Starting phenix.real_space_refine on Mon May 4 13:17:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9unj_64353/05_2026/9unj_64353.cif Found real_map, /net/cci-nas-00/data/ceres_data/9unj_64353/05_2026/9unj_64353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9unj_64353/05_2026/9unj_64353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9unj_64353/05_2026/9unj_64353.map" model { file = "/net/cci-nas-00/data/ceres_data/9unj_64353/05_2026/9unj_64353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9unj_64353/05_2026/9unj_64353.cif" } resolution = 3.93 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= 0.004 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 5 Type Number sf(0) Gaussians S 87 5.16 5 Cl 1 4.86 5 C 13147 2.51 5 N 3535 2.21 5 O 3946 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-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20716 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 5322 Classifications: {'peptide': 790} Incomplete info: {'truncation_to_alanine': 216} Link IDs: {'PTRANS': 34, 'TRANS': 755} Chain breaks: 2 Unresolved non-hydrogen bonds: 947 Unresolved non-hydrogen angles: 1162 Unresolved non-hydrogen dihedrals: 820 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'ARG:plan': 35, 'GLU:plan': 33, 'GLN:plan1': 12, 'TRP:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 17, 'HIS:plan': 5, 'TYR:plan': 5, 'PHE:plan': 14} Unresolved non-hydrogen planarities: 625 Chain: "B" Number of atoms: 4882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 4882 Classifications: {'peptide': 790} Incomplete info: {'truncation_to_alanine': 342} Link IDs: {'PTRANS': 29, 'TRANS': 760} Chain breaks: 1 Unresolved non-hydrogen bonds: 1450 Unresolved non-hydrogen angles: 1847 Unresolved non-hydrogen dihedrals: 1272 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'HIS:plan': 10, 'ASP:plan': 35, 'GLU:plan': 41, 'ARG:plan': 24, 'TRP:plan': 13, 'GLN:plan1': 18, 'PHE:plan': 30, 'TYR:plan': 16, 'ASN:plan1': 18} Unresolved non-hydrogen planarities: 974 Chain: "C" Number of atoms: 5141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 5141 Classifications: {'peptide': 790} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 34, 'TRANS': 755} Chain breaks: 2 Unresolved non-hydrogen bonds: 1157 Unresolved non-hydrogen angles: 1447 Unresolved non-hydrogen dihedrals: 1028 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'ARG:plan': 33, 'GLU:plan': 38, 'GLN:plan1': 17, 'TRP:plan': 10, 'ASN:plan1': 12, 'ASP:plan': 17, 'PHE:plan': 19, 'TYR:plan': 13, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 802 Chain: "D" Number of atoms: 5147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 5147 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 283} Link IDs: {'PTRANS': 30, 'TRANS': 760} Chain breaks: 1 Unresolved non-hydrogen bonds: 1166 Unresolved non-hydrogen angles: 1465 Unresolved non-hydrogen dihedrals: 1030 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'HIS:plan': 8, 'ASP:plan': 33, 'GLU:plan': 39, 'ARG:plan': 20, 'TRP:plan': 10, 'GLN:plan1': 9, 'PHE:plan': 22, 'ASN:plan1': 14, 'TYR:plan': 11} Unresolved non-hydrogen planarities: 772 Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 102 Unusual residues: {'NAG': 7} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 74 Unusual residues: {'NAG': 5} Classifications: {'peptide': 1, 'undetermined': 5} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'JC9': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Time building chain proxies: 5.32, per 1000 atoms: 0.26 Number of scatterers: 20716 At special positions: 0 Unit cell: (106.555, 142.425, 178.295, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 87 16.00 O 3946 8.00 N 3535 7.00 C 13147 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " distance=2.04 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 745 " - pdb=" SG CYS B 800 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 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 D 87 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 456 " distance=2.04 Simple disulfide: pdb=" SG CYS D 745 " - pdb=" SG CYS D 800 " 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 471 " " NAG A 902 " - " ASN A 61 " " NAG A 903 " - " ASN A 350 " " NAG A 904 " - " ASN A 239 " " NAG A 905 " - " ASN A 368 " " NAG A 906 " - " ASN A 276 " " NAG A 907 " - " ASN A 771 " " NAG B 901 " - " ASN B 687 " " NAG C 901 " - " ASN C 61 " " NAG C 902 " - " ASN C 276 " " NAG C 903 " - " ASN C 350 " " NAG C 904 " - " ASN C 471 " " NAG C 905 " - " ASN C 771 " Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 1.1 seconds 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5914 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 29 sheets defined 45.7% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 Processing helix chain 'A' and resid 70 through 82 Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 103 through 114 removed outlier: 4.292A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.785A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.796A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 removed outlier: 4.187A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 4.167A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 256 through 262 Processing helix chain 'A' and resid 277 through 298 Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.100A pdb=" N GLU A 385 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.199A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 583 Processing helix chain 'A' and resid 602 through 615 Processing helix chain 'A' and resid 626 through 657 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 699 through 709 removed outlier: 3.592A pdb=" N HIS A 709 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 767 through 783 removed outlier: 4.672A pdb=" N ASN A 771 " --> pdb=" O PRO A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 792 Processing helix chain 'A' and resid 804 through 808 Processing helix chain 'A' and resid 810 through 836 Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 108 through 121 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 150 through 165 Processing helix chain 'B' and resid 179 through 194 removed outlier: 3.837A pdb=" N PHE B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 222 Processing helix chain 'B' and resid 232 through 246 Processing helix chain 'B' and resid 268 through 272 removed outlier: 4.111A pdb=" N GLU B 271 " --> pdb=" O ILE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 310 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.865A pdb=" N VAL B 339 " --> pdb=" O HIS B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 removed outlier: 3.922A pdb=" N GLY B 345 " --> pdb=" O THR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 472 Processing helix chain 'B' and resid 495 through 502 Processing helix chain 'B' and resid 515 through 522 Processing helix chain 'B' and resid 555 through 579 Processing helix chain 'B' and resid 600 through 613 Processing helix chain 'B' and resid 624 through 655 Processing helix chain 'B' and resid 667 through 672 Processing helix chain 'B' and resid 688 through 698 Processing helix chain 'B' and resid 698 through 708 removed outlier: 3.533A pdb=" N PHE B 708 " --> pdb=" O TYR B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 732 through 742 Processing helix chain 'B' and resid 743 through 745 No H-bonds generated for 'chain 'B' and resid 743 through 745' Processing helix chain 'B' and resid 770 through 785 removed outlier: 4.147A pdb=" N GLN B 774 " --> pdb=" O PRO B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 796 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 817 through 839 Processing helix chain 'C' and resid 35 through 54 Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 83 through 86 Processing helix chain 'C' and resid 103 through 115 removed outlier: 4.557A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.674A pdb=" N SER C 129 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.874A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET C 154 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 Processing helix chain 'C' and resid 204 through 214 Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 251 through 254 Processing helix chain 'C' and resid 256 through 262 Processing helix chain 'C' and resid 277 through 298 Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 556 through 583 removed outlier: 3.710A pdb=" N LEU C 562 " --> pdb=" O PHE C 558 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG C 582 " --> pdb=" O TYR C 578 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE C 583 " --> pdb=" O LEU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 615 Processing helix chain 'C' and resid 626 through 657 Processing helix chain 'C' and resid 668 through 674 removed outlier: 3.708A pdb=" N LEU C 672 " --> pdb=" O ASN C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.666A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 708 Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 768 through 783 Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 804 through 808 Processing helix chain 'C' and resid 810 through 837 removed outlier: 3.917A pdb=" N ALA C 814 " --> pdb=" O PHE C 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 106 through 121 removed outlier: 4.059A pdb=" N ALA D 110 " --> pdb=" O GLN D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 removed outlier: 3.651A pdb=" N THR D 143 " --> pdb=" O PRO D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 211 through 222 removed outlier: 4.192A pdb=" N THR D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 247 Processing helix chain 'D' and resid 287 through 310 Processing helix chain 'D' and resid 329 through 332 Processing helix chain 'D' and resid 333 through 340 removed outlier: 4.051A pdb=" N PHE D 337 " --> pdb=" O THR D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 472 Processing helix chain 'D' and resid 495 through 502 Processing helix chain 'D' and resid 515 through 522 removed outlier: 3.690A pdb=" N VAL D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 580 Processing helix chain 'D' and resid 603 through 613 Processing helix chain 'D' and resid 624 through 655 Processing helix chain 'D' and resid 688 through 698 Processing helix chain 'D' and resid 698 through 706 Processing helix chain 'D' and resid 707 through 709 No H-bonds generated for 'chain 'D' and resid 707 through 709' Processing helix chain 'D' and resid 712 through 722 Processing helix chain 'D' and resid 732 through 742 Processing helix chain 'D' and resid 771 through 785 Processing helix chain 'D' and resid 786 through 796 Processing helix chain 'D' and resid 798 through 803 removed outlier: 3.994A pdb=" N ASN D 802 " --> pdb=" O GLY D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 841 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 65 removed outlier: 3.790A pdb=" N VAL A 65 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 197 removed outlier: 7.583A pdb=" N ILE A 163 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A 194 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU A 165 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLN A 196 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 167 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 222 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 168 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 474 through 478 removed outlier: 3.829A pdb=" N VAL A 514 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ALA A 515 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY A 761 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU A 517 " --> pdb=" O GLY A 759 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 410 through 413 Processing sheet with id=AA5, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA6, first strand: chain 'A' and resid 681 through 682 removed outlier: 3.504A pdb=" N ALA A 682 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 730 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 68 through 73 removed outlier: 6.033A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 199 through 205 removed outlier: 7.679A pdb=" N PHE B 170 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL B 203 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B 172 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N THR B 205 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N THR B 174 " --> pdb=" O THR B 205 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 280 removed outlier: 4.024A pdb=" N SER B 278 " --> pdb=" O ILE B 364 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 475 through 479 removed outlier: 5.568A pdb=" N LEU B 406 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TYR B 478 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE B 408 " --> pdb=" O TYR B 478 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER B 407 " --> pdb=" O MET B 507 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 418 through 421 Processing sheet with id=AB3, first strand: chain 'B' and resid 487 through 489 removed outlier: 3.892A pdb=" N LYS B 487 " --> pdb=" O ASN B 494 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 683 through 684 removed outlier: 7.166A pdb=" N GLY B 683 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 9.500A pdb=" N ASP B 731 " --> pdb=" O GLY B 683 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 683 through 684 removed outlier: 7.166A pdb=" N GLY B 683 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 9.500A pdb=" N ASP B 731 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE B 533 " --> pdb=" O ALA B 757 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ALA B 757 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 60 through 65 removed outlier: 6.192A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 193 through 194 removed outlier: 3.675A pdb=" N ILE C 267 " --> pdb=" O TRP C 247 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 269 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 266 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 380 through 381 Processing sheet with id=AB9, first strand: chain 'C' and resid 474 through 478 removed outlier: 5.949A pdb=" N LYS C 399 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 412 through 413 removed outlier: 3.849A pdb=" N GLN C 453 " --> pdb=" O CYS C 436 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 486 through 489 Processing sheet with id=AC3, first strand: chain 'C' and resid 517 through 518 removed outlier: 4.476A pdb=" N LEU C 517 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N THR C 748 " --> pdb=" O VAL C 542 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VAL C 542 " --> pdb=" O THR C 748 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLY C 750 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE C 540 " --> pdb=" O GLY C 750 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU C 752 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU C 538 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N PHE C 754 " --> pdb=" O GLN C 536 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLN C 536 " --> pdb=" O PHE C 754 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER C 756 " --> pdb=" O LYS C 534 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LYS C 534 " --> pdb=" O SER C 756 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE C 758 " --> pdb=" O PRO C 532 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ILE C 760 " --> pdb=" O SER C 530 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR C 539 " --> pdb=" O TRP C 731 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TRP C 731 " --> pdb=" O THR C 539 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 67 through 73 removed outlier: 5.671A pdb=" N LEU D 34 " --> pdb=" O ASN D 68 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL D 70 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE D 36 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU D 72 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL D 38 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN D 35 " --> pdb=" O HIS D 96 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU D 98 " --> pdb=" O ASN D 35 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA D 37 " --> pdb=" O LEU D 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 200 through 202 removed outlier: 3.570A pdb=" N SER D 171 " --> pdb=" O VAL D 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 256 through 257 removed outlier: 3.956A pdb=" N VAL D 279 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 408 through 410 Processing sheet with id=AC8, first strand: chain 'D' and resid 418 through 421 removed outlier: 5.459A pdb=" N CYS D 455 " --> pdb=" O GLU D 420 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET D 450 " --> pdb=" O VAL D 440 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AD1, first strand: chain 'D' and resid 523 through 524 Processing sheet with id=AD2, first strand: chain 'D' and resid 682 through 683 removed outlier: 6.162A pdb=" N GLY D 683 " --> pdb=" O ILE D 729 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ASP D 731 " --> pdb=" O GLY D 683 " (cutoff:3.500A) 1147 hydrogen bonds defined for protein. 3324 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: 4.28 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6971 1.35 - 1.47: 4738 1.47 - 1.59: 9208 1.59 - 1.71: 0 1.71 - 1.83: 139 Bond restraints: 21056 Sorted by residual: bond pdb=" C5 JC9 D 901 " pdb=" O1 JC9 D 901 " ideal model delta sigma weight residual 1.217 1.418 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C8 JC9 D 901 " pdb="CL1 JC9 D 901 " ideal model delta sigma weight residual 1.735 1.788 -0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" C1 JC9 D 901 " pdb=" N1 JC9 D 901 " ideal model delta sigma weight residual 1.502 1.458 0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" C1 NAG A 905 " pdb=" O5 NAG A 905 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.08e+00 bond pdb=" C1 JC9 D 901 " pdb=" C7 JC9 D 901 " ideal model delta sigma weight residual 1.529 1.561 -0.032 2.00e-02 2.50e+03 2.55e+00 ... (remaining 21051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 28771 2.33 - 4.67: 242 4.67 - 7.00: 27 7.00 - 9.33: 1 9.33 - 11.66: 2 Bond angle restraints: 29043 Sorted by residual: angle pdb=" C SER D 540 " pdb=" CA SER D 540 " pdb=" CB SER D 540 " ideal model delta sigma weight residual 115.89 110.64 5.25 1.32e+00 5.74e-01 1.58e+01 angle pdb=" C1 JC9 D 901 " pdb=" C5 JC9 D 901 " pdb=" O1 JC9 D 901 " ideal model delta sigma weight residual 121.39 109.73 11.66 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C6 JC9 D 901 " pdb=" C5 JC9 D 901 " pdb=" O1 JC9 D 901 " ideal model delta sigma weight residual 121.29 109.90 11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb=" N VAL C 656 " pdb=" CA VAL C 656 " pdb=" C VAL C 656 " ideal model delta sigma weight residual 111.45 108.77 2.68 9.30e-01 1.16e+00 8.28e+00 angle pdb=" N GLY A 365 " pdb=" CA GLY A 365 " pdb=" C GLY A 365 " ideal model delta sigma weight residual 110.91 114.88 -3.97 1.49e+00 4.50e-01 7.11e+00 ... (remaining 29038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.09: 12372 33.09 - 66.18: 172 66.18 - 99.27: 12 99.27 - 132.36: 1 132.36 - 165.45: 4 Dihedral angle restraints: 12561 sinusoidal: 3442 harmonic: 9119 Sorted by residual: dihedral pdb=" CB CYS D 436 " pdb=" SG CYS D 436 " pdb=" SG CYS D 456 " pdb=" CB CYS D 456 " ideal model delta sinusoidal sigma weight residual 93.00 172.85 -79.85 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS D 429 " pdb=" SG CYS D 429 " pdb=" SG CYS D 455 " pdb=" CB CYS D 455 " ideal model delta sinusoidal sigma weight residual 93.00 170.28 -77.28 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS C 79 " pdb=" SG CYS C 79 " pdb=" SG CYS C 308 " pdb=" CB CYS C 308 " ideal model delta sinusoidal sigma weight residual 93.00 160.76 -67.76 1 1.00e+01 1.00e-02 5.97e+01 ... (remaining 12558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3331 0.064 - 0.127: 451 0.127 - 0.191: 15 0.191 - 0.254: 0 0.254 - 0.318: 2 Chirality restraints: 3799 Sorted by residual: chirality pdb=" C1 NAG A 905 " pdb=" ND2 ASN A 368 " pdb=" C2 NAG A 905 " pdb=" O5 NAG A 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 687 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB ILE A 546 " pdb=" CA ILE A 546 " pdb=" CG1 ILE A 546 " pdb=" CG2 ILE A 546 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 3796 not shown) Planarity restraints: 3769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 JC9 D 901 " -0.113 2.00e-02 2.50e+03 1.99e-01 3.95e+02 pdb=" C5 JC9 D 901 " 0.344 2.00e-02 2.50e+03 pdb=" C6 JC9 D 901 " -0.112 2.00e-02 2.50e+03 pdb=" O1 JC9 D 901 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 609 " 0.025 2.00e-02 2.50e+03 2.32e-02 1.34e+01 pdb=" CG TRP D 609 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP D 609 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP D 609 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 609 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 609 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 609 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 609 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 609 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 609 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 659 " 0.048 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO A 660 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 660 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 660 " 0.040 5.00e-02 4.00e+02 ... (remaining 3766 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 422 2.70 - 3.25: 21754 3.25 - 3.80: 34434 3.80 - 4.35: 40077 4.35 - 4.90: 66759 Nonbonded interactions: 163446 Sorted by model distance: nonbonded pdb=" O VAL B 339 " pdb=" OG SER B 349 " model vdw 2.146 3.040 nonbonded pdb=" OH TYR A 114 " pdb=" O CYS A 308 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR C 105 " pdb=" OH TYR C 128 " model vdw 2.230 3.040 nonbonded pdb=" N SER A 126 " pdb=" OE1 GLU A 172 " model vdw 2.241 3.120 nonbonded pdb=" O LEU C 325 " pdb=" OG SER C 328 " model vdw 2.271 3.040 ... (remaining 163441 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 101 or (resid 102 and (name N or n \ ame CA or name C or name O or name CB )) or resid 103 through 114 or (resid 115 \ and (name N or name CA or name C or name O or name CB )) or resid 116 through 15 \ 4 or (resid 155 through 156 and (name N or name CA or name C or name O or name C \ B )) or resid 157 or (resid 158 and (name N or name CA or name C or name O or na \ me CB )) or resid 159 or (resid 160 and (name N or name CA or name C or name O o \ r name CB )) or resid 161 through 168 or (resid 169 and (name N or name CA or na \ me C or name O or name CB )) or resid 170 through 183 or (resid 184 through 188 \ and (name N or name CA or name C or name O or name CB )) or resid 189 through 21 \ 6 or (resid 217 and (name N or name CA or name C or name O or name CB )) or resi \ d 218 through 246 or (resid 247 and (name N or name CA or name C or name O or na \ me CB )) or resid 248 through 269 or (resid 270 and (name N or name CA or name C \ or name O or name CB )) or resid 271 through 293 or (resid 294 and (name N or n \ ame CA or name C or name O or name CB )) or resid 295 or (resid 296 through 301 \ and (name N or name CA or name C or name O or name CB )) or resid 302 through 31 \ 0 or (resid 311 and (name N or name CA or name C or name O or name CB )) or resi \ d 312 through 325 or (resid 326 and (name N or name CA or name C or name O or na \ me CB )) or resid 327 through 350 or (resid 351 and (name N or name CA or name C \ or name O or name CB )) or resid 352 through 355 or (resid 356 through 361 and \ (name N or name CA or name C or name O or name CB )) or resid 362 or (resid 363 \ and (name N or name CA or name C or name O or name CB )) or resid 364 through 40 \ 5 or (resid 406 and (name N or name CA or name C or name O or name CB )) or resi \ d 407 through 421 or (resid 422 through 423 and (name N or name CA or name C or \ name O or name CB )) or resid 424 through 449 or (resid 450 and (name N or name \ CA or name C or name O or name CB )) or resid 451 through 452 or (resid 453 and \ (name N or name CA or name C or name O or name CB )) or resid 454 through 497 or \ (resid 498 and (name N or name CA or name C or name O or name CB )) or resid 49 \ 9 through 500 or (resid 501 through 502 and (name N or name CA or name C or name \ O or name CB )) or resid 503 through 510 or (resid 511 and (name N or name CA o \ r name C or name O or name CB )) or resid 512 through 525 or (resid 526 and (nam \ e N or name CA or name C or name O or name CB )) or resid 527 or (resid 528 and \ (name N or name CA or name C or name O or name CB )) or resid 529 through 555 or \ (resid 556 and (name N or name CA or name C or name O or name CB )) or resid 55 \ 7 through 570 or (resid 571 through 572 and (name N or name CA or name C or name \ O or name CB )) or resid 573 through 579 or (resid 580 and (name N or name CA o \ r name C or name O or name CB )) or resid 581 through 583 or (resid 602 through \ 603 and (name N or name CA or name C or name O or name CB )) or resid 604 throug \ h 608 or (resid 609 through 611 and (name N or name CA or name C or name O or na \ me CB )) or resid 612 through 646 or (resid 647 and (name N or name CA or name C \ or name O or name CB )) or resid 648 through 653 or (resid 654 through 655 and \ (name N or name CA or name C or name O or name CB )) or resid 656 through 660 or \ (resid 661 through 664 and (name N or name CA or name C or name O or name CB )) \ or resid 665 through 683 or (resid 684 through 686 and (name N or name CA or na \ me C or name O or name CB )) or resid 687 through 689 or (resid 690 and (name N \ or name CA or name C or name O or name CB )) or resid 691 or (resid 692 through \ 698 and (name N or name CA or name C or name O or name CB )) or resid 699 throug \ h 702 or (resid 703 through 709 and (name N or name CA or name C or name O or na \ me CB )) or resid 710 or (resid 711 through 712 and (name N or name CA or name C \ or name O or name CB )) or resid 713 through 721 or (resid 722 through 725 and \ (name N or name CA or name C or name O or name CB )) or resid 726 or (resid 727 \ through 729 and (name N or name CA or name C or name O or name CB )) or resid 73 \ 0 or (resid 731 through 732 and (name N or name CA or name C or name O or name C \ B )) or resid 733 through 747 or (resid 748 through 749 and (name N or name CA o \ r name C or name O or name CB )) or (resid 750 through 756 and (name N or name C \ A or name C or name O or name CB )) or resid 757 through 761 or (resid 762 throu \ gh 765 and (name N or name CA or name C or name O or name CB )) or resid 766 thr \ ough 767 or (resid 768 through 770 and (name N or name CA or name C or name O or \ name CB )) or resid 771 through 789 or (resid 790 and (name N or name CA or nam \ e C or name O or name CB )) or resid 791 through 797 or (resid 798 through 804 a \ nd (name N or name CA or name C or name O or name CB )) or resid 805 through 836 \ or resid 902 through 906 or resid 908)) selection = (chain 'C' and (resid 25 through 80 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 123 or (resid 124 and (name N or n \ ame CA or name C or name O or name CB )) or resid 125 through 155 or (resid 156 \ and (name N or name CA or name C or name O or name CB )) or resid 157 through 17 \ 0 or (resid 171 and (name N or name CA or name C or name O or name CB )) or resi \ d 172 through 203 or (resid 204 and (name N or name CA or name C or name O or na \ me CB )) or resid 205 through 226 or (resid 227 through 229 and (name N or name \ CA or name C or name O or name CB )) or resid 230 through 232 or (resid 233 thro \ ugh 237 and (name N or name CA or name C or name O or name CB )) or resid 238 th \ rough 258 or (resid 259 through 260 and (name N or name CA or name C or name O o \ r name CB )) or resid 261 through 274 or (resid 275 and (name N or name CA or na \ me C or name O or name CB )) or resid 276 through 316 or (resid 317 and (name N \ or name CA or name C or name O or name CB )) or resid 318 through 422 or (resid \ 423 and (name N or name CA or name C or name O or name CB )) or resid 424 throug \ h 467 or (resid 468 and (name N or name CA or name C or name O or name CB )) or \ resid 469 through 480 or (resid 481 and (name N or name CA or name C or name O o \ r name CB )) or resid 482 or (resid 483 and (name N or name CA or name C or name \ O or name CB )) or resid 484 through 530 or (resid 531 and (name N or name CA o \ r name C or name O or name CB )) or resid 532 through 550 or (resid 551 through \ 552 and (name N or name CA or name C or name O or name CB )) or resid 553 throug \ h 561 or (resid 562 through 564 and (name N or name CA or name C or name O or na \ me CB )) or resid 565 through 618 or (resid 619 and (name N or name CA or name C \ or name O or name CB )) or resid 620 through 629 or (resid 630 through 631 and \ (name N or name CA or name C or name O or name CB )) or resid 632 through 654 or \ (resid 655 and (name N or name CA or name C or name O or name CB )) or resid 65 \ 6 through 666 or (resid 667 and (name N or name CA or name C or name O or name C \ B )) or resid 668 through 671 or (resid 672 through 674 and (name N or name CA o \ r name C or name O or name CB )) or resid 675 through 695 or (resid 696 through \ 698 and (name N or name CA or name C or name O or name CB )) or resid 699 throug \ h 812 or (resid 813 through 814 and (name N or name CA or name C or name O or na \ me CB )) or resid 815 through 836 or resid 901 through 906)) } ncs_group { reference = (chain 'B' and (resid 33 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB )) or resid 81 through 90 or (resid 91 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 92 through 95 and (name N or na \ me CA or name C or name O or name CB )) or resid 96 through 106 or (resid 107 th \ rough 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 113 or (resid 114 and (name N or name CA or name C or name O or name CB \ )) or resid 115 through 180 or (resid 181 and (name N or name CA or name C or na \ me O or name CB )) or resid 182 through 219 or (resid 220 through 221 and (name \ N or name CA or name C or name O or name CB )) or resid 222 or (resid 223 and (n \ ame N or name CA or name C or name O or name CB )) or resid 224 through 252 or ( \ resid 253 through 255 and (name N or name CA or name C or name O or name CB )) o \ r resid 256 through 280 or (resid 281 through 287 and (name N or name CA or name \ C or name O or name CB )) or resid 288 or (resid 289 through 291 and (name N or \ name CA or name C or name O or name CB )) or resid 292 through 293 or (resid 29 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 295 through \ 303 or (resid 304 and (name N or name CA or name C or name O or name CB )) or re \ sid 305 through 309 or (resid 310 through 313 and (name N or name CA or name C o \ r name O or name CB )) or resid 314 through 318 or (resid 319 and (name N or nam \ e CA or name C or name O or name CB )) or resid 320 through 325 or (resid 326 an \ d (name N or name CA or name C or name O or name CB )) or resid 327 through 330 \ or (resid 331 through 334 and (name N or name CA or name C or name O or name CB \ )) or resid 335 through 337 or (resid 338 and (name N or name CA or name C or na \ me O or name CB )) or resid 339 through 345 or (resid 346 and (name N or name CA \ or name C or name O or name CB )) or resid 347 through 367 or (resid 368 throug \ h 374 and (name N or name CA or name C or name O or name CB )) or resid 375 thro \ ugh 394 or (resid 395 through 400 and (name N or name CA or name C or name O or \ name CB )) or resid 401 through 425 or (resid 426 through 428 and (name N or nam \ e CA or name C or name O or name CB )) or resid 429 through 458 or (resid 459 an \ d (name N or name CA or name C or name O or name CB )) or resid 460 through 469 \ or (resid 470 and (name N or name CA or name C or name O or name CB )) or resid \ 471 through 493 or (resid 494 and (name N or name CA or name C or name O or name \ CB )) or resid 495 or (resid 496 and (name N or name CA or name C or name O or \ name CB )) or resid 497 through 524 or (resid 525 and (name N or name CA or name \ C or name O or name CB )) or resid 526 through 560 or (resid 561 through 562 an \ d (name N or name CA or name C or name O or name CB )) or resid 563 through 579 \ or resid 601 through 604 or (resid 605 through 608 and (name N or name CA or nam \ e C or name O or name CB )) or resid 609 through 625 or (resid 626 through 627 a \ nd (name N or name CA or name C or name O or name CB )) or resid 628 through 631 \ or (resid 632 and (name N or name CA or name C or name O or name CB )) or resid \ 633 through 638 or (resid 639 and (name N or name CA or name C or name O or nam \ e CB )) or resid 640 through 648 or (resid 649 through 653 and (name N or name C \ A or name C or name O or name CB )) or resid 654 through 662 or (resid 663 and ( \ name N or name CA or name C or name O or name CB )) or resid 664 through 699 or \ (resid 700 through 701 and (name N or name CA or name C or name O or name CB )) \ or resid 702 through 806 or (resid 807 through 808 and (name N or name CA or nam \ e C or name O or name CB )) or resid 809 through 812 or (resid 813 and (name N o \ r name CA or name C or name O or name CB )) or resid 814 through 816 or (resid 8 \ 17 through 818 and (name N or name CA or name C or name O or name CB )) or resid \ 819 through 823 or (resid 824 through 830 and (name N or name CA or name C or n \ ame O or name CB )) or resid 831 through 841 or resid 902)) selection = (chain 'D' and ((resid 33 through 34 and (name N or name CA or name C or name O \ or name CB )) or resid 35 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or (resid 41 through 52 and (name N or name CA or nam \ e C or name O or name CB )) or resid 53 through 89 or (resid 90 through 91 and ( \ name N or name CA or name C or name O or name CB )) or resid 92 through 105 or ( \ resid 106 through 108 and (name N or name CA or name C or name O or name CB )) o \ r resid 109 through 124 or (resid 125 and (name N or name CA or name C or name O \ or name CB )) or resid 126 through 127 or (resid 128 and (name N or name CA or \ name C or name O or name CB )) or (resid 129 through 132 and (name N or name CA \ or name C or name O or name CB )) or resid 133 through 134 or (resid 135 through \ 139 and (name N or name CA or name C or name O or name CB )) or resid 140 throu \ gh 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) or \ resid 148 through 151 or (resid 152 and (name N or name CA or name C or name O \ or name CB )) or resid 153 through 155 or (resid 156 and (name N or name CA or n \ ame C or name O or name CB )) or resid 157 through 158 or (resid 159 through 163 \ and (name N or name CA or name C or name O or name CB )) or resid 164 or (resid \ 165 through 166 and (name N or name CA or name C or name O or name CB )) or res \ id 167 through 169 or (resid 170 and (name N or name CA or name C or name O or n \ ame CB )) or resid 171 or (resid 172 and (name N or name CA or name C or name O \ or name CB )) or resid 173 or (resid 174 through 176 and (name N or name CA or n \ ame C or name O or name CB )) or resid 177 through 192 or (resid 193 and (name N \ or name CA or name C or name O or name CB )) or resid 194 through 200 or (resid \ 201 through 202 and (name N or name CA or name C or name O or name CB )) or res \ id 203 through 215 or (resid 216 and (name N or name CA or name C or name O or n \ ame CB )) or resid 217 or (resid 218 and (name N or name CA or name C or name O \ or name CB )) or resid 219 through 227 or (resid 228 through 236 and (name N or \ name CA or name C or name O or name CB )) or resid 237 through 276 or (resid 277 \ and (name N or name CA or name C or name O or name CB )) or resid 278 through 2 \ 83 or (resid 284 through 287 and (name N or name CA or name C or name O or name \ CB )) or resid 288 through 290 or (resid 291 and (name N or name CA or name C or \ name O or name CB )) or resid 292 through 312 or (resid 313 and (name N or name \ CA or name C or name O or name CB )) or resid 314 through 320 or (resid 321 and \ (name N or name CA or name C or name O or name CB )) or resid 322 through 343 o \ r (resid 344 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 45 through 357 or (resid 358 and (name N or name CA or name C or name O or name \ CB )) or resid 359 through 369 or (resid 370 through 374 and (name N or name CA \ or name C or name O or name CB )) or resid 375 through 380 or (resid 381 through \ 384 and (name N or name CA or name C or name O or name CB )) or resid 385 throu \ gh 405 or (resid 406 and (name N or name CA or name C or name O or name CB )) or \ resid 407 through 408 or (resid 409 and (name N or name CA or name C or name O \ or name CB )) or resid 410 or (resid 411 through 414 and (name N or name CA or n \ ame C or name O or name CB )) or resid 415 through 436 or (resid 437 through 448 \ and (name N or name CA or name C or name O or name CB )) or resid 449 or (resid \ 450 and (name N or name CA or name C or name O or name CB )) or resid 451 throu \ gh 474 or (resid 475 through 476 and (name N or name CA or name C or name O or n \ ame CB )) or resid 477 through 484 or (resid 485 and (name N or name CA or name \ C or name O or name CB )) or resid 486 through 501 or (resid 502 through 505 and \ (name N or name CA or name C or name O or name CB )) or resid 506 through 515 o \ r (resid 516 through 518 and (name N or name CA or name C or name O or name CB ) \ ) or resid 519 through 523 or (resid 524 through 525 and (name N or name CA or n \ ame C or name O or name CB )) or resid 526 through 527 or (resid 528 and (name N \ or name CA or name C or name O or name CB )) or resid 529 through 534 or (resid \ 535 through 536 and (name N or name CA or name C or name O or name CB )) or res \ id 537 through 540 or (resid 541 and (name N or name CA or name C or name O or n \ ame CB )) or resid 542 or (resid 543 through 545 and (name N or name CA or name \ C or name O or name CB )) or resid 546 through 548 or (resid 549 through 551 and \ (name N or name CA or name C or name O or name CB )) or resid 552 through 553 o \ r (resid 554 through 557 and (name N or name CA or name C or name O or name CB ) \ ) or resid 558 through 563 or (resid 564 and (name N or name CA or name C or nam \ e O or name CB )) or resid 565 through 566 or (resid 567 and (name N or name CA \ or name C or name O or name CB )) or resid 568 through 578 or (resid 579 and (na \ me N or name CA or name C or name O or name CB )) or resid 601 through 606 or (r \ esid 607 through 608 and (name N or name CA or name C or name O or name CB )) or \ resid 609 through 610 or (resid 611 and (name N or name CA or name C or name O \ or name CB )) or resid 612 through 619 or (resid 620 through 621 and (name N or \ name CA or name C or name O or name CB )) or resid 622 through 630 or (resid 631 \ through 632 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 33 or (resid 634 through 639 and (name N or name CA or name C or name O or name \ CB )) or resid 640 or (resid 641 and (name N or name CA or name C or name O or n \ ame CB )) or resid 642 through 643 or (resid 644 through 645 and (name N or name \ CA or name C or name O or name CB )) or resid 646 through 647 or (resid 648 thr \ ough 653 and (name N or name CA or name C or name O or name CB )) or resid 654 t \ hrough 676 or (resid 677 and (name N or name CA or name C or name O or name CB ) \ ) or resid 678 through 680 or (resid 681 through 682 and (name N or name CA or n \ ame C or name O or name CB )) or resid 683 through 694 or (resid 695 and (name N \ or name CA or name C or name O or name CB )) or resid 696 through 697 or (resid \ 698 and (name N or name CA or name C or name O or name CB )) or resid 699 throu \ gh 700 or (resid 701 and (name N or name CA or name C or name O or name CB )) or \ resid 702 or (resid 703 and (name N or name CA or name C or name O or name CB ) \ ) or resid 704 through 708 or (resid 709 and (name N or name CA or name C or nam \ e O or name CB )) or resid 710 through 712 or (resid 713 through 719 and (name N \ or name CA or name C or name O or name CB )) or resid 720 through 730 or (resid \ 731 through 734 and (name N or name CA or name C or name O or name CB )) or res \ id 735 through 736 or (resid 737 and (name N or name CA or name C or name O or n \ ame CB )) or resid 738 through 749 or (resid 750 and (name N or name CA or name \ C or name O or name CB )) or resid 751 through 762 or (resid 763 through 767 and \ (name N or name CA or name C or name O or name CB )) or resid 768 through 775 o \ r (resid 776 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 77 through 784 or (resid 785 and (name N or name CA or name C or name O or name \ CB )) or resid 786 through 792 or (resid 793 through 797 and (name N or name CA \ or name C or name O or name CB )) or resid 798 through 805 or (resid 806 through \ 808 and (name N or name CA or name C or name O or name CB )) or resid 809 throu \ gh 811 or (resid 812 through 813 and (name N or name CA or name C or name O or n \ ame CB )) or resid 814 through 822 or (resid 823 through 830 and (name N or name \ CA or name C or name O or name CB )) or resid 831 through 833 or (resid 834 thr \ ough 839 and (name N or name CA or name C or name O or name CB )) or resid 840 t \ hrough 841 or resid 902)) } 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.150 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 0.003 0.201 21084 Z= 0.135 Angle : 0.514 11.663 29112 Z= 0.256 Chirality : 0.041 0.318 3799 Planarity : 0.005 0.199 3756 Dihedral : 12.272 165.448 6602 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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 are not related in a simple way. whole: 1.15 (0.16), residues: 3141 helix: 2.62 (0.14), residues: 1330 sheet: -0.52 (0.29), residues: 350 loop : -0.69 (0.17), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 139 TYR 0.006 0.000 TYR D 478 PHE 0.020 0.001 PHE D 183 TRP 0.063 0.001 TRP D 609 HIS 0.004 0.000 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00262 (21056) covalent geometry : angle 0.50575 (29043) SS BOND : bond 0.00248 ( 15) SS BOND : angle 1.05603 ( 30) hydrogen bonds : bond 0.11121 ( 1143) hydrogen bonds : angle 5.01720 ( 3324) link_NAG-ASN : bond 0.00621 ( 13) link_NAG-ASN : angle 2.46797 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8764 (tpp) cc_final: 0.8357 (tpp) REVERT: B 613 PHE cc_start: 0.8026 (m-10) cc_final: 0.7792 (m-10) REVERT: B 817 MET cc_start: 0.9103 (mpp) cc_final: 0.8734 (mpp) REVERT: D 450 MET cc_start: 0.8429 (ppp) cc_final: 0.7766 (pmm) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1150 time to fit residues: 27.5141 Evaluate side-chains 124 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS A 405 GLN C 50 ASN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 ASN C 487 GLN D 736 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.069072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.047798 restraints weight = 163874.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.047661 restraints weight = 130535.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.047415 restraints weight = 136103.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.047668 restraints weight = 126281.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.047771 restraints weight = 114560.543| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21084 Z= 0.209 Angle : 0.590 10.043 29112 Z= 0.307 Chirality : 0.044 0.415 3799 Planarity : 0.004 0.080 3756 Dihedral : 5.300 59.885 3523 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.30 % Allowed : 7.42 % Favored : 92.28 % 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 are not related in a simple way. whole: 0.90 (0.16), residues: 3141 helix: 2.35 (0.14), residues: 1351 sheet: -1.04 (0.26), residues: 420 loop : -0.65 (0.18), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 468 TYR 0.022 0.002 TYR A 144 PHE 0.028 0.002 PHE A 533 TRP 0.028 0.002 TRP D 609 HIS 0.010 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00431 (21056) covalent geometry : angle 0.57967 (29043) SS BOND : bond 0.00232 ( 15) SS BOND : angle 1.00144 ( 30) hydrogen bonds : bond 0.03529 ( 1143) hydrogen bonds : angle 4.50193 ( 3324) link_NAG-ASN : bond 0.00547 ( 13) link_NAG-ASN : angle 2.99516 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8680 (tpp) cc_final: 0.8462 (tpp) REVERT: A 240 MET cc_start: 0.8351 (mmm) cc_final: 0.7964 (tpp) REVERT: B 465 LYS cc_start: 0.9142 (pttm) cc_final: 0.8801 (pttm) REVERT: B 817 MET cc_start: 0.9142 (mpp) cc_final: 0.8820 (mpp) REVERT: C 50 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.7391 (t0) REVERT: C 74 MET cc_start: 0.8599 (mmp) cc_final: 0.8356 (tpp) REVERT: C 240 MET cc_start: 0.8167 (mmm) cc_final: 0.7869 (mmm) REVERT: D 614 ASN cc_start: 0.8383 (p0) cc_final: 0.7648 (t0) outliers start: 5 outliers final: 2 residues processed: 135 average time/residue: 0.1216 time to fit residues: 28.5175 Evaluate side-chains 128 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 614 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 305 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 272 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 chunk 259 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.069515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.048716 restraints weight = 164266.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.048677 restraints weight = 132860.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.048521 restraints weight = 130904.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.048635 restraints weight = 122019.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.048849 restraints weight = 112231.626| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21084 Z= 0.093 Angle : 0.495 10.186 29112 Z= 0.246 Chirality : 0.042 0.401 3799 Planarity : 0.003 0.069 3756 Dihedral : 4.536 55.990 3523 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.24 % Allowed : 10.26 % Favored : 89.50 % 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 are not related in a simple way. whole: 1.08 (0.16), residues: 3141 helix: 2.53 (0.14), residues: 1349 sheet: -1.01 (0.26), residues: 412 loop : -0.57 (0.18), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 468 TYR 0.008 0.001 TYR D 478 PHE 0.017 0.001 PHE A 609 TRP 0.017 0.001 TRP D 609 HIS 0.005 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00196 (21056) covalent geometry : angle 0.48499 (29043) SS BOND : bond 0.00190 ( 15) SS BOND : angle 0.69091 ( 30) hydrogen bonds : bond 0.02836 ( 1143) hydrogen bonds : angle 4.20350 ( 3324) link_NAG-ASN : bond 0.00453 ( 13) link_NAG-ASN : angle 2.67958 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8568 (tpp) cc_final: 0.8340 (tpp) REVERT: A 785 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7167 (ptm) REVERT: B 112 MET cc_start: 0.9015 (mmm) cc_final: 0.8689 (mmm) REVERT: B 465 LYS cc_start: 0.9184 (pttm) cc_final: 0.8841 (pttm) REVERT: B 613 PHE cc_start: 0.8100 (m-10) cc_final: 0.7818 (m-10) REVERT: B 817 MET cc_start: 0.9159 (mpp) cc_final: 0.8943 (mpp) REVERT: C 240 MET cc_start: 0.8225 (mmm) cc_final: 0.7890 (mmm) REVERT: D 564 MET cc_start: 0.8391 (mpp) cc_final: 0.8133 (mpp) REVERT: D 614 ASN cc_start: 0.8373 (p0) cc_final: 0.7699 (t0) outliers start: 4 outliers final: 1 residues processed: 135 average time/residue: 0.1108 time to fit residues: 26.5207 Evaluate side-chains 130 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain D residue 61 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 298 optimal weight: 20.0000 chunk 135 optimal weight: 8.9990 chunk 284 optimal weight: 0.4980 chunk 195 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 229 optimal weight: 20.0000 chunk 232 optimal weight: 3.9990 chunk 186 optimal weight: 0.0570 chunk 301 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 overall best weight: 2.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.068466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.047630 restraints weight = 165101.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.047374 restraints weight = 137326.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.047133 restraints weight = 133120.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.047211 restraints weight = 137446.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.047429 restraints weight = 117999.528| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21084 Z= 0.169 Angle : 0.537 10.494 29112 Z= 0.276 Chirality : 0.042 0.393 3799 Planarity : 0.004 0.078 3756 Dihedral : 4.530 55.257 3523 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.91 % Allowed : 12.98 % Favored : 86.12 % 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 are not related in a simple way. whole: 0.93 (0.16), residues: 3141 helix: 2.39 (0.14), residues: 1351 sheet: -1.08 (0.26), residues: 389 loop : -0.64 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 722 TYR 0.015 0.001 TYR A 144 PHE 0.022 0.001 PHE A 533 TRP 0.020 0.001 TRP D 634 HIS 0.009 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00352 (21056) covalent geometry : angle 0.52661 (29043) SS BOND : bond 0.00233 ( 15) SS BOND : angle 0.80557 ( 30) hydrogen bonds : bond 0.03226 ( 1143) hydrogen bonds : angle 4.36914 ( 3324) link_NAG-ASN : bond 0.00408 ( 13) link_NAG-ASN : angle 2.90868 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 785 MET cc_start: 0.7734 (ptm) cc_final: 0.7454 (ptm) REVERT: B 112 MET cc_start: 0.9139 (mmm) cc_final: 0.8854 (mmm) REVERT: B 465 LYS cc_start: 0.9185 (pttm) cc_final: 0.8836 (pttm) REVERT: B 817 MET cc_start: 0.9111 (mpp) cc_final: 0.8898 (mpp) REVERT: C 41 MET cc_start: 0.8266 (ppp) cc_final: 0.7943 (ppp) REVERT: C 74 MET cc_start: 0.8811 (tpp) cc_final: 0.8500 (tpp) REVERT: C 240 MET cc_start: 0.8211 (mmm) cc_final: 0.7813 (mmm) REVERT: D 112 MET cc_start: 0.9129 (tpp) cc_final: 0.8381 (mmm) REVERT: D 564 MET cc_start: 0.8460 (mpp) cc_final: 0.8158 (mpp) outliers start: 15 outliers final: 7 residues processed: 142 average time/residue: 0.1085 time to fit residues: 26.9045 Evaluate side-chains 132 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 116 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 283 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 280 optimal weight: 8.9990 chunk 296 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 HIS ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.067995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.047310 restraints weight = 164090.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.046712 restraints weight = 129281.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.046801 restraints weight = 124764.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.046826 restraints weight = 117274.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.047240 restraints weight = 110255.566| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21084 Z= 0.175 Angle : 0.554 10.720 29112 Z= 0.282 Chirality : 0.042 0.409 3799 Planarity : 0.004 0.074 3756 Dihedral : 4.397 40.457 3523 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.85 % Favored : 96.12 % Rotamer: Outliers : 1.27 % Allowed : 14.60 % Favored : 84.13 % 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 are not related in a simple way. whole: 0.80 (0.16), residues: 3141 helix: 2.28 (0.14), residues: 1346 sheet: -1.03 (0.26), residues: 393 loop : -0.73 (0.17), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 722 TYR 0.011 0.001 TYR A 144 PHE 0.020 0.001 PHE A 533 TRP 0.021 0.001 TRP D 634 HIS 0.009 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00361 (21056) covalent geometry : angle 0.54203 (29043) SS BOND : bond 0.00197 ( 15) SS BOND : angle 0.88565 ( 30) hydrogen bonds : bond 0.03249 ( 1143) hydrogen bonds : angle 4.43900 ( 3324) link_NAG-ASN : bond 0.00387 ( 13) link_NAG-ASN : angle 3.06382 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 512 MET cc_start: 0.7836 (tpp) cc_final: 0.7460 (tpp) REVERT: A 785 MET cc_start: 0.7595 (ptm) cc_final: 0.7336 (ptm) REVERT: B 112 MET cc_start: 0.9147 (mmm) cc_final: 0.8819 (mmm) REVERT: B 465 LYS cc_start: 0.9241 (pttm) cc_final: 0.8907 (pttm) REVERT: B 817 MET cc_start: 0.9108 (mpp) cc_final: 0.8899 (mpp) REVERT: C 41 MET cc_start: 0.8273 (ppp) cc_final: 0.7995 (ppp) REVERT: C 74 MET cc_start: 0.8866 (tpp) cc_final: 0.8434 (tpp) REVERT: C 118 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.7996 (p) REVERT: C 240 MET cc_start: 0.8437 (mmm) cc_final: 0.8132 (mmm) REVERT: D 175 THR cc_start: 0.5342 (OUTLIER) cc_final: 0.5096 (p) REVERT: D 564 MET cc_start: 0.8414 (mpp) cc_final: 0.8063 (mpp) outliers start: 21 outliers final: 11 residues processed: 149 average time/residue: 0.1146 time to fit residues: 30.0615 Evaluate side-chains 136 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 297 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 254 optimal weight: 0.7980 chunk 162 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 220 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.067986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.047378 restraints weight = 163882.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.046901 restraints weight = 133396.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.046762 restraints weight = 127455.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.047004 restraints weight = 124309.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.047305 restraints weight = 108786.220| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21084 Z= 0.146 Angle : 0.535 10.637 29112 Z= 0.270 Chirality : 0.042 0.413 3799 Planarity : 0.003 0.075 3756 Dihedral : 4.264 41.362 3523 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.89 % Rotamer: Outliers : 0.97 % Allowed : 15.87 % Favored : 83.16 % 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 are not related in a simple way. whole: 0.82 (0.16), residues: 3141 helix: 2.31 (0.14), residues: 1346 sheet: -1.04 (0.26), residues: 407 loop : -0.74 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 722 TYR 0.010 0.001 TYR D 478 PHE 0.018 0.001 PHE A 533 TRP 0.007 0.001 TRP C 151 HIS 0.007 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00305 (21056) covalent geometry : angle 0.52412 (29043) SS BOND : bond 0.00216 ( 15) SS BOND : angle 0.89339 ( 30) hydrogen bonds : bond 0.03118 ( 1143) hydrogen bonds : angle 4.37040 ( 3324) link_NAG-ASN : bond 0.00387 ( 13) link_NAG-ASN : angle 2.95474 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8156 (t) REVERT: A 785 MET cc_start: 0.7797 (ptm) cc_final: 0.7548 (ptm) REVERT: B 112 MET cc_start: 0.9165 (mmm) cc_final: 0.8837 (mmm) REVERT: B 338 MET cc_start: 0.8370 (mmm) cc_final: 0.8150 (mmm) REVERT: B 465 LYS cc_start: 0.9238 (pttm) cc_final: 0.8884 (pttm) REVERT: B 817 MET cc_start: 0.9106 (mpp) cc_final: 0.8891 (mpp) REVERT: C 41 MET cc_start: 0.8292 (ppp) cc_final: 0.8026 (ppp) REVERT: C 74 MET cc_start: 0.8852 (tpp) cc_final: 0.8523 (tpp) REVERT: C 118 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.7982 (p) REVERT: C 178 LYS cc_start: 0.8976 (ptpp) cc_final: 0.8726 (ptpp) REVERT: C 240 MET cc_start: 0.8541 (mmm) cc_final: 0.8317 (mmm) REVERT: C 634 MET cc_start: 0.8574 (tpp) cc_final: 0.8341 (tpp) REVERT: D 112 MET cc_start: 0.9141 (tpp) cc_final: 0.8414 (mmm) outliers start: 16 outliers final: 13 residues processed: 141 average time/residue: 0.1152 time to fit residues: 28.0620 Evaluate side-chains 139 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 133 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 chunk 246 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 283 optimal weight: 50.0000 chunk 44 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 520 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.068307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.047593 restraints weight = 163522.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.047428 restraints weight = 135128.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.047161 restraints weight = 127733.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.047403 restraints weight = 124188.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.047537 restraints weight = 110313.927| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 21084 Z= 0.102 Angle : 0.523 10.460 29112 Z= 0.258 Chirality : 0.042 0.413 3799 Planarity : 0.003 0.071 3756 Dihedral : 3.993 40.434 3523 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.28 % Favored : 96.69 % Rotamer: Outliers : 1.27 % Allowed : 16.35 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.16), residues: 3141 helix: 2.40 (0.14), residues: 1352 sheet: -1.02 (0.26), residues: 401 loop : -0.66 (0.18), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 468 TYR 0.008 0.001 TYR D 478 PHE 0.013 0.001 PHE A 609 TRP 0.009 0.001 TRP D 634 HIS 0.005 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00220 (21056) covalent geometry : angle 0.51284 (29043) SS BOND : bond 0.00197 ( 15) SS BOND : angle 0.75682 ( 30) hydrogen bonds : bond 0.02826 ( 1143) hydrogen bonds : angle 4.20668 ( 3324) link_NAG-ASN : bond 0.00440 ( 13) link_NAG-ASN : angle 2.80218 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 167 VAL cc_start: 0.8250 (OUTLIER) cc_final: 0.7952 (t) REVERT: A 209 MET cc_start: 0.8085 (mmm) cc_final: 0.7865 (tpt) REVERT: A 785 MET cc_start: 0.7643 (ptm) cc_final: 0.7371 (ptm) REVERT: B 112 MET cc_start: 0.9134 (mmm) cc_final: 0.8824 (mmm) REVERT: B 338 MET cc_start: 0.8322 (mmm) cc_final: 0.8112 (mmm) REVERT: B 465 LYS cc_start: 0.9250 (pttm) cc_final: 0.8921 (pttm) REVERT: B 817 MET cc_start: 0.9126 (mpp) cc_final: 0.8904 (mpp) REVERT: C 41 MET cc_start: 0.8252 (ppp) cc_final: 0.7959 (ppp) REVERT: C 74 MET cc_start: 0.8793 (tpp) cc_final: 0.8473 (tpp) REVERT: C 178 LYS cc_start: 0.8963 (ptpp) cc_final: 0.8710 (ptpp) REVERT: C 424 PHE cc_start: 0.9279 (m-80) cc_final: 0.9011 (t80) REVERT: C 643 ILE cc_start: 0.8919 (pt) cc_final: 0.8673 (tt) REVERT: D 112 MET cc_start: 0.9109 (tpp) cc_final: 0.8383 (mmm) REVERT: D 175 THR cc_start: 0.5306 (OUTLIER) cc_final: 0.5074 (p) outliers start: 21 outliers final: 13 residues processed: 147 average time/residue: 0.1172 time to fit residues: 29.9357 Evaluate side-chains 140 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 17 optimal weight: 1.9990 chunk 145 optimal weight: 20.0000 chunk 123 optimal weight: 0.0870 chunk 125 optimal weight: 2.9990 chunk 165 optimal weight: 0.0170 chunk 83 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 254 optimal weight: 40.0000 chunk 288 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 614 ASN C 520 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.068028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.047470 restraints weight = 163543.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.047043 restraints weight = 129368.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.047127 restraints weight = 116697.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.047258 restraints weight = 110771.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.047364 restraints weight = 105605.600| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21084 Z= 0.124 Angle : 0.534 10.490 29112 Z= 0.265 Chirality : 0.042 0.402 3799 Planarity : 0.003 0.073 3756 Dihedral : 3.982 40.613 3523 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 1.21 % Allowed : 16.54 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.16), residues: 3141 helix: 2.38 (0.14), residues: 1352 sheet: -0.95 (0.27), residues: 397 loop : -0.67 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 468 TYR 0.009 0.001 TYR D 478 PHE 0.016 0.001 PHE A 533 TRP 0.017 0.001 TRP D 634 HIS 0.005 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00263 (21056) covalent geometry : angle 0.52405 (29043) SS BOND : bond 0.00175 ( 15) SS BOND : angle 0.73062 ( 30) hydrogen bonds : bond 0.02929 ( 1143) hydrogen bonds : angle 4.23328 ( 3324) link_NAG-ASN : bond 0.00422 ( 13) link_NAG-ASN : angle 2.81638 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 167 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8087 (t) REVERT: A 209 MET cc_start: 0.8129 (mmm) cc_final: 0.7918 (tpt) REVERT: A 785 MET cc_start: 0.7646 (ptm) cc_final: 0.7379 (ptm) REVERT: B 112 MET cc_start: 0.9161 (mmm) cc_final: 0.8833 (mmm) REVERT: B 465 LYS cc_start: 0.9269 (pttm) cc_final: 0.8935 (pttm) REVERT: B 817 MET cc_start: 0.9123 (mpp) cc_final: 0.8903 (mpp) REVERT: C 41 MET cc_start: 0.8275 (ppp) cc_final: 0.7993 (ppp) REVERT: C 74 MET cc_start: 0.8885 (tpp) cc_final: 0.8569 (tpp) REVERT: C 178 LYS cc_start: 0.8968 (ptpp) cc_final: 0.8720 (ptpp) REVERT: C 643 ILE cc_start: 0.8961 (pt) cc_final: 0.8700 (tt) REVERT: D 175 THR cc_start: 0.5398 (OUTLIER) cc_final: 0.5148 (p) REVERT: D 564 MET cc_start: 0.8390 (mpp) cc_final: 0.7836 (mtt) outliers start: 20 outliers final: 15 residues processed: 148 average time/residue: 0.1150 time to fit residues: 29.5086 Evaluate side-chains 142 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 641 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 154 optimal weight: 10.0000 chunk 247 optimal weight: 0.2980 chunk 83 optimal weight: 0.0000 chunk 239 optimal weight: 30.0000 chunk 201 optimal weight: 1.9990 chunk 238 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 92 optimal weight: 30.0000 chunk 81 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 614 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.068176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.047000 restraints weight = 163433.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.047039 restraints weight = 140408.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.046995 restraints weight = 118834.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.047129 restraints weight = 119093.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.047363 restraints weight = 106820.225| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21084 Z= 0.108 Angle : 0.537 11.456 29112 Z= 0.264 Chirality : 0.042 0.402 3799 Planarity : 0.003 0.071 3756 Dihedral : 3.890 40.439 3523 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.59 % Rotamer: Outliers : 1.09 % Allowed : 17.02 % Favored : 81.89 % 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 are not related in a simple way. whole: 0.93 (0.16), residues: 3141 helix: 2.36 (0.14), residues: 1346 sheet: -0.87 (0.27), residues: 392 loop : -0.67 (0.17), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 468 TYR 0.009 0.001 TYR D 478 PHE 0.012 0.001 PHE A 533 TRP 0.017 0.001 TRP D 634 HIS 0.005 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00231 (21056) covalent geometry : angle 0.52773 (29043) SS BOND : bond 0.00183 ( 15) SS BOND : angle 0.71100 ( 30) hydrogen bonds : bond 0.02841 ( 1143) hydrogen bonds : angle 4.18907 ( 3324) link_NAG-ASN : bond 0.00434 ( 13) link_NAG-ASN : angle 2.76319 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 209 MET cc_start: 0.8164 (mmm) cc_final: 0.7962 (tpt) REVERT: A 785 MET cc_start: 0.7610 (ptm) cc_final: 0.7338 (ptm) REVERT: B 112 MET cc_start: 0.9142 (mmm) cc_final: 0.8822 (mmm) REVERT: B 465 LYS cc_start: 0.9274 (pttm) cc_final: 0.8949 (pttm) REVERT: B 817 MET cc_start: 0.9128 (mpp) cc_final: 0.8907 (mpp) REVERT: C 41 MET cc_start: 0.8294 (ppp) cc_final: 0.7992 (ppp) REVERT: C 74 MET cc_start: 0.8842 (tpp) cc_final: 0.8550 (tpp) REVERT: C 178 LYS cc_start: 0.8947 (ptpp) cc_final: 0.8704 (ptpp) REVERT: C 424 PHE cc_start: 0.9298 (m-80) cc_final: 0.9042 (t80) REVERT: C 643 ILE cc_start: 0.8953 (pt) cc_final: 0.8713 (tt) REVERT: D 175 THR cc_start: 0.5360 (OUTLIER) cc_final: 0.5111 (p) REVERT: D 564 MET cc_start: 0.8381 (mpp) cc_final: 0.7825 (mtt) outliers start: 18 outliers final: 13 residues processed: 141 average time/residue: 0.1135 time to fit residues: 27.8715 Evaluate side-chains 137 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 641 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 68 optimal weight: 0.4980 chunk 112 optimal weight: 20.0000 chunk 233 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 0.2980 chunk 125 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 305 optimal weight: 1.9990 chunk 290 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 520 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.068343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.047696 restraints weight = 163803.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.047246 restraints weight = 130867.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.047234 restraints weight = 122652.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.047438 restraints weight = 117442.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.047607 restraints weight = 104384.532| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21084 Z= 0.095 Angle : 0.529 12.053 29112 Z= 0.258 Chirality : 0.042 0.398 3799 Planarity : 0.003 0.071 3756 Dihedral : 3.745 39.940 3523 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 0.97 % Allowed : 17.08 % Favored : 81.96 % 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 are not related in a simple way. whole: 0.96 (0.16), residues: 3141 helix: 2.36 (0.14), residues: 1357 sheet: -0.88 (0.27), residues: 391 loop : -0.64 (0.18), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 722 TYR 0.008 0.001 TYR D 478 PHE 0.012 0.001 PHE A 609 TRP 0.022 0.001 TRP D 634 HIS 0.005 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00206 (21056) covalent geometry : angle 0.51999 (29043) SS BOND : bond 0.00168 ( 15) SS BOND : angle 0.68778 ( 30) hydrogen bonds : bond 0.02717 ( 1143) hydrogen bonds : angle 4.11223 ( 3324) link_NAG-ASN : bond 0.00457 ( 13) link_NAG-ASN : angle 2.68804 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 762 MET cc_start: 0.7798 (mmm) cc_final: 0.7226 (mtp) REVERT: A 785 MET cc_start: 0.7609 (ptm) cc_final: 0.7354 (ptm) REVERT: B 112 MET cc_start: 0.9115 (mmm) cc_final: 0.8789 (mmm) REVERT: B 465 LYS cc_start: 0.9262 (pttm) cc_final: 0.8951 (pttm) REVERT: B 817 MET cc_start: 0.9137 (mpp) cc_final: 0.8906 (mpp) REVERT: C 41 MET cc_start: 0.8269 (ppp) cc_final: 0.7960 (ppp) REVERT: C 74 MET cc_start: 0.8847 (tpp) cc_final: 0.8539 (tpp) REVERT: C 178 LYS cc_start: 0.8944 (ptpp) cc_final: 0.8698 (ptpp) REVERT: C 424 PHE cc_start: 0.9307 (m-80) cc_final: 0.9047 (t80) REVERT: C 643 ILE cc_start: 0.8935 (pt) cc_final: 0.8697 (tt) REVERT: D 175 THR cc_start: 0.5321 (OUTLIER) cc_final: 0.5080 (p) REVERT: D 564 MET cc_start: 0.8376 (mpp) cc_final: 0.7851 (mtt) outliers start: 16 outliers final: 12 residues processed: 141 average time/residue: 0.1217 time to fit residues: 29.6143 Evaluate side-chains 136 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 190 optimal weight: 9.9990 chunk 35 optimal weight: 0.0670 chunk 15 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 246 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 310 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 overall best weight: 2.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 520 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.067738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.047160 restraints weight = 163999.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.046778 restraints weight = 127533.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.046840 restraints weight = 117582.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.047007 restraints weight = 108915.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.047087 restraints weight = 106185.580| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21084 Z= 0.154 Angle : 0.565 12.579 29112 Z= 0.282 Chirality : 0.042 0.388 3799 Planarity : 0.003 0.072 3756 Dihedral : 4.036 41.196 3523 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.14 % Favored : 95.83 % Rotamer: Outliers : 0.97 % Allowed : 17.32 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.16), residues: 3141 helix: 2.28 (0.14), residues: 1352 sheet: -0.96 (0.27), residues: 401 loop : -0.71 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 468 TYR 0.010 0.001 TYR D 478 PHE 0.019 0.001 PHE A 533 TRP 0.035 0.001 TRP D 634 HIS 0.006 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00324 (21056) covalent geometry : angle 0.55564 (29043) SS BOND : bond 0.00199 ( 15) SS BOND : angle 0.73436 ( 30) hydrogen bonds : bond 0.03104 ( 1143) hydrogen bonds : angle 4.32212 ( 3324) link_NAG-ASN : bond 0.00456 ( 13) link_NAG-ASN : angle 2.87330 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3719.76 seconds wall clock time: 64 minutes 59.36 seconds (3899.36 seconds total)