Starting phenix.real_space_refine on Wed May 21 11:36:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9arg_43781/05_2025/9arg_43781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9arg_43781/05_2025/9arg_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/cci-nas-00/data/ceres_data/9arg_43781/05_2025/9arg_43781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9arg_43781/05_2025/9arg_43781.map" model { file = "/net/cci-nas-00/data/ceres_data/9arg_43781/05_2025/9arg_43781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9arg_43781/05_2025/9arg_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-5687/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: 21.09, per 1000 atoms: 1.00 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=16, 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 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.04 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 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: 5.34 Conformation dependent library (CDL) restraints added in 3.0 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: 3.26 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: 8.41 Time building geometry restraints manager: 6.25 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: 11567 11.21 - 22.42: 493 22.42 - 33.63: 184 33.63 - 44.84: 68 44.84 - 56.05: 34 Dihedral angle restraints: 12346 sinusoidal: 3200 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 12343 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: 2.11 - 2.67: 243 2.67 - 3.23: 20217 3.23 - 3.78: 30575 3.78 - 4.34: 36739 4.34 - 4.90: 62111 Nonbonded interactions: 149885 Sorted by model distance: nonbonded pdb=" OG SER A 628 " pdb=" OG SER B 832 " model vdw 2.112 3.040 nonbonded pdb=" O ASP C 81 " pdb=" OG SER C 85 " model vdw 2.253 3.040 nonbonded pdb=" O ASP A 81 " pdb=" OG SER A 85 " model vdw 2.253 3.040 nonbonded pdb=" OG SER D 832 " pdb=" OG SER C 628 " model vdw 2.256 3.040 nonbonded pdb=" O CYS B 321 " pdb=" OG1 THR B 324 " model vdw 2.261 3.040 ... (remaining 149880 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: 0.13 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: 5.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.030 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 58.650 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.260 ------------------------------------------------------------------------------- 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 21464 Z= 0.131 Angle : 0.568 7.091 29660 Z= 0.353 Chirality : 0.039 0.343 3834 Planarity : 0.004 0.047 3730 Dihedral : 9.079 56.051 6382 Min Nonbonded Distance : 2.112 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 Details of bonding type rmsd hydrogen bonds : bond 0.17444 ( 1086) hydrogen bonds : angle 6.37135 ( 3138) SS BOND : bond 0.00233 ( 16) SS BOND : angle 0.73159 ( 32) covalent geometry : bond 0.00213 (21448) covalent geometry : angle 0.56758 (29628) *********************** 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 to be fit. rotamer outliers: 86 poor density : 482 time to evaluate : 2.311 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: 0.2376 time to fit residues: 223.9485 Evaluate side-chains 310 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 284 time to evaluate : 2.421 ------------------------------------------------------------------------------- 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 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN B 118 GLN B 616 ASN B 817 ASN D 616 ASN D 817 ASN ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.137807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.109873 restraints weight = 69873.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.105790 restraints weight = 99589.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.104668 restraints weight = 68681.793| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 21464 Z= 0.297 Angle : 0.735 8.071 29660 Z= 0.391 Chirality : 0.046 0.244 3834 Planarity : 0.005 0.053 3730 Dihedral : 4.312 30.284 3246 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.45 % Allowed : 5.66 % Favored : 93.89 % 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: -2.11 (0.14), residues: 3142 helix: 0.20 (0.14), residues: 1330 sheet: -1.94 (0.25), residues: 368 loop : -2.88 (0.14), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 256 HIS 0.006 0.001 HIS C 780 PHE 0.029 0.003 PHE D 729 TYR 0.014 0.001 TYR C 578 ARG 0.006 0.001 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.05733 ( 1086) hydrogen bonds : angle 5.48632 ( 3138) SS BOND : bond 0.00979 ( 16) SS BOND : angle 2.26879 ( 32) covalent geometry : bond 0.00686 (21448) covalent geometry : angle 0.73188 (29628) *********************** 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 297 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 289 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 LEU cc_start: 0.7706 (tp) cc_final: 0.7475 (tp) REVERT: B 249 LEU cc_start: 0.6959 (pt) cc_final: 0.6194 (mp) REVERT: B 554 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7701 (m-10) REVERT: B 721 LEU cc_start: 0.7024 (tp) cc_final: 0.6464 (pp) REVERT: B 818 MET cc_start: 0.7875 (mmm) cc_final: 0.7633 (mmp) REVERT: D 171 ILE cc_start: 0.8008 (mp) cc_final: 0.7744 (mp) REVERT: D 249 LEU cc_start: 0.6885 (pt) cc_final: 0.6047 (mp) REVERT: D 554 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7518 (m-10) REVERT: D 706 MET cc_start: 0.8525 (ttp) cc_final: 0.8322 (ttp) REVERT: D 721 LEU cc_start: 0.7048 (tp) cc_final: 0.6459 (pp) REVERT: C 166 LEU cc_start: 0.9347 (tt) cc_final: 0.9086 (mt) REVERT: C 184 LEU cc_start: 0.8954 (mt) cc_final: 0.8541 (tp) REVERT: C 247 TRP cc_start: 0.8277 (m100) cc_final: 0.8015 (m100) outliers start: 8 outliers final: 2 residues processed: 297 average time/residue: 0.2496 time to fit residues: 127.0004 Evaluate side-chains 231 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 227 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 119 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 130 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 244 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 245 optimal weight: 9.9990 chunk 243 optimal weight: 20.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 C 134 HIS C 363 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.140080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.117106 restraints weight = 70004.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.114174 restraints weight = 97970.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.112034 restraints weight = 87207.493| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21464 Z= 0.160 Angle : 0.587 6.857 29660 Z= 0.310 Chirality : 0.042 0.191 3834 Planarity : 0.004 0.047 3730 Dihedral : 4.235 30.274 3246 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.06 % Allowed : 5.38 % Favored : 94.56 % 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: -1.60 (0.15), residues: 3142 helix: 0.69 (0.14), residues: 1324 sheet: -1.77 (0.25), residues: 404 loop : -2.64 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 256 HIS 0.004 0.001 HIS A 780 PHE 0.046 0.002 PHE D 114 TYR 0.068 0.001 TYR C 109 ARG 0.002 0.000 ARG A 755 Details of bonding type rmsd hydrogen bonds : bond 0.04714 ( 1086) hydrogen bonds : angle 4.98908 ( 3138) SS BOND : bond 0.00856 ( 16) SS BOND : angle 2.00266 ( 32) covalent geometry : bond 0.00365 (21448) covalent geometry : angle 0.58391 (29628) *********************** 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 281 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 MET cc_start: 0.0893 (tpp) cc_final: 0.0692 (ttp) REVERT: B 171 ILE cc_start: 0.7598 (mp) cc_final: 0.7351 (mp) REVERT: B 249 LEU cc_start: 0.6251 (pt) cc_final: 0.5738 (mp) REVERT: B 497 MET cc_start: 0.8930 (mmm) cc_final: 0.8714 (mmm) REVERT: B 721 LEU cc_start: 0.6727 (tp) cc_final: 0.6223 (pp) REVERT: D 142 MET cc_start: 0.1135 (tpp) cc_final: 0.0837 (ttp) REVERT: D 249 LEU cc_start: 0.6213 (pt) cc_final: 0.5569 (mp) REVERT: D 721 LEU cc_start: 0.6783 (tp) cc_final: 0.6269 (pp) REVERT: C 184 LEU cc_start: 0.8807 (mt) cc_final: 0.8406 (tp) REVERT: C 219 ILE cc_start: 0.8556 (mt) cc_final: 0.8182 (mt) REVERT: C 247 TRP cc_start: 0.8206 (m100) cc_final: 0.7948 (m100) outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.2463 time to fit residues: 118.0644 Evaluate side-chains 233 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 190 optimal weight: 2.9990 chunk 238 optimal weight: 0.0060 chunk 138 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 32 optimal weight: 30.0000 chunk 90 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 272 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 153 GLN C 134 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.140557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.117692 restraints weight = 70604.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.115702 restraints weight = 100016.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.113861 restraints weight = 79734.262| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21464 Z= 0.124 Angle : 0.556 8.301 29660 Z= 0.289 Chirality : 0.041 0.214 3834 Planarity : 0.004 0.049 3730 Dihedral : 4.087 29.101 3246 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % 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: -1.24 (0.15), residues: 3142 helix: 1.00 (0.14), residues: 1330 sheet: -1.73 (0.25), residues: 410 loop : -2.42 (0.15), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 256 HIS 0.004 0.001 HIS A 780 PHE 0.030 0.001 PHE D 653 TYR 0.017 0.001 TYR A 578 ARG 0.002 0.000 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 1086) hydrogen bonds : angle 4.70107 ( 3138) SS BOND : bond 0.00407 ( 16) SS BOND : angle 1.44966 ( 32) covalent geometry : bond 0.00281 (21448) covalent geometry : angle 0.55420 (29628) *********************** 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 281 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 229 LEU cc_start: 0.7323 (pp) cc_final: 0.7092 (tp) REVERT: B 249 LEU cc_start: 0.5926 (pt) cc_final: 0.5512 (mp) REVERT: B 497 MET cc_start: 0.8822 (mmm) cc_final: 0.8162 (mmt) REVERT: B 721 LEU cc_start: 0.6640 (tp) cc_final: 0.6133 (pp) REVERT: D 249 LEU cc_start: 0.5873 (pt) cc_final: 0.5382 (mp) REVERT: D 497 MET cc_start: 0.8719 (mmm) cc_final: 0.8057 (mmt) REVERT: D 721 LEU cc_start: 0.6812 (tp) cc_final: 0.6280 (pp) REVERT: C 184 LEU cc_start: 0.8748 (mt) cc_final: 0.8362 (tp) REVERT: C 502 MET cc_start: 0.6464 (mtp) cc_final: 0.6254 (mmt) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.2386 time to fit residues: 115.6070 Evaluate side-chains 229 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 17 optimal weight: 7.9990 chunk 311 optimal weight: 1.9990 chunk 300 optimal weight: 0.4980 chunk 304 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 215 optimal weight: 0.5980 chunk 263 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN D 153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.141636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.119615 restraints weight = 70952.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.116515 restraints weight = 95303.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.114521 restraints weight = 81542.486| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 21464 Z= 0.107 Angle : 0.539 6.968 29660 Z= 0.278 Chirality : 0.041 0.153 3834 Planarity : 0.004 0.048 3730 Dihedral : 3.974 27.377 3246 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % 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 : 0.00 % 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: -0.97 (0.15), residues: 3142 helix: 1.18 (0.14), residues: 1332 sheet: -1.36 (0.26), residues: 382 loop : -2.31 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 247 HIS 0.005 0.001 HIS A 780 PHE 0.033 0.001 PHE D 653 TYR 0.019 0.001 TYR C 109 ARG 0.002 0.000 ARG C 755 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 1086) hydrogen bonds : angle 4.52859 ( 3138) SS BOND : bond 0.00487 ( 16) SS BOND : angle 1.36216 ( 32) covalent geometry : bond 0.00233 (21448) covalent geometry : angle 0.53730 (29628) *********************** 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 286 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 TRP cc_start: 0.8104 (m100) cc_final: 0.7464 (m100) REVERT: A 813 MET cc_start: 0.8175 (ttp) cc_final: 0.7941 (ttp) REVERT: B 249 LEU cc_start: 0.5931 (pt) cc_final: 0.5518 (mp) REVERT: B 497 MET cc_start: 0.8792 (mmm) cc_final: 0.8163 (mmt) REVERT: D 249 LEU cc_start: 0.5948 (pt) cc_final: 0.5439 (mp) REVERT: D 497 MET cc_start: 0.8668 (mmm) cc_final: 0.8045 (mmt) REVERT: D 721 LEU cc_start: 0.6925 (tp) cc_final: 0.6263 (pp) REVERT: C 184 LEU cc_start: 0.8766 (mt) cc_final: 0.8384 (tp) outliers start: 1 outliers final: 0 residues processed: 285 average time/residue: 0.2374 time to fit residues: 115.8463 Evaluate side-chains 235 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 229 optimal weight: 0.9980 chunk 216 optimal weight: 0.9990 chunk 199 optimal weight: 0.7980 chunk 241 optimal weight: 50.0000 chunk 273 optimal weight: 0.6980 chunk 103 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN B 688 ASN D 153 GLN D 688 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.140290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.117261 restraints weight = 70441.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.114127 restraints weight = 102593.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.112177 restraints weight = 87192.786| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21464 Z= 0.137 Angle : 0.566 8.522 29660 Z= 0.293 Chirality : 0.041 0.177 3834 Planarity : 0.004 0.055 3730 Dihedral : 4.071 28.380 3246 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % 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: -0.90 (0.15), residues: 3142 helix: 1.25 (0.14), residues: 1338 sheet: -1.73 (0.26), residues: 362 loop : -2.16 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 247 HIS 0.004 0.001 HIS A 780 PHE 0.031 0.002 PHE D 653 TYR 0.016 0.001 TYR A 795 ARG 0.002 0.000 ARG C 755 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 1086) hydrogen bonds : angle 4.58401 ( 3138) SS BOND : bond 0.00488 ( 16) SS BOND : angle 1.15888 ( 32) covalent geometry : bond 0.00314 (21448) covalent geometry : angle 0.56475 (29628) *********************** 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 277 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 171 ILE cc_start: 0.7731 (mp) cc_final: 0.7457 (mp) REVERT: B 249 LEU cc_start: 0.6146 (pt) cc_final: 0.5619 (mp) REVERT: B 497 MET cc_start: 0.8763 (mmm) cc_final: 0.8146 (mmt) REVERT: D 153 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7684 (tp40) REVERT: D 249 LEU cc_start: 0.6147 (pt) cc_final: 0.5536 (mp) REVERT: D 280 VAL cc_start: 0.7954 (t) cc_final: 0.7720 (p) REVERT: D 497 MET cc_start: 0.8729 (mmm) cc_final: 0.8076 (mmt) REVERT: D 721 LEU cc_start: 0.6970 (tp) cc_final: 0.6249 (pp) REVERT: C 184 LEU cc_start: 0.8865 (mt) cc_final: 0.8453 (tp) REVERT: C 247 TRP cc_start: 0.8232 (m100) cc_final: 0.8032 (m100) outliers start: 1 outliers final: 0 residues processed: 276 average time/residue: 0.2376 time to fit residues: 112.8654 Evaluate side-chains 237 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 179 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 192 optimal weight: 0.7980 chunk 257 optimal weight: 0.0370 chunk 313 optimal weight: 0.8980 chunk 294 optimal weight: 0.9990 chunk 233 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.140842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.118329 restraints weight = 70383.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.115062 restraints weight = 100393.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.113368 restraints weight = 83400.549| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21464 Z= 0.122 Angle : 0.557 7.493 29660 Z= 0.288 Chirality : 0.041 0.151 3834 Planarity : 0.004 0.047 3730 Dihedral : 4.023 27.983 3246 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: -0.77 (0.15), residues: 3142 helix: 1.31 (0.14), residues: 1350 sheet: -1.31 (0.25), residues: 390 loop : -2.18 (0.15), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 247 HIS 0.004 0.001 HIS C 780 PHE 0.034 0.001 PHE D 653 TYR 0.014 0.001 TYR C 109 ARG 0.002 0.000 ARG C 755 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 1086) hydrogen bonds : angle 4.47444 ( 3138) SS BOND : bond 0.00910 ( 16) SS BOND : angle 1.43763 ( 32) covalent geometry : bond 0.00278 (21448) covalent geometry : angle 0.55576 (29628) *********************** 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 275 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 249 LEU cc_start: 0.5842 (pt) cc_final: 0.5392 (mp) REVERT: B 497 MET cc_start: 0.8745 (mmm) cc_final: 0.8152 (mmt) REVERT: D 249 LEU cc_start: 0.5973 (pt) cc_final: 0.5385 (mp) REVERT: D 256 TRP cc_start: 0.4280 (m100) cc_final: 0.4067 (m100) REVERT: D 497 MET cc_start: 0.8720 (mmm) cc_final: 0.7997 (mmt) REVERT: D 721 LEU cc_start: 0.6855 (tp) cc_final: 0.6062 (pp) REVERT: C 184 LEU cc_start: 0.8832 (mt) cc_final: 0.8426 (tp) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.2574 time to fit residues: 122.1200 Evaluate side-chains 229 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 109 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 280 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 276 optimal weight: 0.5980 chunk 268 optimal weight: 10.0000 chunk 134 optimal weight: 0.0970 chunk 144 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4325 r_free = 0.4325 target = 0.141439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.119245 restraints weight = 70825.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.116795 restraints weight = 93529.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.113788 restraints weight = 81637.174| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 21464 Z= 0.108 Angle : 0.549 9.934 29660 Z= 0.280 Chirality : 0.041 0.200 3834 Planarity : 0.004 0.049 3730 Dihedral : 3.914 26.977 3246 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: -0.62 (0.15), residues: 3142 helix: 1.42 (0.14), residues: 1350 sheet: -1.15 (0.26), residues: 362 loop : -2.10 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 247 HIS 0.005 0.001 HIS C 780 PHE 0.032 0.001 PHE D 653 TYR 0.015 0.001 TYR C 109 ARG 0.002 0.000 ARG C 755 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 1086) hydrogen bonds : angle 4.34723 ( 3138) SS BOND : bond 0.00502 ( 16) SS BOND : angle 1.03938 ( 32) covalent geometry : bond 0.00236 (21448) covalent geometry : angle 0.54853 (29628) *********************** 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 284 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.6441 (mtp) cc_final: 0.6190 (mmt) REVERT: B 158 LEU cc_start: 0.9172 (tt) cc_final: 0.8958 (tp) REVERT: B 161 MET cc_start: 0.8159 (ptm) cc_final: 0.7591 (ppp) REVERT: B 249 LEU cc_start: 0.5832 (pt) cc_final: 0.5373 (mp) REVERT: B 256 TRP cc_start: 0.4386 (m100) cc_final: 0.4163 (m100) REVERT: B 497 MET cc_start: 0.8782 (mmm) cc_final: 0.8135 (mmt) REVERT: D 142 MET cc_start: -0.0028 (ptt) cc_final: -0.0456 (ttt) REVERT: D 249 LEU cc_start: 0.6011 (pt) cc_final: 0.5428 (mp) REVERT: D 497 MET cc_start: 0.8678 (mmm) cc_final: 0.8009 (mmt) REVERT: D 721 LEU cc_start: 0.6938 (tp) cc_final: 0.6101 (pp) REVERT: C 184 LEU cc_start: 0.8828 (mt) cc_final: 0.8419 (tp) REVERT: C 354 MET cc_start: 0.4355 (mmm) cc_final: 0.2885 (mmm) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.2433 time to fit residues: 118.1152 Evaluate side-chains 232 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 117 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 129 optimal weight: 5.9990 chunk 167 optimal weight: 0.0470 chunk 115 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.138337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.115971 restraints weight = 70552.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.113298 restraints weight = 107347.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.110950 restraints weight = 93067.980| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21464 Z= 0.193 Angle : 0.627 9.226 29660 Z= 0.327 Chirality : 0.043 0.166 3834 Planarity : 0.004 0.057 3730 Dihedral : 4.271 30.086 3246 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: -0.77 (0.15), residues: 3142 helix: 1.28 (0.14), residues: 1340 sheet: -1.53 (0.26), residues: 372 loop : -2.05 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 391 HIS 0.007 0.001 HIS C 780 PHE 0.034 0.002 PHE D 653 TYR 0.017 0.001 TYR C 109 ARG 0.002 0.001 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.04880 ( 1086) hydrogen bonds : angle 4.68215 ( 3138) SS BOND : bond 0.00313 ( 16) SS BOND : angle 1.13636 ( 32) covalent geometry : bond 0.00450 (21448) covalent geometry : angle 0.62669 (29628) *********************** 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 264 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 158 LEU cc_start: 0.9137 (tt) cc_final: 0.8875 (tp) REVERT: B 161 MET cc_start: 0.8249 (ptm) cc_final: 0.7651 (ppp) REVERT: B 249 LEU cc_start: 0.5866 (pt) cc_final: 0.5318 (mp) REVERT: B 256 TRP cc_start: 0.4129 (m100) cc_final: 0.3853 (m100) REVERT: B 497 MET cc_start: 0.8803 (mmm) cc_final: 0.8218 (mmt) REVERT: D 142 MET cc_start: 0.0289 (ptt) cc_final: -0.0196 (ttp) REVERT: D 158 LEU cc_start: 0.9103 (tt) cc_final: 0.8892 (tp) REVERT: D 161 MET cc_start: 0.8139 (ptm) cc_final: 0.7619 (ppp) REVERT: D 249 LEU cc_start: 0.5990 (pt) cc_final: 0.5353 (mp) REVERT: D 497 MET cc_start: 0.8771 (mmm) cc_final: 0.8028 (mmt) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2485 time to fit residues: 113.1275 Evaluate side-chains 218 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 76 optimal weight: 0.0980 chunk 126 optimal weight: 4.9990 chunk 307 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 302 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.138824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.115371 restraints weight = 70796.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.113926 restraints weight = 106000.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.111766 restraints weight = 88507.486| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21464 Z= 0.155 Angle : 0.597 9.097 29660 Z= 0.308 Chirality : 0.042 0.178 3834 Planarity : 0.004 0.062 3730 Dihedral : 4.221 29.998 3246 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % 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 : 0.00 % 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: -0.65 (0.15), residues: 3142 helix: 1.35 (0.14), residues: 1342 sheet: -1.32 (0.26), residues: 356 loop : -2.00 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 391 HIS 0.004 0.001 HIS A 780 PHE 0.033 0.002 PHE D 653 TYR 0.017 0.001 TYR C 109 ARG 0.002 0.000 ARG C 755 Details of bonding type rmsd hydrogen bonds : bond 0.04428 ( 1086) hydrogen bonds : angle 4.51124 ( 3138) SS BOND : bond 0.00420 ( 16) SS BOND : angle 1.53445 ( 32) covalent geometry : bond 0.00361 (21448) covalent geometry : angle 0.59525 (29628) ********************** 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 268 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 158 LEU cc_start: 0.9068 (tt) cc_final: 0.8868 (tp) REVERT: B 161 MET cc_start: 0.8128 (ptm) cc_final: 0.7611 (ppp) REVERT: B 249 LEU cc_start: 0.5699 (pt) cc_final: 0.5164 (mp) REVERT: B 497 MET cc_start: 0.8795 (mmm) cc_final: 0.8143 (mmt) REVERT: D 142 MET cc_start: 0.0286 (ptt) cc_final: -0.0222 (ttp) REVERT: D 161 MET cc_start: 0.8122 (ptm) cc_final: 0.7586 (ppp) REVERT: D 249 LEU cc_start: 0.5729 (pt) cc_final: 0.5157 (mp) REVERT: D 497 MET cc_start: 0.8732 (mmm) cc_final: 0.7980 (mmt) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2405 time to fit residues: 110.8743 Evaluate side-chains 227 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 99 optimal weight: 6.9990 chunk 213 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 57 optimal weight: 0.4980 chunk 166 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 167 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.139423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.116016 restraints weight = 70390.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.114332 restraints weight = 104368.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.113612 restraints weight = 76936.563| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21464 Z= 0.128 Angle : 0.580 8.533 29660 Z= 0.298 Chirality : 0.041 0.157 3834 Planarity : 0.004 0.060 3730 Dihedral : 4.117 29.392 3246 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % 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 : 0.00 % 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: -0.56 (0.15), residues: 3142 helix: 1.39 (0.14), residues: 1336 sheet: -1.42 (0.26), residues: 364 loop : -1.85 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 256 HIS 0.004 0.001 HIS A 780 PHE 0.029 0.001 PHE D 653 TYR 0.017 0.001 TYR C 109 ARG 0.002 0.000 ARG A 755 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 1086) hydrogen bonds : angle 4.42051 ( 3138) SS BOND : bond 0.00408 ( 16) SS BOND : angle 1.78925 ( 32) covalent geometry : bond 0.00296 (21448) covalent geometry : angle 0.57727 (29628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6512.01 seconds wall clock time: 114 minutes 36.38 seconds (6876.38 seconds total)