 271 optimal weight: 30.0000 chunk 81 optimal weight: 50.0000 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN C 134 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21448 Z= 0.216 Angle : 0.563 7.615 29628 Z= 0.295 Chirality : 0.041 0.183 3834 Planarity : 0.004 0.053 3730 Dihedral : 4.203 30.065 3246 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.15), residues: 3142 helix: 0.90 (0.14), residues: 1342 sheet: -1.87 (0.25), residues: 420 loop : -2.46 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 247 HIS 0.003 0.001 HIS A 780 PHE 0.017 0.001 PHE B 822 TYR 0.022 0.001 TYR C 109 ARG 0.002 0.000 ARG C 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 249 LEU cc_start: 0.6612 (pt) cc_final: 0.5906 (mp) REVERT: B 497 MET cc_start: 0.8777 (mmm) cc_final: 0.8173 (mmt) REVERT: D 142 MET cc_start: 0.1688 (tpp) cc_final: 0.1437 (ttp) REVERT: D 249 LEU cc_start: 0.6679 (pt) cc_final: 0.5839 (mp) REVERT: D 497 MET cc_start: 0.8772 (mmm) cc_final: 0.8284 (mmt) REVERT: D 721 LEU cc_start: 0.6930 (tp) cc_final: 0.6201 (pp) REVERT: C 184 LEU cc_start: 0.8858 (mt) cc_final: 0.8430 (tp) REVERT: C 219 ILE cc_start: 0.8726 (mt) cc_final: 0.8291 (mt) REVERT: C 247 TRP cc_start: 0.8220 (m100) cc_final: 0.7958 (m100) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2410 time to fit residues: 110.8960 Evaluate side-chains 221 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 0.0970 chunk 172 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 225 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 259 optimal weight: 0.0870 chunk 209 optimal weight: 0.9990 chunk 0 optimal weight: 60.0000 chunk 154 optimal weight: 0.9980 chunk 272 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN D 153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21448 Z= 0.174 Angle : 0.544 6.822 29628 Z= 0.283 Chirality : 0.041 0.150 3834 Planarity : 0.004 0.049 3730 Dihedral : 4.077 28.741 3246 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.06 % Allowed : 2.91 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.06 (0.15), residues: 3142 helix: 1.11 (0.14), residues: 1336 sheet: -1.65 (0.25), residues: 404 loop : -2.28 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 256 HIS 0.005 0.001 HIS A 134 PHE 0.036 0.001 PHE D 114 TYR 0.016 0.001 TYR A 578 ARG 0.002 0.000 ARG C 755 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 275 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 249 LEU cc_start: 0.6506 (pt) cc_final: 0.5833 (mp) REVERT: B 497 MET cc_start: 0.8714 (mmm) cc_final: 0.8188 (mmt) REVERT: D 249 LEU cc_start: 0.6607 (pt) cc_final: 0.5777 (mp) REVERT: D 497 MET cc_start: 0.8692 (mmm) cc_final: 0.8230 (mmt) REVERT: D 721 LEU cc_start: 0.6887 (tp) cc_final: 0.6140 (pp) REVERT: C 184 LEU cc_start: 0.8852 (mt) cc_final: 0.8435 (tp) outliers start: 1 outliers final: 0 residues processed: 275 average time/residue: 0.2386 time to fit residues: 112.6898 Evaluate side-chains 230 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 9.9990 chunk 273 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 178 optimal weight: 0.0070 chunk 74 optimal weight: 0.9990 chunk 303 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 159 optimal weight: 7.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 21448 Z= 0.148 Angle : 0.534 7.183 29628 Z= 0.274 Chirality : 0.041 0.251 3834 Planarity : 0.004 0.050 3730 Dihedral : 3.942 27.782 3246 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.06 % Allowed : 2.02 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.15), residues: 3142 helix: 1.32 (0.15), residues: 1330 sheet: -1.63 (0.27), residues: 358 loop : -2.11 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 256 HIS 0.005 0.001 HIS C 780 PHE 0.039 0.001 PHE D 653 TYR 0.016 0.001 TYR A 795 ARG 0.002 0.000 ARG A 755 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 2.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 610 SER cc_start: 0.9364 (t) cc_final: 0.9152 (p) REVERT: A 813 MET cc_start: 0.8009 (ttp) cc_final: 0.7803 (ttp) REVERT: B 249 LEU cc_start: 0.6495 (pt) cc_final: 0.5837 (mp) REVERT: B 497 MET cc_start: 0.8687 (mmm) cc_final: 0.8161 (mmt) REVERT: D 249 LEU cc_start: 0.6399 (pt) cc_final: 0.5702 (mp) REVERT: D 497 MET cc_start: 0.8672 (mmm) cc_final: 0.8211 (mmt) REVERT: D 721 LEU cc_start: 0.6892 (tp) cc_final: 0.6072 (pp) REVERT: C 184 LEU cc_start: 0.8858 (mt) cc_final: 0.8448 (tp) REVERT: C 607 MET cc_start: 0.6903 (ttp) cc_final: 0.6677 (ttm) REVERT: C 610 SER cc_start: 0.9403 (t) cc_final: 0.9100 (p) outliers start: 1 outliers final: 0 residues processed: 283 average time/residue: 0.2453 time to fit residues: 119.3321 Evaluate side-chains 231 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 0.5980 chunk 34 optimal weight: 0.0570 chunk 173 optimal weight: 7.9990 chunk 221 optimal weight: 20.0000 chunk 171 optimal weight: 20.0000 chunk 255 optimal weight: 20.0000 chunk 169 optimal weight: 8.9990 chunk 302 optimal weight: 7.9990 chunk 189 optimal weight: 8.9990 chunk 184 optimal weight: 40.0000 chunk 139 optimal weight: 20.0000 overall best weight: 5.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 21448 Z= 0.498 Angle : 0.760 10.325 29628 Z= 0.404 Chirality : 0.047 0.206 3834 Planarity : 0.005 0.067 3730 Dihedral : 4.948 34.911 3246 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.15), residues: 3142 helix: 0.75 (0.14), residues: 1322 sheet: -1.60 (0.27), residues: 342 loop : -2.28 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP C 247 HIS 0.012 0.002 HIS A 780 PHE 0.039 0.003 PHE D 653 TYR 0.027 0.002 TYR A 647 ARG 0.004 0.001 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 253 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 TRP cc_start: 0.8317 (m100) cc_final: 0.8022 (m100) REVERT: B 249 LEU cc_start: 0.6774 (pt) cc_final: 0.5827 (mp) REVERT: B 497 MET cc_start: 0.8862 (mmm) cc_final: 0.8315 (mmt) REVERT: B 537 MET cc_start: 0.8259 (mmm) cc_final: 0.7760 (mmm) REVERT: D 153 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: D 249 LEU cc_start: 0.6736 (pt) cc_final: 0.5689 (mp) REVERT: D 497 MET cc_start: 0.8837 (mmm) cc_final: 0.8352 (mmt) REVERT: D 508 MET cc_start: 0.8422 (tpt) cc_final: 0.8077 (tpt) outliers start: 1 outliers final: 0 residues processed: 253 average time/residue: 0.2682 time to fit residues: 117.9629 Evaluate side-chains 214 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 192 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 237 optimal weight: 40.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21448 Z= 0.167 Angle : 0.576 10.992 29628 Z= 0.296 Chirality : 0.042 0.179 3834 Planarity : 0.004 0.055 3730 Dihedral : 4.297 30.972 3246 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.15), residues: 3142 helix: 1.17 (0.14), residues: 1350 sheet: -1.75 (0.25), residues: 388 loop : -2.10 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 563 HIS 0.002 0.000 HIS A 780 PHE 0.031 0.002 PHE D 653 TYR 0.017 0.001 TYR A 109 ARG 0.002 0.000 ARG C 755 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 786 GLU cc_start: 0.6793 (tp30) cc_final: 0.6470 (tp30) REVERT: B 161 MET cc_start: 0.8281 (ptm) cc_final: 0.7747 (ppp) REVERT: B 249 LEU cc_start: 0.6556 (pt) cc_final: 0.5698 (mp) REVERT: B 497 MET cc_start: 0.8698 (mmm) cc_final: 0.8193 (mmt) REVERT: D 157 MET cc_start: 0.8335 (ppp) cc_final: 0.8121 (ppp) REVERT: D 161 MET cc_start: 0.8294 (ptm) cc_final: 0.7754 (ppp) REVERT: D 249 LEU cc_start: 0.6594 (pt) cc_final: 0.5653 (mp) REVERT: D 497 MET cc_start: 0.8666 (mmm) cc_final: 0.8165 (mmt) REVERT: C 184 LEU cc_start: 0.8885 (mt) cc_final: 0.8424 (tp) REVERT: C 247 TRP cc_start: 0.8123 (m100) cc_final: 0.7799 (m100) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2421 time to fit residues: 113.0796 Evaluate side-chains 225 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 9.9990 chunk 289 optimal weight: 4.9990 chunk 264 optimal weight: 6.9990 chunk 282 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 254 optimal weight: 6.9990 chunk 266 optimal weight: 20.0000 chunk 281 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 812 GLN D 812 GLN C 134 HIS C 311 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 21448 Z= 0.647 Angle : 0.858 13.622 29628 Z= 0.456 Chirality : 0.049 0.201 3834 Planarity : 0.005 0.080 3730 Dihedral : 5.388 39.112 3246 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.92 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 (0.15), residues: 3142 helix: 0.56 (0.14), residues: 1312 sheet: -1.95 (0.28), residues: 318 loop : -2.23 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP C 247 HIS 0.015 0.003 HIS A 780 PHE 0.025 0.003 PHE D 114 TYR 0.028 0.002 TYR C 647 ARG 0.006 0.001 ARG C 523 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 TRP cc_start: 0.8337 (m100) cc_final: 0.7953 (m100) REVERT: B 161 MET cc_start: 0.8284 (ptm) cc_final: 0.7799 (ppp) REVERT: B 249 LEU cc_start: 0.6801 (pt) cc_final: 0.5673 (mp) REVERT: B 497 MET cc_start: 0.8879 (mmm) cc_final: 0.8235 (mmt) REVERT: D 157 MET cc_start: 0.8552 (ppp) cc_final: 0.8320 (ppp) REVERT: D 161 MET cc_start: 0.8454 (ptm) cc_final: 0.7885 (ppp) REVERT: D 249 LEU cc_start: 0.6806 (pt) cc_final: 0.5648 (mp) REVERT: D 497 MET cc_start: 0.8915 (mmm) cc_final: 0.8290 (mmt) REVERT: D 508 MET cc_start: 0.8456 (tpt) cc_final: 0.8042 (tpt) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.2474 time to fit residues: 106.9114 Evaluate side-chains 209 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 0.0570 chunk 298 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 312 optimal weight: 0.9990 chunk 287 optimal weight: 0.9990 chunk 249 optimal weight: 10.0000 chunk 25 optimal weight: 40.0000 chunk 192 optimal weight: 0.5980 chunk 152 optimal weight: 6.9990 overall best weight: 0.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 GLN A 571 HIS C 525 GLN C 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21448 Z= 0.183 Angle : 0.615 11.737 29628 Z= 0.314 Chirality : 0.042 0.158 3834 Planarity : 0.004 0.057 3730 Dihedral : 4.521 33.702 3246 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 3142 helix: 1.10 (0.14), residues: 1326 sheet: -1.72 (0.26), residues: 352 loop : -2.07 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 391 HIS 0.007 0.001 HIS A 571 PHE 0.034 0.002 PHE D 653 TYR 0.020 0.001 TYR A 109 ARG 0.002 0.000 ARG A 755 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.8202 (ptm) cc_final: 0.7776 (ppp) REVERT: B 249 LEU cc_start: 0.6586 (pt) cc_final: 0.5644 (mp) REVERT: B 497 MET cc_start: 0.8764 (mmm) cc_final: 0.8231 (mmt) REVERT: D 157 MET cc_start: 0.8414 (ppp) cc_final: 0.8188 (ppp) REVERT: D 158 LEU cc_start: 0.9297 (tt) cc_final: 0.9077 (tt) REVERT: D 161 MET cc_start: 0.8320 (ptm) cc_final: 0.7826 (ppp) REVERT: D 229 LEU cc_start: 0.7594 (pp) cc_final: 0.7206 (tp) REVERT: D 249 LEU cc_start: 0.6601 (pt) cc_final: 0.5521 (mp) REVERT: D 497 MET cc_start: 0.8731 (mmm) cc_final: 0.7945 (mmt) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.2458 time to fit residues: 118.2336 Evaluate side-chains 224 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.7980 chunk 265 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 229 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 249 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 256 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 45 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.140011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.118148 restraints weight = 71679.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.116587 restraints weight = 97330.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.114114 restraints weight = 78634.064| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21448 Z= 0.163 Angle : 0.581 10.255 29628 Z= 0.294 Chirality : 0.041 0.165 3834 Planarity : 0.004 0.051 3730 Dihedral : 4.208 30.192 3246 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 3142 helix: 1.35 (0.14), residues: 1322 sheet: -1.68 (0.26), residues: 364 loop : -1.91 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 391 HIS 0.002 0.000 HIS C 477 PHE 0.040 0.002 PHE D 653 TYR 0.019 0.001 TYR A 109 ARG 0.002 0.000 ARG C 755 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3849.61 seconds wall clock time: 72 minutes 27.56 seconds (4347.56 seconds total)