Starting phenix.real_space_refine on Fri Sep 19 00:00:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9arg_43781/09_2025/9arg_43781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9arg_43781/09_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_43781/09_2025/9arg_43781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9arg_43781/09_2025/9arg_43781.map" model { file = "/net/cci-nas-00/data/ceres_data/9arg_43781/09_2025/9arg_43781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9arg_43781/09_2025/9arg_43781.cif" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASN:plan1': 14, 'ARG:plan': 37, 'HIS:plan': 10, 'GLU:plan': 46, 'GLN:plan1': 25, 'PHE:plan': 8, 'ASP:plan': 26, 'TYR:plan': 4, 'TRP:plan': 1} 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: {'ASP:plan': 33, 'GLU:plan': 50, 'HIS:plan': 7, 'PHE:plan': 9, 'ARG:plan': 23, 'ASN:plan1': 13, 'GLN:plan1': 21, 'TYR:plan': 14, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 742 Restraints were copied for chains: C, D Time building chain proxies: 7.79, per 1000 atoms: 0.37 Number of scatterers: 21008 At special positions: 0 Unit cell: (151.512, 118.984, 181.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3856 8.00 N 3442 7.00 C 13626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.04 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.04 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.76 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: 3.73 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6714 1.34 - 1.46: 5127 1.46 - 1.58: 9477 1.58 - 1.71: 0 1.71 - 1.83: 130 Bond restraints: 21448 Sorted by residual: bond pdb=" CA ASN D 615 " pdb=" CB ASN D 615 " ideal model delta sigma weight residual 1.539 1.514 0.025 1.20e-02 6.94e+03 4.36e+00 bond pdb=" CA ASN B 615 " pdb=" CB ASN B 615 " ideal model delta sigma weight residual 1.539 1.514 0.024 1.20e-02 6.94e+03 4.07e+00 bond pdb=" C PHE D 614 " pdb=" N ASN D 615 " ideal model delta sigma weight residual 1.332 1.308 0.024 1.36e-02 5.41e+03 3.20e+00 bond pdb=" C PHE B 614 " pdb=" N ASN B 615 " ideal model delta sigma weight residual 1.332 1.309 0.023 1.36e-02 5.41e+03 2.85e+00 bond pdb=" CA PRO A 447 " pdb=" C PRO A 447 " ideal model delta sigma weight residual 1.526 1.516 0.010 8.50e-03 1.38e+04 1.50e+00 ... (remaining 21443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 28718 1.42 - 2.84: 777 2.84 - 4.25: 103 4.25 - 5.67: 25 5.67 - 7.09: 5 Bond angle restraints: 29628 Sorted by residual: angle pdb=" C ASN B 615 " pdb=" CA ASN B 615 " pdb=" CB ASN B 615 " ideal model delta sigma weight residual 109.83 116.92 -7.09 9.90e-01 1.02e+00 5.13e+01 angle pdb=" C ASN D 615 " pdb=" CA ASN D 615 " pdb=" CB ASN D 615 " ideal model delta sigma weight residual 109.83 116.29 -6.46 9.90e-01 1.02e+00 4.26e+01 angle pdb=" N ASN B 615 " pdb=" CA ASN B 615 " pdb=" CB ASN B 615 " ideal model delta sigma weight residual 114.10 108.25 5.85 1.00e+00 1.00e+00 3.42e+01 angle pdb=" N ASN D 615 " pdb=" CA ASN D 615 " pdb=" CB ASN D 615 " ideal model delta sigma weight residual 114.10 108.98 5.12 1.00e+00 1.00e+00 2.62e+01 angle pdb=" CA ASN D 615 " pdb=" CB ASN D 615 " pdb=" CG ASN D 615 " ideal model delta sigma weight residual 112.60 109.07 3.53 1.00e+00 1.00e+00 1.24e+01 ... (remaining 29623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.21: 11567 11.21 - 22.42: 493 22.42 - 33.63: 184 33.63 - 44.84: 68 44.84 - 56.05: 34 Dihedral angle restraints: 12346 sinusoidal: 3200 harmonic: 9146 Sorted by residual: dihedral pdb=" CA GLN A 491 " pdb=" C GLN A 491 " pdb=" N ASN A 492 " pdb=" CA ASN A 492 " ideal model delta harmonic sigma weight residual 180.00 152.04 27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLN C 491 " pdb=" C GLN C 491 " pdb=" N ASN C 492 " pdb=" CA ASN C 492 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA MET D 503 " pdb=" C MET D 503 " pdb=" N LYS D 504 " pdb=" CA LYS D 504 " ideal model delta harmonic sigma weight residual -180.00 -158.21 -21.79 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 12343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3470 0.069 - 0.137: 362 0.137 - 0.206: 0 0.206 - 0.274: 0 0.274 - 0.343: 2 Chirality restraints: 3834 Sorted by residual: chirality pdb=" CA ASN D 615 " pdb=" N ASN D 615 " pdb=" C ASN D 615 " pdb=" CB ASN D 615 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ASN B 615 " pdb=" N ASN B 615 " pdb=" C ASN B 615 " pdb=" CB ASN B 615 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA ILE B 766 " pdb=" N ILE B 766 " pdb=" C ILE B 766 " pdb=" CB ILE B 766 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 3831 not shown) Planarity restraints: 3730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 615 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C ASN B 615 " 0.060 2.00e-02 2.50e+03 pdb=" O ASN B 615 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN B 616 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 615 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C ASN D 615 " -0.058 2.00e-02 2.50e+03 pdb=" O ASN D 615 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN D 616 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 318 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO C 319 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 319 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 319 " -0.026 5.00e-02 4.00e+02 ... (remaining 3727 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 243 2.67 - 3.23: 20217 3.23 - 3.78: 30575 3.78 - 4.34: 36739 4.34 - 4.90: 62111 Nonbonded interactions: 149885 Sorted by model distance: nonbonded pdb=" OG SER A 628 " pdb=" OG SER B 832 " model vdw 2.112 3.040 nonbonded pdb=" O ASP C 81 " pdb=" OG SER C 85 " model vdw 2.253 3.040 nonbonded pdb=" O ASP A 81 " pdb=" OG SER A 85 " model vdw 2.253 3.040 nonbonded pdb=" OG SER D 832 " pdb=" OG SER C 628 " model vdw 2.256 3.040 nonbonded pdb=" O CYS B 321 " pdb=" OG1 THR B 324 " model vdw 2.261 3.040 ... (remaining 149880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 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: 5.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 23.170 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 21464 Z= 0.131 Angle : 0.568 7.091 29660 Z= 0.353 Chirality : 0.039 0.343 3834 Planarity : 0.004 0.047 3730 Dihedral : 9.079 56.051 6382 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 4.82 % Allowed : 8.46 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG C 663 TYR 0.008 0.001 TYR B 356 PHE 0.007 0.001 PHE D 550 TRP 0.006 0.001 TRP C 636 HIS 0.001 0.000 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00213 (21448) covalent geometry : angle 0.56758 (29628) SS BOND : bond 0.00233 ( 16) SS BOND : angle 0.73159 ( 32) hydrogen bonds : bond 0.17444 ( 1086) hydrogen bonds : angle 6.37135 ( 3138) *********************** 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 : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 TRP cc_start: 0.8668 (m-10) cc_final: 0.8105 (m-90) REVERT: A 184 LEU cc_start: 0.8794 (mt) cc_final: 0.8485 (tp) REVERT: A 830 LEU cc_start: 0.8937 (mm) cc_final: 0.8716 (mm) REVERT: B 230 LEU cc_start: 0.7097 (tp) cc_final: 0.6844 (tp) REVERT: B 626 THR cc_start: 0.4909 (OUTLIER) cc_final: 0.4388 (m) REVERT: D 230 LEU cc_start: 0.7106 (tp) cc_final: 0.6846 (tp) REVERT: D 626 THR cc_start: 0.4472 (OUTLIER) cc_final: 0.3840 (m) REVERT: D 653 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.7211 (t80) REVERT: C 184 LEU cc_start: 0.8727 (mt) cc_final: 0.8425 (tp) REVERT: C 219 ILE cc_start: 0.8000 (mt) cc_final: 0.7543 (mt) REVERT: C 296 LEU cc_start: 0.0938 (OUTLIER) cc_final: 0.0646 (tt) REVERT: C 541 LEU cc_start: 0.7698 (tp) cc_final: 0.7459 (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: 0.8794 (mt) outliers start: 86 outliers final: 20 residues processed: 556 average time/residue: 0.1047 time to fit residues: 100.0017 Evaluate side-chains 308 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 282 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.0980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN A 571 HIS ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 616 ASN B 817 ASN D 817 ASN C 393 GLN C 571 HIS ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.144672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.119182 restraints weight = 71224.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.114003 restraints weight = 86642.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.112820 restraints weight = 72598.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.113007 restraints weight = 56257.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.113223 restraints weight = 47408.669| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21464 Z= 0.131 Angle : 0.578 7.697 29660 Z= 0.299 Chirality : 0.042 0.196 3834 Planarity : 0.004 0.044 3730 Dihedral : 3.731 28.696 3246 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.11 % Allowed : 4.09 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.14), residues: 3142 helix: 0.44 (0.14), residues: 1308 sheet: -1.96 (0.25), residues: 374 loop : -2.84 (0.14), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 523 TYR 0.010 0.001 TYR B 507 PHE 0.028 0.002 PHE D 653 TRP 0.032 0.002 TRP B 256 HIS 0.010 0.001 HIS A 571 Details of bonding type rmsd covalent geometry : bond 0.00285 (21448) covalent geometry : angle 0.57470 (29628) SS BOND : bond 0.01042 ( 16) SS BOND : angle 1.89470 ( 32) hydrogen bonds : bond 0.03843 ( 1086) hydrogen bonds : angle 5.04039 ( 3138) *********************** 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 335 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 333 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8976 (mt) cc_final: 0.8607 (tp) REVERT: B 171 ILE cc_start: 0.7963 (mp) cc_final: 0.7569 (mp) REVERT: B 249 LEU cc_start: 0.6839 (pt) cc_final: 0.6314 (mp) REVERT: D 157 MET cc_start: 0.8121 (ppp) cc_final: 0.7910 (ppp) REVERT: D 171 ILE cc_start: 0.7882 (mp) cc_final: 0.7640 (mp) REVERT: D 230 LEU cc_start: 0.7358 (tp) cc_final: 0.7133 (tp) REVERT: D 249 LEU cc_start: 0.6913 (pt) cc_final: 0.6284 (mp) REVERT: D 706 MET cc_start: 0.8506 (ttp) cc_final: 0.8299 (ttp) REVERT: D 721 LEU cc_start: 0.6867 (mm) cc_final: 0.6412 (pp) REVERT: C 166 LEU cc_start: 0.9290 (tt) cc_final: 0.9090 (mt) REVERT: C 184 LEU cc_start: 0.8856 (mt) cc_final: 0.8444 (tp) REVERT: C 219 ILE cc_start: 0.8568 (mt) cc_final: 0.8197 (mt) REVERT: C 247 TRP cc_start: 0.8205 (m100) cc_final: 0.7887 (m100) REVERT: C 607 MET cc_start: 0.7396 (ttp) cc_final: 0.7173 (ttm) outliers start: 2 outliers final: 0 residues processed: 335 average time/residue: 0.1059 time to fit residues: 61.4668 Evaluate side-chains 253 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 125 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 34 optimal weight: 30.0000 chunk 94 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 240 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 296 optimal weight: 0.0870 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN B 622 ASN B 688 ASN D 153 GLN D 616 ASN ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.136837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.110878 restraints weight = 70463.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.107238 restraints weight = 100122.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.104341 restraints weight = 84981.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.104579 restraints weight = 81429.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.104627 restraints weight = 59884.815| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 21464 Z= 0.286 Angle : 0.717 8.259 29660 Z= 0.381 Chirality : 0.045 0.205 3834 Planarity : 0.005 0.050 3730 Dihedral : 4.498 30.498 3246 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.45 % Allowed : 6.89 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.14), residues: 3142 helix: 0.41 (0.14), residues: 1340 sheet: -1.84 (0.25), residues: 410 loop : -2.75 (0.14), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 630 TYR 0.015 0.001 TYR A 410 PHE 0.033 0.003 PHE D 653 TRP 0.022 0.003 TRP C 731 HIS 0.006 0.002 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00666 (21448) covalent geometry : angle 0.71459 (29628) SS BOND : bond 0.00821 ( 16) SS BOND : angle 1.90434 ( 32) hydrogen bonds : bond 0.05832 ( 1086) hydrogen bonds : angle 5.39528 ( 3138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 266 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8630 (mt) cc_final: 0.8355 (mt) REVERT: B 229 LEU cc_start: 0.7982 (pp) cc_final: 0.7316 (tp) REVERT: B 249 LEU cc_start: 0.6512 (pt) cc_final: 0.5883 (mp) REVERT: B 554 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7394 (m-10) REVERT: D 229 LEU cc_start: 0.7956 (pp) cc_final: 0.7228 (tp) REVERT: D 249 LEU cc_start: 0.6482 (pt) cc_final: 0.5732 (mp) REVERT: D 554 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7226 (m-10) REVERT: C 166 LEU cc_start: 0.9321 (tt) cc_final: 0.9120 (mt) REVERT: C 184 LEU cc_start: 0.8897 (mt) cc_final: 0.8453 (tp) REVERT: C 219 ILE cc_start: 0.8604 (mt) cc_final: 0.8141 (mt) REVERT: C 247 TRP cc_start: 0.8255 (m100) cc_final: 0.7933 (m100) outliers start: 8 outliers final: 1 residues processed: 272 average time/residue: 0.1134 time to fit residues: 53.4658 Evaluate side-chains 231 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 228 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 16 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 310 optimal weight: 0.7980 chunk 190 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 79 optimal weight: 30.0000 chunk 52 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 176 optimal weight: 30.0000 chunk 130 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN B 153 GLN D 118 GLN D 153 GLN C 363 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.140467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.117054 restraints weight = 70801.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.115655 restraints weight = 101427.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.114233 restraints weight = 81722.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.114382 restraints weight = 70736.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.113643 restraints weight = 62516.014| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21464 Z= 0.132 Angle : 0.566 7.924 29660 Z= 0.296 Chirality : 0.042 0.206 3834 Planarity : 0.004 0.049 3730 Dihedral : 4.169 30.381 3246 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.15), residues: 3142 helix: 0.91 (0.14), residues: 1342 sheet: -1.55 (0.26), residues: 392 loop : -2.52 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 763 TYR 0.016 0.001 TYR A 578 PHE 0.030 0.002 PHE D 653 TRP 0.024 0.002 TRP A 247 HIS 0.002 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00295 (21448) covalent geometry : angle 0.56311 (29628) SS BOND : bond 0.00713 ( 16) SS BOND : angle 1.72771 ( 32) hydrogen bonds : bond 0.04460 ( 1086) hydrogen bonds : angle 4.78647 ( 3138) *********************** 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 272 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 249 LEU cc_start: 0.5822 (pt) cc_final: 0.5465 (mp) REVERT: B 497 MET cc_start: 0.8781 (mmm) cc_final: 0.8547 (tpp) REVERT: D 249 LEU cc_start: 0.5836 (pt) cc_final: 0.5359 (mp) REVERT: D 497 MET cc_start: 0.8782 (mmm) cc_final: 0.8133 (mmt) REVERT: C 184 LEU cc_start: 0.8709 (mt) cc_final: 0.8350 (tp) REVERT: C 219 ILE cc_start: 0.8533 (mt) cc_final: 0.8082 (mt) REVERT: C 247 TRP cc_start: 0.8122 (m100) cc_final: 0.7921 (m100) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.1084 time to fit residues: 50.7606 Evaluate side-chains 232 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 142 optimal weight: 5.9990 chunk 304 optimal weight: 0.7980 chunk 148 optimal weight: 0.0040 chunk 137 optimal weight: 0.5980 chunk 221 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 25 optimal weight: 8.9990 chunk 295 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 38 optimal weight: 0.0570 chunk 227 optimal weight: 6.9990 overall best weight: 0.3110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN A 405 GLN C 650 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.142664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.120238 restraints weight = 70864.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.116334 restraints weight = 95377.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.114002 restraints weight = 84779.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.114328 restraints weight = 77013.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.114548 restraints weight = 57964.183| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21464 Z= 0.103 Angle : 0.541 7.761 29660 Z= 0.279 Chirality : 0.041 0.165 3834 Planarity : 0.004 0.045 3730 Dihedral : 3.933 26.863 3246 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.15), residues: 3142 helix: 1.20 (0.15), residues: 1332 sheet: -1.15 (0.27), residues: 368 loop : -2.26 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 755 TYR 0.016 0.001 TYR A 578 PHE 0.036 0.001 PHE D 653 TRP 0.020 0.001 TRP B 256 HIS 0.004 0.000 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00213 (21448) covalent geometry : angle 0.53962 (29628) SS BOND : bond 0.00521 ( 16) SS BOND : angle 1.31601 ( 32) hydrogen bonds : bond 0.03681 ( 1086) hydrogen bonds : angle 4.49207 ( 3138) *********************** 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 291 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 TRP cc_start: 0.8154 (m100) cc_final: 0.7902 (m100) REVERT: A 321 PHE cc_start: 0.7647 (t80) cc_final: 0.7391 (t80) REVERT: B 249 LEU cc_start: 0.6235 (pt) cc_final: 0.5735 (mp) REVERT: B 497 MET cc_start: 0.8750 (mmm) cc_final: 0.8138 (mmt) REVERT: B 818 MET cc_start: 0.7868 (mmp) cc_final: 0.7611 (mmt) REVERT: D 249 LEU cc_start: 0.6184 (pt) cc_final: 0.5595 (mp) REVERT: D 497 MET cc_start: 0.8760 (mmm) cc_final: 0.8183 (mmt) REVERT: C 184 LEU cc_start: 0.8834 (mt) cc_final: 0.8453 (tp) REVERT: C 219 ILE cc_start: 0.8690 (mt) cc_final: 0.8171 (mt) REVERT: C 247 TRP cc_start: 0.8192 (m100) cc_final: 0.7929 (m100) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.0990 time to fit residues: 49.9987 Evaluate side-chains 231 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 152 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 293 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 289 optimal weight: 4.9990 chunk 110 optimal weight: 40.0000 chunk 13 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 223 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 D 688 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.139970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.117240 restraints weight = 70730.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.113687 restraints weight = 109707.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.112416 restraints weight = 90461.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.112816 restraints weight = 86200.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.112280 restraints weight = 68277.320| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21464 Z= 0.160 Angle : 0.580 6.948 29660 Z= 0.302 Chirality : 0.041 0.164 3834 Planarity : 0.004 0.056 3730 Dihedral : 4.076 28.550 3246 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.11 % Allowed : 3.31 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.15), residues: 3142 helix: 1.14 (0.14), residues: 1350 sheet: -1.47 (0.27), residues: 346 loop : -2.18 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 755 TYR 0.012 0.001 TYR A 795 PHE 0.036 0.002 PHE D 653 TRP 0.015 0.002 TRP A 563 HIS 0.004 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00369 (21448) covalent geometry : angle 0.57908 (29628) SS BOND : bond 0.00542 ( 16) SS BOND : angle 1.30431 ( 32) hydrogen bonds : bond 0.04375 ( 1086) hydrogen bonds : angle 4.63040 ( 3138) *********************** 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 272 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 270 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 249 LEU cc_start: 0.6141 (pt) cc_final: 0.5586 (mp) REVERT: B 497 MET cc_start: 0.8805 (mmm) cc_final: 0.8173 (mmt) REVERT: D 153 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7530 (tp40) REVERT: D 249 LEU cc_start: 0.6103 (pt) cc_final: 0.5483 (mp) REVERT: D 280 VAL cc_start: 0.8213 (t) cc_final: 0.7973 (p) REVERT: D 497 MET cc_start: 0.8808 (mmm) cc_final: 0.8247 (mmt) REVERT: C 184 LEU cc_start: 0.8874 (mt) cc_final: 0.8463 (tp) REVERT: C 219 ILE cc_start: 0.8714 (mt) cc_final: 0.8238 (mt) REVERT: C 247 TRP cc_start: 0.8182 (m100) cc_final: 0.7914 (m100) outliers start: 2 outliers final: 0 residues processed: 270 average time/residue: 0.1078 time to fit residues: 49.9999 Evaluate side-chains 224 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 267 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 294 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 256 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4320 r_free = 0.4320 target = 0.141095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.118394 restraints weight = 71009.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.117568 restraints weight = 96734.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.115230 restraints weight = 74594.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.115261 restraints weight = 79938.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.114938 restraints weight = 61116.479| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21464 Z= 0.119 Angle : 0.549 6.540 29660 Z= 0.286 Chirality : 0.041 0.182 3834 Planarity : 0.004 0.050 3730 Dihedral : 4.001 27.837 3246 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.06 % Allowed : 1.63 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.15), residues: 3142 helix: 1.33 (0.14), residues: 1338 sheet: -1.12 (0.27), residues: 354 loop : -2.13 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 397 TYR 0.009 0.001 TYR A 410 PHE 0.034 0.001 PHE D 653 TRP 0.033 0.001 TRP A 247 HIS 0.003 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00266 (21448) covalent geometry : angle 0.54779 (29628) SS BOND : bond 0.00376 ( 16) SS BOND : angle 1.42632 ( 32) hydrogen bonds : bond 0.04004 ( 1086) hydrogen bonds : angle 4.46581 ( 3138) *********************** 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 272 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 249 LEU cc_start: 0.5772 (pt) cc_final: 0.5343 (mp) REVERT: B 497 MET cc_start: 0.8751 (mmm) cc_final: 0.8101 (mmt) REVERT: D 142 MET cc_start: -0.0241 (ptt) cc_final: -0.0488 (ttt) REVERT: D 249 LEU cc_start: 0.5821 (pt) cc_final: 0.5287 (mp) REVERT: C 184 LEU cc_start: 0.8786 (mt) cc_final: 0.8383 (tp) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.1082 time to fit residues: 51.0668 Evaluate side-chains 220 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 259 optimal weight: 0.0170 chunk 93 optimal weight: 10.0000 chunk 232 optimal weight: 0.6980 chunk 160 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 HIS ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.141863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.118684 restraints weight = 70891.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.116443 restraints weight = 95687.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.114811 restraints weight = 82633.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.114966 restraints weight = 75105.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.114574 restraints weight = 61921.363| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21464 Z= 0.103 Angle : 0.542 6.885 29660 Z= 0.278 Chirality : 0.041 0.183 3834 Planarity : 0.004 0.049 3730 Dihedral : 3.902 27.107 3246 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.15), residues: 3142 helix: 1.47 (0.14), residues: 1334 sheet: -1.20 (0.26), residues: 366 loop : -2.06 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 755 TYR 0.011 0.001 TYR A 795 PHE 0.034 0.001 PHE D 653 TRP 0.021 0.001 TRP C 247 HIS 0.006 0.001 HIS A 571 Details of bonding type rmsd covalent geometry : bond 0.00223 (21448) covalent geometry : angle 0.54143 (29628) SS BOND : bond 0.00462 ( 16) SS BOND : angle 1.08486 ( 32) hydrogen bonds : bond 0.03702 ( 1086) hydrogen bonds : angle 4.34716 ( 3138) *********************** 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 278 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 PHE cc_start: 0.7630 (t80) cc_final: 0.7427 (t80) REVERT: A 818 MET cc_start: 0.7938 (ptm) cc_final: 0.7716 (ptt) REVERT: B 153 GLN cc_start: 0.8148 (pp30) cc_final: 0.7928 (pp30) REVERT: B 249 LEU cc_start: 0.5810 (pt) cc_final: 0.5389 (mp) REVERT: B 497 MET cc_start: 0.8800 (mmm) cc_final: 0.8193 (mmt) REVERT: D 142 MET cc_start: -0.0173 (ptt) cc_final: -0.0503 (ttt) REVERT: D 249 LEU cc_start: 0.5847 (pt) cc_final: 0.5300 (mp) REVERT: D 497 MET cc_start: 0.8686 (mmm) cc_final: 0.8387 (mmt) REVERT: C 184 LEU cc_start: 0.8791 (mt) cc_final: 0.8398 (tp) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.1094 time to fit residues: 52.7789 Evaluate side-chains 219 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 24 optimal weight: 0.0030 chunk 172 optimal weight: 9.9990 chunk 259 optimal weight: 10.0000 chunk 294 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 109 optimal weight: 30.0000 chunk 152 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 301 optimal weight: 0.0670 overall best weight: 1.9532 ------------------------------------------------------------------------------- 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 = 0.4300 r_free = 0.4300 target = 0.139679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.116767 restraints weight = 70118.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.113667 restraints weight = 108156.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.111315 restraints weight = 86576.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.111864 restraints weight = 82205.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.111712 restraints weight = 64803.662| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21464 Z= 0.149 Angle : 0.575 6.549 29660 Z= 0.299 Chirality : 0.042 0.190 3834 Planarity : 0.004 0.051 3730 Dihedral : 4.073 28.353 3246 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.15), residues: 3142 helix: 1.46 (0.15), residues: 1328 sheet: -1.11 (0.27), residues: 354 loop : -2.01 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 755 TYR 0.009 0.001 TYR C 474 PHE 0.033 0.002 PHE D 653 TRP 0.057 0.002 TRP C 247 HIS 0.006 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00343 (21448) covalent geometry : angle 0.57413 (29628) SS BOND : bond 0.00327 ( 16) SS BOND : angle 1.05383 ( 32) hydrogen bonds : bond 0.04302 ( 1086) hydrogen bonds : angle 4.49032 ( 3138) *********************** 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 268 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 MET cc_start: 0.8135 (tpp) cc_final: 0.7836 (mmm) REVERT: B 161 MET cc_start: 0.8280 (ptm) cc_final: 0.7691 (ppp) REVERT: B 249 LEU cc_start: 0.6144 (pt) cc_final: 0.5529 (mp) REVERT: B 256 TRP cc_start: 0.4679 (m100) cc_final: 0.4418 (m100) REVERT: B 497 MET cc_start: 0.8778 (mmm) cc_final: 0.8151 (mmt) REVERT: B 818 MET cc_start: 0.7645 (mmt) cc_final: 0.7360 (mmt) REVERT: D 142 MET cc_start: 0.0020 (ptt) cc_final: -0.0274 (ttp) REVERT: D 157 MET cc_start: 0.8198 (ppp) cc_final: 0.7990 (ppp) REVERT: D 161 MET cc_start: 0.8242 (ptm) cc_final: 0.7681 (ppp) REVERT: D 249 LEU cc_start: 0.6236 (pt) cc_final: 0.5517 (mp) REVERT: D 497 MET cc_start: 0.8672 (mmm) cc_final: 0.8346 (mmt) REVERT: C 184 LEU cc_start: 0.8885 (mt) cc_final: 0.8438 (tp) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1112 time to fit residues: 51.8831 Evaluate side-chains 214 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 127 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 249 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 104 optimal weight: 0.0000 chunk 139 optimal weight: 1.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- 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 = 0.4314 r_free = 0.4314 target = 0.140682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.118098 restraints weight = 70696.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.114388 restraints weight = 98791.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.112379 restraints weight = 87787.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.113073 restraints weight = 75329.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.112401 restraints weight = 61293.271| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21464 Z= 0.114 Angle : 0.565 8.375 29660 Z= 0.288 Chirality : 0.041 0.225 3834 Planarity : 0.004 0.055 3730 Dihedral : 3.985 27.450 3246 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.15), residues: 3142 helix: 1.44 (0.14), residues: 1348 sheet: -1.03 (0.27), residues: 354 loop : -1.96 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 755 TYR 0.008 0.001 TYR A 795 PHE 0.030 0.001 PHE D 653 TRP 0.032 0.002 TRP C 247 HIS 0.005 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00257 (21448) covalent geometry : angle 0.56153 (29628) SS BOND : bond 0.00409 ( 16) SS BOND : angle 1.93257 ( 32) hydrogen bonds : bond 0.03907 ( 1086) hydrogen bonds : angle 4.34063 ( 3138) ********************** 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 275 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 LEU cc_start: 0.9180 (tt) cc_final: 0.8973 (tt) REVERT: B 161 MET cc_start: 0.8242 (ptm) cc_final: 0.7683 (ppp) REVERT: B 249 LEU cc_start: 0.6003 (pt) cc_final: 0.5478 (mp) REVERT: B 256 TRP cc_start: 0.4453 (m100) cc_final: 0.4231 (m100) REVERT: B 497 MET cc_start: 0.8763 (mmm) cc_final: 0.8267 (mmt) REVERT: D 142 MET cc_start: 0.0008 (ptt) cc_final: -0.0251 (ttp) REVERT: D 161 MET cc_start: 0.8213 (ptm) cc_final: 0.7674 (ppp) REVERT: D 229 LEU cc_start: 0.7595 (pp) cc_final: 0.7168 (tp) REVERT: D 249 LEU cc_start: 0.6093 (pt) cc_final: 0.5463 (mp) REVERT: D 497 MET cc_start: 0.8668 (mmm) cc_final: 0.8393 (mmt) REVERT: C 184 LEU cc_start: 0.8865 (mt) cc_final: 0.8421 (tp) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1119 time to fit residues: 53.6668 Evaluate side-chains 218 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 277 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 228 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 212 optimal weight: 0.0670 chunk 311 optimal weight: 0.3980 chunk 254 optimal weight: 0.1980 chunk 251 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.142367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.119079 restraints weight = 71254.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.117107 restraints weight = 96502.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.114924 restraints weight = 80973.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.115355 restraints weight = 80710.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.115394 restraints weight = 60277.767| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21464 Z= 0.099 Angle : 0.544 8.738 29660 Z= 0.277 Chirality : 0.041 0.195 3834 Planarity : 0.004 0.045 3730 Dihedral : 3.827 25.828 3246 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.15), residues: 3142 helix: 1.56 (0.14), residues: 1348 sheet: -0.77 (0.27), residues: 366 loop : -1.92 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 397 TYR 0.008 0.001 TYR A 795 PHE 0.031 0.001 PHE D 653 TRP 0.031 0.002 TRP B 391 HIS 0.006 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00214 (21448) covalent geometry : angle 0.54214 (29628) SS BOND : bond 0.00438 ( 16) SS BOND : angle 1.62754 ( 32) hydrogen bonds : bond 0.03442 ( 1086) hydrogen bonds : angle 4.20553 ( 3138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3524.40 seconds wall clock time: 61 minutes 19.28 seconds (3679.28 seconds total)