Starting phenix.real_space_refine on Fri Jan 24 05:37:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9arg_43781/01_2025/9arg_43781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9arg_43781/01_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_43781/01_2025/9arg_43781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9arg_43781/01_2025/9arg_43781.map" model { file = "/net/cci-nas-00/data/ceres_data/9arg_43781/01_2025/9arg_43781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9arg_43781/01_2025/9arg_43781.cif" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 266 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 13626 2.51 5 N 3442 2.21 5 O 3856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 20.58, per 1000 atoms: 0.98 Number of scatterers: 21008 At special positions: 0 Unit cell: (151.512, 118.984, 181.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3856 8.00 N 3442 7.00 C 13626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.04 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.50 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: 2.71 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: 7.40 Time building geometry restraints manager: 6.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6714 1.34 - 1.46: 5127 1.46 - 1.58: 9477 1.58 - 1.71: 0 1.71 - 1.83: 130 Bond restraints: 21448 Sorted by residual: bond pdb=" CA ASN D 615 " pdb=" CB ASN D 615 " ideal model delta sigma weight residual 1.539 1.514 0.025 1.20e-02 6.94e+03 4.36e+00 bond pdb=" CA ASN B 615 " pdb=" CB ASN B 615 " ideal model delta sigma weight residual 1.539 1.514 0.024 1.20e-02 6.94e+03 4.07e+00 bond pdb=" C PHE D 614 " pdb=" N ASN D 615 " ideal model delta sigma weight residual 1.332 1.308 0.024 1.36e-02 5.41e+03 3.20e+00 bond pdb=" C PHE B 614 " pdb=" N ASN B 615 " ideal model delta sigma weight residual 1.332 1.309 0.023 1.36e-02 5.41e+03 2.85e+00 bond pdb=" CA PRO A 447 " pdb=" C PRO A 447 " ideal model delta sigma weight residual 1.526 1.516 0.010 8.50e-03 1.38e+04 1.50e+00 ... (remaining 21443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 28718 1.42 - 2.84: 777 2.84 - 4.25: 103 4.25 - 5.67: 25 5.67 - 7.09: 5 Bond angle restraints: 29628 Sorted by residual: angle pdb=" C ASN B 615 " pdb=" CA ASN B 615 " pdb=" CB ASN B 615 " ideal model delta sigma weight residual 109.83 116.92 -7.09 9.90e-01 1.02e+00 5.13e+01 angle pdb=" C ASN D 615 " pdb=" CA ASN D 615 " pdb=" CB ASN D 615 " ideal model delta sigma weight residual 109.83 116.29 -6.46 9.90e-01 1.02e+00 4.26e+01 angle pdb=" N ASN B 615 " pdb=" CA ASN B 615 " pdb=" CB ASN B 615 " ideal model delta sigma weight residual 114.10 108.25 5.85 1.00e+00 1.00e+00 3.42e+01 angle pdb=" N ASN D 615 " pdb=" CA ASN D 615 " pdb=" CB ASN D 615 " ideal model delta sigma weight residual 114.10 108.98 5.12 1.00e+00 1.00e+00 2.62e+01 angle pdb=" CA ASN D 615 " pdb=" CB ASN D 615 " pdb=" CG ASN D 615 " ideal model delta sigma weight residual 112.60 109.07 3.53 1.00e+00 1.00e+00 1.24e+01 ... (remaining 29623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.21: 11555 11.21 - 22.42: 484 22.42 - 33.63: 182 33.63 - 44.84: 67 44.84 - 56.05: 34 Dihedral angle restraints: 12322 sinusoidal: 3176 harmonic: 9146 Sorted by residual: dihedral pdb=" CA GLN A 491 " pdb=" C GLN A 491 " pdb=" N ASN A 492 " pdb=" CA ASN A 492 " ideal model delta harmonic sigma weight residual 180.00 152.04 27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLN C 491 " pdb=" C GLN C 491 " pdb=" N ASN C 492 " pdb=" CA ASN C 492 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA MET D 503 " pdb=" C MET D 503 " pdb=" N LYS D 504 " pdb=" CA LYS D 504 " ideal model delta harmonic sigma weight residual -180.00 -158.21 -21.79 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 12319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3470 0.069 - 0.137: 362 0.137 - 0.206: 0 0.206 - 0.274: 0 0.274 - 0.343: 2 Chirality restraints: 3834 Sorted by residual: chirality pdb=" CA ASN D 615 " pdb=" N ASN D 615 " pdb=" C ASN D 615 " pdb=" CB ASN D 615 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ASN B 615 " pdb=" N ASN B 615 " pdb=" C ASN B 615 " pdb=" CB ASN B 615 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA ILE B 766 " pdb=" N ILE B 766 " pdb=" C ILE B 766 " pdb=" CB ILE B 766 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 3831 not shown) Planarity restraints: 3730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 615 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C ASN B 615 " 0.060 2.00e-02 2.50e+03 pdb=" O ASN B 615 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN B 616 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 615 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C ASN D 615 " -0.058 2.00e-02 2.50e+03 pdb=" O ASN D 615 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN D 616 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 318 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO C 319 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 319 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 319 " -0.026 5.00e-02 4.00e+02 ... (remaining 3727 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 92 2.60 - 3.18: 18166 3.18 - 3.75: 31038 3.75 - 4.33: 37294 4.33 - 4.90: 63319 Nonbonded interactions: 149909 Sorted by model distance: nonbonded pdb=" SG CYS D 86 " pdb=" SG CYS D 321 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS D 436 " pdb=" SG CYS D 457 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS C 744 " pdb=" SG CYS C 798 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS D 429 " pdb=" SG CYS D 456 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS D 746 " pdb=" SG CYS D 801 " model vdw 2.032 3.760 ... (remaining 149904 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 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: 5.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 55.070 Find NCS groups from input model: 0.520 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: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 21448 Z= 0.146 Angle : 0.568 7.091 29628 Z= 0.353 Chirality : 0.039 0.343 3834 Planarity : 0.004 0.047 3730 Dihedral : 9.079 56.051 6382 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 4.82 % Allowed : 8.46 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.13), residues: 3142 helix: -0.41 (0.13), residues: 1278 sheet: -2.65 (0.23), residues: 378 loop : -3.32 (0.13), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 636 HIS 0.001 0.000 HIS A 162 PHE 0.007 0.001 PHE D 550 TYR 0.008 0.001 TYR B 356 ARG 0.001 0.000 ARG C 663 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 482 time to evaluate : 2.275 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: 0.2507 time to fit residues: 235.7965 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 : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 9.9990 chunk 237 optimal weight: 30.0000 chunk 132 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 160 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 246 optimal weight: 8.9990 chunk 95 optimal weight: 20.0000 chunk 149 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 285 optimal weight: 4.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN B 118 GLN B 616 ASN B 688 ASN B 817 ASN D 616 ASN D 688 ASN D 817 ASN ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.137575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.110795 restraints weight = 70259.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.106569 restraints weight = 101743.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.104082 restraints weight = 72151.304| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 21448 Z= 0.465 Angle : 0.747 8.314 29628 Z= 0.395 Chirality : 0.046 0.228 3834 Planarity : 0.005 0.055 3730 Dihedral : 4.434 30.493 3246 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.56 % Allowed : 5.77 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.14), residues: 3142 helix: 0.21 (0.14), residues: 1328 sheet: -1.97 (0.25), residues: 380 loop : -2.85 (0.14), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 256 HIS 0.006 0.002 HIS C 780 PHE 0.033 0.003 PHE D 653 TYR 0.015 0.002 TYR A 410 ARG 0.006 0.001 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 284 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8553 (mt) cc_final: 0.7979 (mt) REVERT: A 247 TRP cc_start: 0.8177 (m100) cc_final: 0.7835 (m100) REVERT: B 249 LEU cc_start: 0.6775 (pt) cc_final: 0.6058 (mp) REVERT: B 554 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7819 (m-10) REVERT: B 818 MET cc_start: 0.8001 (mmm) cc_final: 0.7798 (mmp) REVERT: D 171 ILE cc_start: 0.7874 (mp) cc_final: 0.7591 (mp) REVERT: D 230 LEU cc_start: 0.7444 (tp) cc_final: 0.7173 (tp) REVERT: D 249 LEU cc_start: 0.6693 (pt) cc_final: 0.5885 (mp) REVERT: D 554 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7490 (m-10) REVERT: C 166 LEU cc_start: 0.9283 (tt) cc_final: 0.9054 (mt) REVERT: C 184 LEU cc_start: 0.8914 (mt) cc_final: 0.8500 (tp) REVERT: C 219 ILE cc_start: 0.8600 (mt) cc_final: 0.8382 (mt) REVERT: C 247 TRP cc_start: 0.8235 (m100) cc_final: 0.7942 (m100) outliers start: 10 outliers final: 3 residues processed: 294 average time/residue: 0.2493 time to fit residues: 125.6886 Evaluate side-chains 225 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 220 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: 30.0000 chunk 103 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 244 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 271 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 245 optimal weight: 6.9990 chunk 243 optimal weight: 10.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 118 GLN B 153 GLN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 ASN C 134 HIS C 650 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.138710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.116177 restraints weight = 70302.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.115068 restraints weight = 97735.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.111986 restraints weight = 93621.926| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21448 Z= 0.301 Angle : 0.612 6.885 29628 Z= 0.323 Chirality : 0.043 0.200 3834 Planarity : 0.004 0.050 3730 Dihedral : 4.360 31.046 3246 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.11 % Allowed : 4.88 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.15), residues: 3142 helix: 0.57 (0.14), residues: 1342 sheet: -1.80 (0.25), residues: 408 loop : -2.68 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 373 HIS 0.004 0.001 HIS A 780 PHE 0.058 0.002 PHE D 114 TYR 0.057 0.001 TYR C 109 ARG 0.002 0.000 ARG A 763 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 264 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 249 LEU cc_start: 0.5795 (pt) cc_final: 0.5366 (mp) REVERT: D 142 MET cc_start: 0.1190 (tpp) cc_final: 0.0913 (ttp) REVERT: D 249 LEU cc_start: 0.5830 (pt) cc_final: 0.5290 (mp) REVERT: C 184 LEU cc_start: 0.8671 (mt) cc_final: 0.8297 (tp) REVERT: C 219 ILE cc_start: 0.8493 (mt) cc_final: 0.8044 (mt) REVERT: C 247 TRP cc_start: 0.8136 (m100) cc_final: 0.7936 (m100) outliers start: 2 outliers final: 1 residues processed: 266 average time/residue: 0.2519 time to fit residues: 115.1057 Evaluate side-chains 225 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 2.351 ------------------------------------------------------------------------------- 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: 8.9990 chunk 238 optimal weight: 0.0020 chunk 138 optimal weight: 0.4980 chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 32 optimal weight: 30.0000 chunk 90 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 272 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 overall best weight: 1.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN C 134 HIS C 363 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.139834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.118032 restraints weight = 70895.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.115708 restraints weight = 99785.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.113562 restraints weight = 89500.770| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21448 Z= 0.197 Angle : 0.555 7.826 29628 Z= 0.290 Chirality : 0.041 0.180 3834 Planarity : 0.004 0.052 3730 Dihedral : 4.160 29.607 3246 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % 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: -1.29 (0.15), residues: 3142 helix: 0.95 (0.14), residues: 1342 sheet: -1.85 (0.25), residues: 420 loop : -2.42 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 247 HIS 0.003 0.001 HIS C 134 PHE 0.020 0.001 PHE D 653 TYR 0.023 0.001 TYR C 109 ARG 0.002 0.000 ARG C 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 TRP cc_start: 0.8089 (m100) cc_final: 0.7553 (m100) REVERT: B 249 LEU cc_start: 0.5849 (pt) cc_final: 0.5427 (mp) REVERT: B 497 MET cc_start: 0.8820 (mmm) cc_final: 0.7910 (mmt) REVERT: D 142 MET cc_start: 0.1409 (tpp) cc_final: 0.1204 (ttp) REVERT: D 249 LEU cc_start: 0.5951 (pt) cc_final: 0.5380 (mp) REVERT: D 497 MET cc_start: 0.8778 (mmm) cc_final: 0.8110 (mmt) REVERT: D 721 LEU cc_start: 0.6652 (tp) cc_final: 0.6043 (pp) REVERT: C 184 LEU cc_start: 0.8741 (mt) cc_final: 0.8347 (tp) REVERT: C 219 ILE cc_start: 0.8651 (mt) cc_final: 0.8261 (mt) REVERT: C 502 MET cc_start: 0.6494 (mtp) cc_final: 0.6256 (mmt) REVERT: C 813 MET cc_start: 0.8299 (ttm) cc_final: 0.8080 (ttm) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2551 time to fit residues: 117.9141 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 : 2.272 ------------------------------------------------------------------------------- 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: 0.7980 chunk 311 optimal weight: 0.3980 chunk 300 optimal weight: 0.9980 chunk 304 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.0980 chunk 135 optimal weight: 0.6980 chunk 215 optimal weight: 0.6980 chunk 263 optimal weight: 30.0000 chunk 22 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN D 153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.141557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.118982 restraints weight = 70971.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.115871 restraints weight = 100475.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.114543 restraints weight = 83283.947| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 21448 Z= 0.151 Angle : 0.538 8.055 29628 Z= 0.277 Chirality : 0.041 0.155 3834 Planarity : 0.004 0.049 3730 Dihedral : 4.003 27.771 3246 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.14 % 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: -0.96 (0.15), residues: 3142 helix: 1.21 (0.15), residues: 1318 sheet: -1.64 (0.25), residues: 406 loop : -2.19 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 247 HIS 0.006 0.001 HIS A 134 PHE 0.037 0.001 PHE B 114 TYR 0.016 0.001 TYR A 578 ARG 0.002 0.000 ARG C 755 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 TRP cc_start: 0.8181 (m100) cc_final: 0.7924 (m100) REVERT: A 321 PHE cc_start: 0.7680 (t80) cc_final: 0.7464 (t80) REVERT: B 249 LEU cc_start: 0.6258 (pt) cc_final: 0.5702 (mp) REVERT: B 497 MET cc_start: 0.8748 (mmm) cc_final: 0.8206 (mmt) REVERT: D 249 LEU cc_start: 0.6255 (pt) cc_final: 0.5593 (mp) REVERT: D 497 MET cc_start: 0.8744 (mmm) cc_final: 0.8288 (mmt) REVERT: D 721 LEU cc_start: 0.6869 (tp) cc_final: 0.6100 (pp) REVERT: C 184 LEU cc_start: 0.8814 (mt) cc_final: 0.8416 (tp) outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.2520 time to fit residues: 121.8488 Evaluate side-chains 237 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 2.404 ------------------------------------------------------------------------------- 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: 5.9990 chunk 216 optimal weight: 0.5980 chunk 199 optimal weight: 0.7980 chunk 241 optimal weight: 30.0000 chunk 273 optimal weight: 0.0470 chunk 103 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 246 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 overall best weight: 1.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.139529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.117854 restraints weight = 70349.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.115986 restraints weight = 95517.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.113420 restraints weight = 85518.718| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21448 Z= 0.233 Angle : 0.573 8.897 29628 Z= 0.296 Chirality : 0.041 0.158 3834 Planarity : 0.004 0.057 3730 Dihedral : 4.112 29.089 3246 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.86 % 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: -0.92 (0.15), residues: 3142 helix: 1.21 (0.14), residues: 1332 sheet: -1.80 (0.27), residues: 366 loop : -2.12 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 247 HIS 0.003 0.001 HIS C 477 PHE 0.030 0.002 PHE D 653 TYR 0.015 0.001 TYR C 109 ARG 0.002 0.000 ARG A 755 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 249 LEU cc_start: 0.5756 (pt) cc_final: 0.5319 (mp) REVERT: B 497 MET cc_start: 0.8779 (mmm) cc_final: 0.8259 (mmt) REVERT: D 153 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7294 (tp40) REVERT: D 249 LEU cc_start: 0.5794 (pt) cc_final: 0.5261 (mp) REVERT: D 280 VAL cc_start: 0.7735 (t) cc_final: 0.7492 (p) REVERT: D 497 MET cc_start: 0.8731 (mmm) cc_final: 0.8257 (mmt) REVERT: D 508 MET cc_start: 0.8354 (tpt) cc_final: 0.8065 (tpt) REVERT: D 721 LEU cc_start: 0.6734 (tp) cc_final: 0.6037 (pp) REVERT: C 184 LEU cc_start: 0.8747 (mt) cc_final: 0.8361 (tp) outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.2763 time to fit residues: 129.7305 Evaluate side-chains 231 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 2.274 ------------------------------------------------------------------------------- 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: 20.0000 chunk 240 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 257 optimal weight: 2.9990 chunk 313 optimal weight: 0.9990 chunk 294 optimal weight: 0.9980 chunk 233 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 chunk 205 optimal weight: 0.0170 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.140736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.117882 restraints weight = 70371.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.115757 restraints weight = 98444.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.113254 restraints weight = 77440.380| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21448 Z= 0.175 Angle : 0.549 7.590 29628 Z= 0.282 Chirality : 0.041 0.220 3834 Planarity : 0.004 0.053 3730 Dihedral : 4.007 28.200 3246 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.76 (0.15), residues: 3142 helix: 1.31 (0.14), residues: 1350 sheet: -1.47 (0.25), residues: 402 loop : -2.11 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 247 HIS 0.004 0.001 HIS C 780 PHE 0.036 0.001 PHE D 653 TYR 0.014 0.001 TYR C 109 ARG 0.002 0.000 ARG C 755 *********************** 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 278 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.6349 (mtp) cc_final: 0.6049 (mmt) REVERT: B 249 LEU cc_start: 0.5764 (pt) cc_final: 0.5315 (mp) REVERT: B 497 MET cc_start: 0.8650 (mmm) cc_final: 0.8154 (mmt) REVERT: D 249 LEU cc_start: 0.5803 (pt) cc_final: 0.5256 (mp) REVERT: D 497 MET cc_start: 0.8631 (mmm) cc_final: 0.8160 (mmt) REVERT: C 184 LEU cc_start: 0.8773 (mt) cc_final: 0.8382 (tp) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2542 time to fit residues: 121.1983 Evaluate side-chains 230 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 2.377 ------------------------------------------------------------------------------- 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: 3.9990 chunk 24 optimal weight: 0.0060 chunk 241 optimal weight: 30.0000 chunk 280 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 276 optimal weight: 0.4980 chunk 268 optimal weight: 6.9990 chunk 134 optimal weight: 0.0770 chunk 144 optimal weight: 0.9980 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.141968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.119886 restraints weight = 70918.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.117775 restraints weight = 96639.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.115843 restraints weight = 76812.637| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 21448 Z= 0.146 Angle : 0.541 7.603 29628 Z= 0.273 Chirality : 0.041 0.175 3834 Planarity : 0.004 0.050 3730 Dihedral : 3.857 26.609 3246 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % 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: -0.53 (0.15), residues: 3142 helix: 1.51 (0.14), residues: 1338 sheet: -1.24 (0.26), residues: 394 loop : -2.00 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 563 HIS 0.005 0.001 HIS C 780 PHE 0.042 0.001 PHE D 653 TYR 0.015 0.001 TYR C 109 ARG 0.002 0.000 ARG A 755 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.8165 (ptm) cc_final: 0.7559 (ppp) REVERT: B 249 LEU cc_start: 0.5811 (pt) cc_final: 0.5332 (mp) REVERT: B 497 MET cc_start: 0.8660 (mmm) cc_final: 0.8198 (mmt) REVERT: D 157 MET cc_start: 0.8130 (ppp) cc_final: 0.7886 (ppp) REVERT: D 161 MET cc_start: 0.8113 (ptm) cc_final: 0.7544 (ppp) REVERT: D 249 LEU cc_start: 0.5855 (pt) cc_final: 0.5297 (mp) REVERT: D 497 MET cc_start: 0.8651 (mmm) cc_final: 0.8235 (mmt) REVERT: D 721 LEU cc_start: 0.6896 (tp) cc_final: 0.6093 (pp) REVERT: C 184 LEU cc_start: 0.8790 (mt) cc_final: 0.8397 (tp) REVERT: C 354 MET cc_start: 0.4222 (mmm) cc_final: 0.2879 (mmm) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.2454 time to fit residues: 124.2044 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 : 2.216 ------------------------------------------------------------------------------- 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: 8.9990 chunk 200 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 129 optimal weight: 0.9990 chunk 167 optimal weight: 0.0470 chunk 115 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 67 optimal weight: 0.0670 chunk 141 optimal weight: 4.9990 overall best weight: 1.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.139793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.118234 restraints weight = 70820.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.114694 restraints weight = 98964.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.112272 restraints weight = 91970.377| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21448 Z= 0.227 Angle : 0.571 8.174 29628 Z= 0.293 Chirality : 0.042 0.195 3834 Planarity : 0.004 0.060 3730 Dihedral : 3.981 28.040 3246 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 3142 helix: 1.44 (0.14), residues: 1344 sheet: -1.40 (0.25), residues: 388 loop : -1.96 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 391 HIS 0.005 0.001 HIS C 780 PHE 0.032 0.002 PHE D 653 TYR 0.021 0.001 TYR A 109 ARG 0.002 0.000 ARG A 755 *********************** 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 274 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 249 LEU cc_start: 0.5921 (pt) cc_final: 0.5358 (mp) REVERT: B 497 MET cc_start: 0.8658 (mmm) cc_final: 0.8161 (mmt) REVERT: D 161 MET cc_start: 0.8200 (ptm) cc_final: 0.7657 (ppp) REVERT: D 229 LEU cc_start: 0.7492 (pp) cc_final: 0.7105 (tp) REVERT: D 249 LEU cc_start: 0.5980 (pt) cc_final: 0.5342 (mp) REVERT: D 497 MET cc_start: 0.8676 (mmm) cc_final: 0.8128 (mmt) REVERT: D 508 MET cc_start: 0.8263 (tpt) cc_final: 0.7977 (tpt) REVERT: D 721 LEU cc_start: 0.6897 (tp) cc_final: 0.6097 (pp) REVERT: C 184 LEU cc_start: 0.8794 (mt) cc_final: 0.8366 (tp) REVERT: C 354 MET cc_start: 0.4548 (mmm) cc_final: 0.3064 (mmm) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.2484 time to fit residues: 116.6688 Evaluate side-chains 228 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 2.333 ------------------------------------------------------------------------------- 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: 6.9990 chunk 307 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 302 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 100 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 622 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.138937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.117407 restraints weight = 70733.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.113861 restraints weight = 98238.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.112690 restraints weight = 89317.345| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21448 Z= 0.245 Angle : 0.585 8.753 29628 Z= 0.301 Chirality : 0.042 0.152 3834 Planarity : 0.004 0.052 3730 Dihedral : 4.139 29.468 3246 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.06 % Allowed : 0.50 % Favored : 99.44 % 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: -0.57 (0.15), residues: 3142 helix: 1.41 (0.14), residues: 1342 sheet: -1.40 (0.26), residues: 364 loop : -1.91 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 391 HIS 0.006 0.001 HIS C 780 PHE 0.033 0.002 PHE D 653 TYR 0.018 0.001 TYR A 109 ARG 0.002 0.000 ARG C 755 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 277 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 TRP cc_start: 0.8257 (m100) cc_final: 0.7923 (m100) REVERT: B 161 MET cc_start: 0.8234 (ptm) cc_final: 0.7706 (ppp) REVERT: B 249 LEU cc_start: 0.5946 (pt) cc_final: 0.5295 (mp) REVERT: B 497 MET cc_start: 0.8675 (mmm) cc_final: 0.8144 (mmt) REVERT: D 161 MET cc_start: 0.8258 (ptm) cc_final: 0.7719 (ppp) REVERT: D 229 LEU cc_start: 0.7424 (pp) cc_final: 0.6983 (tp) REVERT: D 249 LEU cc_start: 0.5995 (pt) cc_final: 0.5276 (mp) REVERT: D 497 MET cc_start: 0.8724 (mmm) cc_final: 0.8113 (mmt) REVERT: C 184 LEU cc_start: 0.8794 (mt) cc_final: 0.8319 (tp) REVERT: C 354 MET cc_start: 0.4586 (mmm) cc_final: 0.3027 (mmm) outliers start: 1 outliers final: 0 residues processed: 278 average time/residue: 0.2446 time to fit residues: 117.0922 Evaluate side-chains 228 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 2.406 ------------------------------------------------------------------------------- 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: 8.9990 chunk 213 optimal weight: 0.0040 chunk 132 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 166 optimal weight: 0.0970 chunk 97 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.0870 overall best weight: 0.5770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 153 GLN ** 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 = 0.4317 r_free = 0.4317 target = 0.140740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.117483 restraints weight = 70994.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.115854 restraints weight = 100529.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.114539 restraints weight = 82536.655| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 21448 Z= 0.153 Angle : 0.552 8.486 29628 Z= 0.280 Chirality : 0.041 0.190 3834 Planarity : 0.004 0.049 3730 Dihedral : 3.922 27.402 3246 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: -0.40 (0.15), residues: 3142 helix: 1.53 (0.14), residues: 1348 sheet: -1.26 (0.26), residues: 360 loop : -1.82 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 391 HIS 0.002 0.000 HIS C 780 PHE 0.035 0.001 PHE D 653 TYR 0.016 0.001 TYR A 109 ARG 0.002 0.000 ARG A 755 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6023.56 seconds wall clock time: 109 minutes 32.50 seconds (6572.50 seconds total)