Starting phenix.real_space_refine on Wed Jun 18 15:09:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9arg_43781/06_2025/9arg_43781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9arg_43781/06_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_43781/06_2025/9arg_43781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9arg_43781/06_2025/9arg_43781.map" model { file = "/net/cci-nas-00/data/ceres_data/9arg_43781/06_2025/9arg_43781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9arg_43781/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21008 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 5321 Classifications: {'peptide': 798} Incomplete info: {'truncation_to_alanine': 239} Link IDs: {'PTRANS': 35, 'TRANS': 762} Chain breaks: 2 Unresolved non-hydrogen bonds: 1016 Unresolved non-hydrogen angles: 1231 Unresolved non-hydrogen dihedrals: 856 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 26, 'TYR:plan': 4, 'ASN:plan1': 14, 'TRP:plan': 1, 'HIS:plan': 10, 'PHE:plan': 8, 'GLU:plan': 46, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 724 Chain: "B" Number of atoms: 5183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5183 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 245} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 1055 Unresolved non-hydrogen angles: 1285 Unresolved non-hydrogen dihedrals: 913 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 21, 'ASP:plan': 33, 'TYR:plan': 14, 'ASN:plan1': 13, 'TRP:plan': 2, 'HIS:plan': 7, 'PHE:plan': 9, 'GLU:plan': 50, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 742 Restraints were copied for chains: C, D Time building chain proxies: 20.37, per 1000 atoms: 0.97 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: 5.37 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: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 35 through 52 Processing helix chain 'A' and resid 71 through 86 Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.945A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 removed outlier: 3.882A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.757A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 261 removed outlier: 3.974A pdb=" N ALA A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 4.024A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.927A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.571A pdb=" N VAL A 575 " --> pdb=" O HIS A 571 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 616 removed outlier: 3.767A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 657 Processing helix chain 'A' and resid 669 through 674 removed outlier: 3.505A pdb=" N ASN A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.521A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 708 removed outlier: 4.277A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.677A pdb=" N GLN A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 723 " --> pdb=" O GLN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 742 removed outlier: 3.664A pdb=" N LEU A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 783 removed outlier: 4.049A pdb=" N GLN A 770 " --> pdb=" O SER A 766 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 810 through 812 No H-bonds generated for 'chain 'A' and resid 810 through 812' Processing helix chain 'A' and resid 813 through 841 removed outlier: 4.300A pdb=" N PHE A 817 " --> pdb=" O MET A 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.061A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 4.019A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 119 removed outlier: 3.960A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.612A pdb=" N MET B 132 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 165 removed outlier: 3.658A pdb=" N MET B 161 " --> pdb=" O MET B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 3.553A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 291 through 311 Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.732A pdb=" N ARG B 328 " --> pdb=" O HIS B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 340 Processing helix chain 'B' and resid 460 through 472 Processing helix chain 'B' and resid 489 through 493 removed outlier: 3.741A pdb=" N GLY B 492 " --> pdb=" O LYS B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 removed outlier: 3.848A pdb=" N MET B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 523 Processing helix chain 'B' and resid 548 through 552 removed outlier: 4.010A pdb=" N LEU B 551 " --> pdb=" O SER B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 578 removed outlier: 4.113A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 612 Processing helix chain 'B' and resid 626 through 654 Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 714 through 723 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 771 through 787 removed outlier: 4.163A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 Processing helix chain 'B' and resid 800 through 804 Processing helix chain 'B' and resid 814 through 817 Processing helix chain 'B' and resid 818 through 845 removed outlier: 3.925A pdb=" N GLN B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 55 removed outlier: 4.061A pdb=" N GLU D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 removed outlier: 4.019A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 119 removed outlier: 3.960A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 removed outlier: 3.613A pdb=" N MET D 132 " --> pdb=" O GLY D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 165 removed outlier: 3.659A pdb=" N MET D 161 " --> pdb=" O MET D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 192 removed outlier: 3.552A pdb=" N ASN D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 291 through 311 Processing helix chain 'D' and resid 324 through 328 removed outlier: 3.733A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 340 Processing helix chain 'D' and resid 460 through 472 Processing helix chain 'D' and resid 489 through 493 removed outlier: 3.741A pdb=" N GLY D 492 " --> pdb=" O LYS D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 503 removed outlier: 3.848A pdb=" N MET D 503 " --> pdb=" O GLY D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 523 Processing helix chain 'D' and resid 548 through 552 removed outlier: 4.009A pdb=" N LEU D 551 " --> pdb=" O SER D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 578 removed outlier: 4.112A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 612 Processing helix chain 'D' and resid 626 through 654 Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 708 through 710 No H-bonds generated for 'chain 'D' and resid 708 through 710' Processing helix chain 'D' and resid 714 through 723 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 771 through 787 removed outlier: 4.163A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 Processing helix chain 'D' and resid 800 through 804 Processing helix chain 'D' and resid 814 through 817 Processing helix chain 'D' and resid 818 through 845 removed outlier: 3.925A pdb=" N GLN D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.945A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 158 removed outlier: 3.882A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 224 through 238 removed outlier: 3.757A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.973A pdb=" N ALA C 258 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 296 removed outlier: 4.023A pdb=" N HIS C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 500 through 508 Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.927A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.570A pdb=" N VAL C 575 " --> pdb=" O HIS C 571 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 616 removed outlier: 3.766A pdb=" N LEU C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 657 Processing helix chain 'C' and resid 669 through 674 removed outlier: 3.504A pdb=" N ASN C 674 " --> pdb=" O PRO C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.521A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 708 removed outlier: 4.277A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.676A pdb=" N GLN C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP C 723 " --> pdb=" O GLN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 742 removed outlier: 3.664A pdb=" N LEU C 736 " --> pdb=" O ASP C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 783 removed outlier: 4.049A pdb=" N GLN C 770 " --> pdb=" O SER C 766 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 777 " --> pdb=" O SER C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 810 through 812 No H-bonds generated for 'chain 'C' and resid 810 through 812' Processing helix chain 'C' and resid 813 through 841 removed outlier: 4.300A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 removed outlier: 3.522A pdb=" N VAL A 65 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.816A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 222 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER A 168 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 268 removed outlier: 6.721A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 373 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A 371 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 340 removed outlier: 3.867A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 402 removed outlier: 3.675A pdb=" N ILE A 400 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR A 402 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 412 removed outlier: 3.649A pdb=" N LYS A 412 " --> pdb=" O CYS A 454 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS A 454 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 486 through 488 removed outlier: 3.661A pdb=" N THR A 486 " --> pdb=" O ASN A 499 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU A 497 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 513 through 517 removed outlier: 5.737A pdb=" N ALA A 515 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLY A 759 " --> pdb=" O ALA A 515 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 729 through 731 removed outlier: 6.413A pdb=" N GLN A 536 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ARG A 755 " --> pdb=" O GLN A 536 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 753 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE A 540 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N GLU A 751 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL A 542 " --> pdb=" O THR A 749 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR A 749 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 67 through 72 removed outlier: 5.700A pdb=" N GLY B 36 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL B 98 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA B 100 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE B 40 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 144 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 199 removed outlier: 3.894A pdb=" N PHE B 169 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE B 227 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.948A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 277 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 281 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 343 through 344 removed outlier: 3.596A pdb=" N PHE B 344 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 405 through 410 removed outlier: 4.045A pdb=" N ASP B 477 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 408 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 410 " --> pdb=" O TYR B 479 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 417 through 420 removed outlier: 3.690A pdb=" N CYS B 456 " --> pdb=" O GLU B 420 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 508 through 509 removed outlier: 3.657A pdb=" N ILE B 766 " --> pdb=" O ASP B 524 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP B 524 " --> pdb=" O ILE B 766 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 531 through 532 removed outlier: 3.508A pdb=" N THR B 760 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 729 through 732 removed outlier: 3.643A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 538 " --> pdb=" O VAL B 749 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 749 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 67 through 72 removed outlier: 5.700A pdb=" N GLY D 36 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL D 98 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA D 100 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE D 40 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE D 144 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 198 through 199 removed outlier: 3.894A pdb=" N PHE D 169 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE D 227 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 277 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 281 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 343 through 344 removed outlier: 3.596A pdb=" N PHE D 344 " --> pdb=" O ARG D 347 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 405 through 410 removed outlier: 4.045A pdb=" N ASP D 477 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 408 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR D 410 " --> pdb=" O TYR D 479 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 417 through 420 removed outlier: 3.691A pdb=" N CYS D 456 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 508 through 509 removed outlier: 3.657A pdb=" N ILE D 766 " --> pdb=" O ASP D 524 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP D 524 " --> pdb=" O ILE D 766 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 531 through 532 removed outlier: 3.507A pdb=" N THR D 760 " --> pdb=" O THR D 532 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 729 through 732 removed outlier: 3.642A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 538 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 749 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 59 through 65 removed outlier: 3.522A pdb=" N VAL C 65 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 193 through 197 removed outlier: 6.817A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER C 222 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER C 168 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 267 through 268 removed outlier: 6.721A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C 373 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS C 371 " --> pdb=" O ASN C 368 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 339 through 340 removed outlier: 3.867A pdb=" N GLU C 339 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 397 through 402 removed outlier: 3.675A pdb=" N ILE C 400 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR C 402 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 409 through 412 removed outlier: 3.649A pdb=" N LYS C 412 " --> pdb=" O CYS C 454 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS C 454 " --> pdb=" O LYS C 412 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 486 through 488 removed outlier: 3.661A pdb=" N THR C 486 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU C 497 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 513 through 517 removed outlier: 5.738A pdb=" N ALA C 515 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLY C 759 " --> pdb=" O ALA C 515 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 729 through 731 removed outlier: 6.414A pdb=" N GLN C 536 " --> pdb=" O ARG C 755 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ARG C 755 " --> pdb=" O GLN C 536 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE C 753 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE C 540 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N GLU C 751 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL C 542 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR C 749 " --> pdb=" O VAL C 542 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 3138 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.81 Time building geometry restraints manager: 6.03 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: 0.12 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: 5.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.880 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 55.740 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.400 ------------------------------------------------------------------------------- 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 : 2.436 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: 0.2466 time to fit residues: 232.0294 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 : 2.417 ------------------------------------------------------------------------------- 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 = 0.109874 restraints weight = 69873.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.105981 restraints weight = 99253.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.104646 restraints weight = 69001.275| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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 : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 LEU cc_start: 0.7680 (tp) cc_final: 0.7457 (tp) REVERT: B 249 LEU cc_start: 0.6943 (pt) cc_final: 0.6182 (mp) REVERT: B 554 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7700 (m-10) REVERT: B 721 LEU cc_start: 0.7016 (tp) cc_final: 0.6460 (pp) REVERT: B 818 MET cc_start: 0.7874 (mmm) cc_final: 0.7635 (mmp) REVERT: D 171 ILE cc_start: 0.7990 (mp) cc_final: 0.7727 (mp) REVERT: D 249 LEU cc_start: 0.6866 (pt) cc_final: 0.6034 (mp) REVERT: D 554 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7524 (m-10) REVERT: D 706 MET cc_start: 0.8522 (ttp) cc_final: 0.8320 (ttp) REVERT: D 721 LEU cc_start: 0.7042 (tp) cc_final: 0.6454 (pp) REVERT: C 166 LEU cc_start: 0.9340 (tt) cc_final: 0.9085 (mt) REVERT: C 184 LEU cc_start: 0.8951 (mt) cc_final: 0.8539 (tp) REVERT: C 247 TRP cc_start: 0.8274 (m100) cc_final: 0.8016 (m100) outliers start: 8 outliers final: 2 residues processed: 297 average time/residue: 0.2481 time to fit residues: 127.7126 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 : 2.475 ------------------------------------------------------------------------------- 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: 5.9990 chunk 130 optimal weight: 0.6980 chunk 100 optimal weight: 0.3980 chunk 244 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 271 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 245 optimal weight: 7.9990 chunk 243 optimal weight: 7.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.138698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.115627 restraints weight = 70167.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.112461 restraints weight = 104719.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.109966 restraints weight = 92000.947| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21464 Z= 0.207 Angle : 0.631 7.376 29660 Z= 0.335 Chirality : 0.043 0.195 3834 Planarity : 0.004 0.048 3730 Dihedral : 4.393 31.059 3246 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.06 % Allowed : 5.61 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.14), residues: 3142 helix: 0.51 (0.14), residues: 1342 sheet: -1.81 (0.25), residues: 402 loop : -2.72 (0.14), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 373 HIS 0.005 0.001 HIS C 780 PHE 0.037 0.002 PHE D 114 TYR 0.063 0.001 TYR C 109 ARG 0.002 0.001 ARG A 755 Details of bonding type rmsd hydrogen bonds : bond 0.05145 ( 1086) hydrogen bonds : angle 5.17219 ( 3138) SS BOND : bond 0.00616 ( 16) SS BOND : angle 2.26261 ( 32) covalent geometry : bond 0.00481 (21448) covalent geometry : angle 0.62732 (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 274 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8584 (mt) cc_final: 0.8354 (mt) REVERT: B 171 ILE cc_start: 0.7505 (mp) cc_final: 0.7259 (mp) REVERT: B 249 LEU cc_start: 0.6217 (pt) cc_final: 0.5626 (mp) REVERT: D 142 MET cc_start: 0.1202 (tpp) cc_final: 0.0873 (ttp) REVERT: D 249 LEU cc_start: 0.6235 (pt) cc_final: 0.5572 (mp) REVERT: D 497 MET cc_start: 0.8935 (mmm) cc_final: 0.8282 (mmt) REVERT: D 721 LEU cc_start: 0.6826 (tp) cc_final: 0.6281 (pp) REVERT: C 184 LEU cc_start: 0.8824 (mt) cc_final: 0.8424 (tp) REVERT: C 219 ILE cc_start: 0.8578 (mt) cc_final: 0.8172 (mt) REVERT: C 247 TRP cc_start: 0.8216 (m100) cc_final: 0.7953 (m100) outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.2467 time to fit residues: 116.1428 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 : 2.240 ------------------------------------------------------------------------------- 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: 0.3980 chunk 138 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 32 optimal weight: 30.0000 chunk 90 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 272 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 247 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 650 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.139827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.117791 restraints weight = 70698.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.116247 restraints weight = 99494.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.113305 restraints weight = 87732.801| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3423 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= 0.138 Angle : 0.572 8.096 29660 Z= 0.298 Chirality : 0.042 0.211 3834 Planarity : 0.004 0.052 3730 Dihedral : 4.234 30.084 3246 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % 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 : 0.07 % 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: -1.36 (0.15), residues: 3142 helix: 0.92 (0.14), residues: 1336 sheet: -1.89 (0.25), residues: 420 loop : -2.49 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 247 HIS 0.004 0.001 HIS A 780 PHE 0.019 0.001 PHE D 653 TYR 0.021 0.001 TYR A 578 ARG 0.002 0.000 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.04462 ( 1086) hydrogen bonds : angle 4.80424 ( 3138) SS BOND : bond 0.01515 ( 16) SS BOND : angle 1.39756 ( 32) covalent geometry : bond 0.00310 (21448) covalent geometry : angle 0.57016 (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 273 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 LEU cc_start: 0.7121 (pp) cc_final: 0.6920 (tp) REVERT: B 249 LEU cc_start: 0.5695 (pt) cc_final: 0.5346 (mp) REVERT: B 497 MET cc_start: 0.8750 (mmm) cc_final: 0.8015 (mmt) REVERT: D 249 LEU cc_start: 0.5765 (pt) cc_final: 0.5319 (mp) REVERT: D 497 MET cc_start: 0.8826 (mmm) cc_final: 0.8186 (mmt) REVERT: D 721 LEU cc_start: 0.6607 (tp) cc_final: 0.6059 (pp) REVERT: C 184 LEU cc_start: 0.8685 (mt) cc_final: 0.8317 (tp) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2464 time to fit residues: 115.0397 Evaluate side-chains 225 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 2.134 ------------------------------------------------------------------------------- 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: 0.8980 chunk 311 optimal weight: 0.9980 chunk 300 optimal weight: 0.6980 chunk 304 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 263 optimal weight: 40.0000 chunk 22 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.141299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.118665 restraints weight = 70890.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.116159 restraints weight = 102695.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.113814 restraints weight = 81334.758| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3486 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= 0.111 Angle : 0.549 6.620 29660 Z= 0.284 Chirality : 0.041 0.183 3834 Planarity : 0.004 0.048 3730 Dihedral : 4.088 28.068 3246 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -1.01 (0.15), residues: 3142 helix: 1.19 (0.15), residues: 1318 sheet: -1.50 (0.26), residues: 392 loop : -2.30 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 256 HIS 0.006 0.001 HIS A 780 PHE 0.036 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 0.03994 ( 1086) hydrogen bonds : angle 4.59454 ( 3138) SS BOND : bond 0.00608 ( 16) SS BOND : angle 1.09150 ( 32) covalent geometry : bond 0.00236 (21448) covalent geometry : angle 0.54788 (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 283 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 TRP cc_start: 0.8143 (m100) cc_final: 0.7744 (m100) REVERT: B 229 LEU cc_start: 0.7695 (pp) cc_final: 0.7357 (tp) REVERT: B 249 LEU cc_start: 0.6092 (pt) cc_final: 0.5575 (mp) REVERT: B 497 MET cc_start: 0.8720 (mmm) cc_final: 0.8057 (mmt) REVERT: D 249 LEU cc_start: 0.6211 (pt) cc_final: 0.5575 (mp) REVERT: D 497 MET cc_start: 0.8795 (mmm) cc_final: 0.8190 (mmt) REVERT: C 184 LEU cc_start: 0.8828 (mt) cc_final: 0.8423 (tp) outliers start: 1 outliers final: 0 residues processed: 282 average time/residue: 0.2373 time to fit residues: 115.6911 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 : 2.123 ------------------------------------------------------------------------------- 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: 4.9990 chunk 216 optimal weight: 0.0870 chunk 199 optimal weight: 0.8980 chunk 241 optimal weight: 40.0000 chunk 273 optimal weight: 0.0970 chunk 103 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 chunk 246 optimal weight: 0.0370 chunk 21 optimal weight: 0.0370 chunk 35 optimal weight: 1.9990 overall best weight: 0.2312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.142786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.120232 restraints weight = 70900.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.118053 restraints weight = 98665.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.116482 restraints weight = 77812.528| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3547 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= 0.101 Angle : 0.540 8.590 29660 Z= 0.276 Chirality : 0.041 0.167 3834 Planarity : 0.004 0.049 3730 Dihedral : 3.939 27.719 3246 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: -0.85 (0.15), residues: 3142 helix: 1.31 (0.14), residues: 1330 sheet: -1.46 (0.27), residues: 342 loop : -2.21 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 247 HIS 0.006 0.001 HIS A 780 PHE 0.039 0.001 PHE D 653 TYR 0.014 0.001 TYR A 795 ARG 0.005 0.001 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 1086) hydrogen bonds : angle 4.40250 ( 3138) SS BOND : bond 0.00475 ( 16) SS BOND : angle 1.06762 ( 32) covalent geometry : bond 0.00212 (21448) covalent geometry : angle 0.53916 (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 297 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 2.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 TRP cc_start: 0.8091 (m100) cc_final: 0.7843 (m100) REVERT: A 813 MET cc_start: 0.7940 (ttp) cc_final: 0.7714 (ttp) REVERT: B 249 LEU cc_start: 0.5813 (pt) cc_final: 0.5436 (mp) REVERT: B 497 MET cc_start: 0.8645 (mmm) cc_final: 0.7847 (mmt) REVERT: D 249 LEU cc_start: 0.5727 (pt) cc_final: 0.5312 (mp) REVERT: D 497 MET cc_start: 0.8782 (mmm) cc_final: 0.8272 (mmt) REVERT: D 721 LEU cc_start: 0.6659 (tp) cc_final: 0.5917 (pp) REVERT: C 184 LEU cc_start: 0.8745 (mt) cc_final: 0.8365 (tp) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.3092 time to fit residues: 162.6553 Evaluate side-chains 238 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 2.358 ------------------------------------------------------------------------------- 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: 2.9990 chunk 240 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 257 optimal weight: 20.0000 chunk 313 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 170 optimal weight: 8.9990 chunk 205 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 688 ASN D 153 GLN D 688 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.138509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.116210 restraints weight = 70436.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.113794 restraints weight = 108216.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.111573 restraints weight = 86557.687| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21464 Z= 0.192 Angle : 0.618 7.732 29660 Z= 0.324 Chirality : 0.042 0.157 3834 Planarity : 0.004 0.061 3730 Dihedral : 4.263 29.599 3246 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.06 % Allowed : 2.13 % Favored : 97.81 % 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: -0.94 (0.15), residues: 3142 helix: 1.16 (0.14), residues: 1336 sheet: -1.52 (0.25), residues: 384 loop : -2.18 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 635 HIS 0.005 0.001 HIS C 780 PHE 0.033 0.002 PHE D 653 TYR 0.015 0.001 TYR C 109 ARG 0.003 0.001 ARG C 630 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 1086) hydrogen bonds : angle 4.73331 ( 3138) SS BOND : bond 0.00510 ( 16) SS BOND : angle 1.41672 ( 32) covalent geometry : bond 0.00445 (21448) covalent geometry : angle 0.61612 (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 263 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 249 LEU cc_start: 0.5988 (pt) cc_final: 0.5423 (mp) REVERT: B 497 MET cc_start: 0.8682 (mmm) cc_final: 0.7932 (mmt) REVERT: D 153 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7413 (tp40) REVERT: D 249 LEU cc_start: 0.6012 (pt) cc_final: 0.5388 (mp) REVERT: D 280 VAL cc_start: 0.7825 (t) cc_final: 0.7575 (p) REVERT: D 497 MET cc_start: 0.8781 (mmm) cc_final: 0.8176 (mmt) REVERT: D 508 MET cc_start: 0.8376 (tpt) cc_final: 0.8081 (tpt) REVERT: C 184 LEU cc_start: 0.8780 (mt) cc_final: 0.8319 (tp) outliers start: 1 outliers final: 0 residues processed: 262 average time/residue: 0.2546 time to fit residues: 115.1654 Evaluate side-chains 222 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 2.257 ------------------------------------------------------------------------------- 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: 0.8980 chunk 241 optimal weight: 10.0000 chunk 280 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 233 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 276 optimal weight: 0.6980 chunk 268 optimal weight: 20.0000 chunk 134 optimal weight: 0.6980 chunk 144 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 GLN ** D 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.139823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.117405 restraints weight = 70755.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.115023 restraints weight = 97506.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.112858 restraints weight = 82296.001| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.4110 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= 0.128 Angle : 0.563 6.501 29660 Z= 0.291 Chirality : 0.042 0.198 3834 Planarity : 0.004 0.057 3730 Dihedral : 4.122 29.186 3246 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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: -0.79 (0.15), residues: 3142 helix: 1.29 (0.14), residues: 1350 sheet: -1.44 (0.25), residues: 384 loop : -2.14 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 247 HIS 0.005 0.001 HIS C 780 PHE 0.035 0.001 PHE D 653 TYR 0.015 0.001 TYR C 109 ARG 0.002 0.000 ARG A 755 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 1086) hydrogen bonds : angle 4.48361 ( 3138) SS BOND : bond 0.00433 ( 16) SS BOND : angle 1.22655 ( 32) covalent geometry : bond 0.00290 (21448) covalent geometry : angle 0.56167 (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 268 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 249 LEU cc_start: 0.5636 (pt) cc_final: 0.5209 (mp) REVERT: B 497 MET cc_start: 0.8698 (mmm) cc_final: 0.7937 (mmt) REVERT: D 142 MET cc_start: 0.0235 (ptt) cc_final: -0.0035 (ttt) REVERT: D 249 LEU cc_start: 0.5700 (pt) cc_final: 0.5176 (mp) REVERT: D 256 TRP cc_start: 0.3955 (m100) cc_final: 0.3754 (m100) REVERT: D 497 MET cc_start: 0.8747 (mmm) cc_final: 0.8138 (mmt) REVERT: C 184 LEU cc_start: 0.8702 (mt) cc_final: 0.8245 (tp) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2535 time to fit residues: 117.2215 Evaluate side-chains 222 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 2.219 ------------------------------------------------------------------------------- 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: 20.0000 chunk 200 optimal weight: 8.9990 chunk 103 optimal weight: 0.0470 chunk 89 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 167 optimal weight: 0.5980 chunk 115 optimal weight: 10.0000 chunk 153 optimal weight: 30.0000 chunk 127 optimal weight: 0.0980 chunk 67 optimal weight: 10.0000 chunk 141 optimal weight: 0.0170 overall best weight: 1.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4310 r_free = 0.4310 target = 0.140339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.117935 restraints weight = 71044.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.115914 restraints weight = 97015.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.114055 restraints weight = 85647.032| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.4219 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= 0.121 Angle : 0.554 8.254 29660 Z= 0.286 Chirality : 0.041 0.158 3834 Planarity : 0.004 0.054 3730 Dihedral : 4.080 28.624 3246 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: -0.63 (0.15), residues: 3142 helix: 1.37 (0.14), residues: 1350 sheet: -1.19 (0.27), residues: 344 loop : -2.05 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 391 HIS 0.005 0.001 HIS C 780 PHE 0.036 0.001 PHE D 653 TYR 0.015 0.001 TYR C 109 ARG 0.002 0.000 ARG A 755 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 1086) hydrogen bonds : angle 4.41788 ( 3138) SS BOND : bond 0.00318 ( 16) SS BOND : angle 1.05784 ( 32) covalent geometry : bond 0.00275 (21448) covalent geometry : angle 0.55273 (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 269 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.8221 (ptm) cc_final: 0.7680 (ppp) REVERT: B 249 LEU cc_start: 0.5585 (pt) cc_final: 0.5166 (mp) REVERT: B 497 MET cc_start: 0.8662 (mmm) cc_final: 0.7936 (mmt) REVERT: D 142 MET cc_start: 0.0205 (ptt) cc_final: -0.0124 (ttp) REVERT: D 161 MET cc_start: 0.8136 (ptm) cc_final: 0.7600 (ppp) REVERT: D 249 LEU cc_start: 0.5612 (pt) cc_final: 0.5096 (mp) REVERT: D 497 MET cc_start: 0.8743 (mmm) cc_final: 0.8203 (mmt) REVERT: D 508 MET cc_start: 0.8319 (tpt) cc_final: 0.7985 (tpt) REVERT: C 184 LEU cc_start: 0.8699 (mt) cc_final: 0.8251 (tp) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2443 time to fit residues: 113.3788 Evaluate side-chains 217 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 2.974 ------------------------------------------------------------------------------- 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: 0.6980 chunk 126 optimal weight: 2.9990 chunk 307 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 302 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 121 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4303 r_free = 0.4303 target = 0.139765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.116817 restraints weight = 70890.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.115022 restraints weight = 101821.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.112877 restraints weight = 80782.950| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.4373 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= 0.133 Angle : 0.574 8.725 29660 Z= 0.295 Chirality : 0.041 0.177 3834 Planarity : 0.004 0.055 3730 Dihedral : 4.092 29.011 3246 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % 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: -0.62 (0.15), residues: 3142 helix: 1.34 (0.14), residues: 1350 sheet: -1.31 (0.26), residues: 356 loop : -1.96 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 391 HIS 0.005 0.001 HIS C 780 PHE 0.036 0.001 PHE D 653 TYR 0.016 0.001 TYR C 109 ARG 0.002 0.000 ARG A 755 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 1086) hydrogen bonds : angle 4.43437 ( 3138) SS BOND : bond 0.00478 ( 16) SS BOND : angle 1.54843 ( 32) covalent geometry : bond 0.00307 (21448) covalent geometry : angle 0.57156 (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 266 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.8253 (ptm) cc_final: 0.7733 (ppp) REVERT: B 249 LEU cc_start: 0.5747 (pt) cc_final: 0.5217 (mp) REVERT: B 497 MET cc_start: 0.8678 (mmm) cc_final: 0.7950 (mmt) REVERT: D 142 MET cc_start: 0.0264 (ptt) cc_final: -0.0181 (ttt) REVERT: D 161 MET cc_start: 0.8106 (ptm) cc_final: 0.7648 (ppp) REVERT: D 249 LEU cc_start: 0.5771 (pt) cc_final: 0.5192 (mp) REVERT: D 497 MET cc_start: 0.8768 (mmm) cc_final: 0.8239 (mmt) REVERT: C 184 LEU cc_start: 0.8735 (mt) cc_final: 0.8331 (tp) REVERT: C 354 MET cc_start: 0.4399 (mmm) cc_final: 0.2853 (mmm) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.2820 time to fit residues: 128.1522 Evaluate side-chains 219 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 2.348 ------------------------------------------------------------------------------- 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: 30.0000 chunk 213 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 166 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 167 optimal weight: 20.0000 chunk 200 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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** B 812 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.135638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.112548 restraints weight = 70619.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.109687 restraints weight = 105799.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.106679 restraints weight = 91204.947| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 21464 Z= 0.277 Angle : 0.736 10.562 29660 Z= 0.387 Chirality : 0.046 0.201 3834 Planarity : 0.005 0.068 3730 Dihedral : 4.843 34.659 3246 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: -1.05 (0.15), residues: 3142 helix: 0.89 (0.14), residues: 1336 sheet: -1.59 (0.28), residues: 316 loop : -2.04 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 391 HIS 0.014 0.002 HIS A 780 PHE 0.030 0.003 PHE D 653 TYR 0.023 0.002 TYR A 647 ARG 0.004 0.001 ARG C 523 Details of bonding type rmsd hydrogen bonds : bond 0.05875 ( 1086) hydrogen bonds : angle 5.12607 ( 3138) SS BOND : bond 0.00684 ( 16) SS BOND : angle 2.06497 ( 32) covalent geometry : bond 0.00645 (21448) covalent geometry : angle 0.73288 (29628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7288.29 seconds wall clock time: 129 minutes 57.60 seconds (7797.60 seconds total)